Table of Content
I.Project Summary
II.Workflow Checklist
III.NGS Sequencing Results
IV.Complete Report Download
V.Raw Sequence Data Download
VI.Analysis - DADA2 Read Processing
 Sample Meta Info
 Read Count by Sample
VII.Analysis - Read Taxonomy Assignment
 Taxonomy Barplots
VIII.Analysis - Alpha Diversity
IX.Analysis - Beta Diversity
X.Analysis - Differential Abundance
 ANCOM Result
 LEfSe Result
XI.Analysis - Heatmap Profile
XII.Analysis - Network Association

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FOMC Service Report

16S rRNA Gene V1V3 Amplicon Sequencing

Version V1.41

Version History

The Forsyth Institute, Cambridge, MA, USA
May 03, 2022

Project ID: FOMC5677

I. Project Summary

Project FOMC5677 services include NGS sequencing of the V1V3 region of the 16S rRNA amplicons from the samples. First and foremost, please download this report, as well as the sequence raw data from the download links provided below. These links will expire after 60 days. We cannot guarantee the availability of your data after 60 days.

Full Bioinformatics analysis service was requested. We provide many analyses, starting from the raw sequence quality and noise filtering, pair reads merging, as well as chimera filtering for the sequences, using the DADA2 denosing algorithm and pipeline.

We also provide many downstream analyses such as taxonomy assignment, alpha and beta diversity analyses, and differential abundance analysis.

For taxonomy assignment, most informative would be the taxonomy barplots. We provide an interactive barplots to show the relative abundance of microbes at different taxonomy levels (from Phylum to species) that you can choose.

If you specify which groups of samples you want to compare for differential abundance, we provide both ANCOM and LEfSe differential abundance analysis.

 

II. Workflow Checklist

☑1.Sample Received
☑2.Sample Quality Evaluated
☑3.Sample Prepared for Sequencing
☑4.Next-Gen Sequencing
☑5.Sequence Quality Check
☑6.Absolute Abundance
☑7.Report and Raw Sequence Data Available for Download
☑8.Bioinformatics Analysis - Reads Processing (DADA2 Quality Trimming, Denoising, Paired Reads Merging)
☑9.Bioinformatics Analysis - Reads Taxonomy Assignment
☑10.Bioinformatics Analysis - Alpha Diversity Analysis
☑11.Bioinformatics Analysis - Beta Diversity Analysis
☑12.Bioinformatics Analysis - Differential Abundance Analysis
☑13.Bioinformatics Analysis - Heatmap Profile
☑14.Bioinformatics Analysis - Network Association
 

III. NGS Sequencing

The samples were processed and analyzed with the ZymoBIOMICS® Service: Targeted Metagenomic Sequencing (Zymo Research, Irvine, CA).

DNA Extraction: If DNA extraction was performed, one of three different DNA extraction kits was used depending on the sample type and sample volume and were used according to the manufacturer’s instructions, unless otherwise stated. The kit used in this project is marked below:

☐ZymoBIOMICS® DNA Miniprep Kit (Zymo Research, Irvine, CA)
☐ZymoBIOMICS® DNA Microprep Kit (Zymo Research, Irvine, CA)
☐ZymoBIOMICS®-96 MagBead DNA Kit (Zymo Research, Irvine, CA)
☑N/A (DNA Extraction Not Performed)
Elution Volume: 50µL
Additional Notes: NA

Targeted Library Preparation: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). These primers were custom designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity. The primer sets used in this project are marked below:

☐Quick-16S™ Primer Set V1-V2 (Zymo Research, Irvine, CA)
☑Quick-16S™ Primer Set V1-V3 (Zymo Research, Irvine, CA)
☐Quick-16S™ Primer Set V3-V4 (Zymo Research, Irvine, CA)
☐Quick-16S™ Primer Set V4 (Zymo Research, Irvine, CA)
☐Quick-16S™ Primer Set V6-V8 (Zymo Research, Irvine, CA)
☐Other: NA
Additional Notes: NA

The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).

Control Samples: The ZymoBIOMICS® Microbial Community Standard (Zymo Research, Irvine, CA) was used as a positive control for each DNA extraction, if performed. The ZymoBIOMICS® Microbial Community DNA Standard (Zymo Research, Irvine, CA) was used as a positive control for each targeted library preparation. Negative controls (i.e. blank extraction control, blank library preparation control) were included to assess the level of bioburden carried by the wet-lab process.

Sequencing: The final library was sequenced on Illumina® MiSeq™ with a V3 reagent kit (600 cycles). The sequencing was performed with 10% PhiX spike-in.

 

IV. Complete Report Download

The complete report of your project, including all links in this report, can be downloaded by clicking the link provided below. The downloaded file is a compressed ZIP file and once unzipped, open the file “REPORT.html” (may only shown as "REPORT" in your computer) by double clicking it. Your default web browser will open it and you will see the exact content of this report.

Please download and save the file to your computer storage device. The download link will expire after 60 days upon your receiving of this report.

Complete report download link:

To view the report, please follow the following steps:
1.Download the .zip file from the report link above.
2.Extract all the contents of the downloaded .zip file to your desktop.
3.Open the extracted folder and find the "REPORT.html" (may shown as only "REPORT").
4.Open (double-clicking) the REPORT.html file. Your default browser will open the top age of the complete report. Within the report, there are links to view all the analyses performed for the project.

 

V. Raw Sequence Data Download

The raw NGS sequence data is available for download with the link provided below. The data is a compressed ZIP file and can be unzipped to individual sequence files. Since this is a pair-end sequencing, each of your samples is represented by two sequence files, one for READ 1, with the file extension “*_R1.fastq.gz”, another READ 2, with the file extension “*_R1.fastq.gz”. The files are in FASTQ format and are compressed. FASTQ format is a text-based data format for storing both a biological sequence and its corresponding quality scores. Most sequence analysis software will be able to open them. The Sample IDs associated with the R1 and R2 fastq files are listed in the table below:



Sample IDOriginal Sample IDRead 1 File NameRead 2 File Name


S001zr5677_100V1V3_R1.fastq.gzzr5677_100V1V3_R2.fastq.gz


S002zr5677_101V1V3_R1.fastq.gzzr5677_101V1V3_R2.fastq.gz


S003zr5677_102V1V3_R1.fastq.gzzr5677_102V1V3_R2.fastq.gz


S004zr5677_103V1V3_R1.fastq.gzzr5677_103V1V3_R2.fastq.gz


S005zr5677_104V1V3_R1.fastq.gzzr5677_104V1V3_R2.fastq.gz


S006zr5677_105V1V3_R1.fastq.gzzr5677_105V1V3_R2.fastq.gz


S007zr5677_106V1V3_R1.fastq.gzzr5677_106V1V3_R2.fastq.gz


S008zr5677_107V1V3_R1.fastq.gzzr5677_107V1V3_R2.fastq.gz


S009zr5677_108V1V3_R1.fastq.gzzr5677_108V1V3_R2.fastq.gz


S010zr5677_109V1V3_R1.fastq.gzzr5677_109V1V3_R2.fastq.gz


S011zr5677_10V1V3_R1.fastq.gzzr5677_10V1V3_R2.fastq.gz


S012zr5677_110V1V3_R1.fastq.gzzr5677_110V1V3_R2.fastq.gz


S013zr5677_111V1V3_R1.fastq.gzzr5677_111V1V3_R2.fastq.gz


S014zr5677_112V1V3_R1.fastq.gzzr5677_112V1V3_R2.fastq.gz


S015zr5677_113V1V3_R1.fastq.gzzr5677_113V1V3_R2.fastq.gz


S016zr5677_114V1V3_R1.fastq.gzzr5677_114V1V3_R2.fastq.gz


S017zr5677_115V1V3_R1.fastq.gzzr5677_115V1V3_R2.fastq.gz


S018zr5677_116V1V3_R1.fastq.gzzr5677_116V1V3_R2.fastq.gz


S019zr5677_117V1V3_R1.fastq.gzzr5677_117V1V3_R2.fastq.gz


S020zr5677_118V1V3_R1.fastq.gzzr5677_118V1V3_R2.fastq.gz


S021zr5677_119V1V3_R1.fastq.gzzr5677_119V1V3_R2.fastq.gz


S022zr5677_11V1V3_R1.fastq.gzzr5677_11V1V3_R2.fastq.gz


S023zr5677_120V1V3_R1.fastq.gzzr5677_120V1V3_R2.fastq.gz


S024zr5677_121V1V3_R1.fastq.gzzr5677_121V1V3_R2.fastq.gz


S025zr5677_122V1V3_R1.fastq.gzzr5677_122V1V3_R2.fastq.gz


S026zr5677_123V1V3_R1.fastq.gzzr5677_123V1V3_R2.fastq.gz


S027zr5677_124V1V3_R1.fastq.gzzr5677_124V1V3_R2.fastq.gz


S028zr5677_125V1V3_R1.fastq.gzzr5677_125V1V3_R2.fastq.gz


S029zr5677_126V1V3_R1.fastq.gzzr5677_126V1V3_R2.fastq.gz


S030zr5677_127V1V3_R1.fastq.gzzr5677_127V1V3_R2.fastq.gz


S031zr5677_128V1V3_R1.fastq.gzzr5677_128V1V3_R2.fastq.gz


S032zr5677_129V1V3_R1.fastq.gzzr5677_129V1V3_R2.fastq.gz


S033zr5677_12V1V3_R1.fastq.gzzr5677_12V1V3_R2.fastq.gz


S034zr5677_130V1V3_R1.fastq.gzzr5677_130V1V3_R2.fastq.gz


S035zr5677_131V1V3_R1.fastq.gzzr5677_131V1V3_R2.fastq.gz


S036zr5677_132V1V3_R1.fastq.gzzr5677_132V1V3_R2.fastq.gz


S037zr5677_133V1V3_R1.fastq.gzzr5677_133V1V3_R2.fastq.gz


S038zr5677_134V1V3_R1.fastq.gzzr5677_134V1V3_R2.fastq.gz


S039zr5677_135V1V3_R1.fastq.gzzr5677_135V1V3_R2.fastq.gz


S040zr5677_136V1V3_R1.fastq.gzzr5677_136V1V3_R2.fastq.gz


S041zr5677_137V1V3_R1.fastq.gzzr5677_137V1V3_R2.fastq.gz


S042zr5677_138V1V3_R1.fastq.gzzr5677_138V1V3_R2.fastq.gz


S043zr5677_139V1V3_R1.fastq.gzzr5677_139V1V3_R2.fastq.gz


S044zr5677_13V1V3_R1.fastq.gzzr5677_13V1V3_R2.fastq.gz


S045zr5677_140V1V3_R1.fastq.gzzr5677_140V1V3_R2.fastq.gz


S046zr5677_141V1V3_R1.fastq.gzzr5677_141V1V3_R2.fastq.gz


S047zr5677_142V1V3_R1.fastq.gzzr5677_142V1V3_R2.fastq.gz


S048zr5677_143V1V3_R1.fastq.gzzr5677_143V1V3_R2.fastq.gz


S049zr5677_144V1V3_R1.fastq.gzzr5677_144V1V3_R2.fastq.gz


S050zr5677_145V1V3_R1.fastq.gzzr5677_145V1V3_R2.fastq.gz


S051zr5677_146V1V3_R1.fastq.gzzr5677_146V1V3_R2.fastq.gz


S052zr5677_147V1V3_R1.fastq.gzzr5677_147V1V3_R2.fastq.gz


S053zr5677_148V1V3_R1.fastq.gzzr5677_148V1V3_R2.fastq.gz


S054zr5677_149V1V3_R1.fastq.gzzr5677_149V1V3_R2.fastq.gz


S055zr5677_14V1V3_R1.fastq.gzzr5677_14V1V3_R2.fastq.gz


S056zr5677_150V1V3_R1.fastq.gzzr5677_150V1V3_R2.fastq.gz


S057zr5677_151V1V3_R1.fastq.gzzr5677_151V1V3_R2.fastq.gz


S058zr5677_152V1V3_R1.fastq.gzzr5677_152V1V3_R2.fastq.gz


S059zr5677_153V1V3_R1.fastq.gzzr5677_153V1V3_R2.fastq.gz


S060zr5677_154V1V3_R1.fastq.gzzr5677_154V1V3_R2.fastq.gz


S061zr5677_155V1V3_R1.fastq.gzzr5677_155V1V3_R2.fastq.gz


S062zr5677_156V1V3_R1.fastq.gzzr5677_156V1V3_R2.fastq.gz


S063zr5677_157V1V3_R1.fastq.gzzr5677_157V1V3_R2.fastq.gz


S064zr5677_158V1V3_R1.fastq.gzzr5677_158V1V3_R2.fastq.gz


S065zr5677_159V1V3_R1.fastq.gzzr5677_159V1V3_R2.fastq.gz


S066zr5677_15V1V3_R1.fastq.gzzr5677_15V1V3_R2.fastq.gz


S067zr5677_160V1V3_R1.fastq.gzzr5677_160V1V3_R2.fastq.gz


S068zr5677_161V1V3_R1.fastq.gzzr5677_161V1V3_R2.fastq.gz


S069zr5677_162V1V3_R1.fastq.gzzr5677_162V1V3_R2.fastq.gz


S070zr5677_163V1V3_R1.fastq.gzzr5677_163V1V3_R2.fastq.gz


S071zr5677_164V1V3_R1.fastq.gzzr5677_164V1V3_R2.fastq.gz


S072zr5677_165V1V3_R1.fastq.gzzr5677_165V1V3_R2.fastq.gz


S073zr5677_166V1V3_R1.fastq.gzzr5677_166V1V3_R2.fastq.gz


S074zr5677_167V1V3_R1.fastq.gzzr5677_167V1V3_R2.fastq.gz


S075zr5677_168V1V3_R1.fastq.gzzr5677_168V1V3_R2.fastq.gz


S076zr5677_169V1V3_R1.fastq.gzzr5677_169V1V3_R2.fastq.gz


S077zr5677_16V1V3_R1.fastq.gzzr5677_16V1V3_R2.fastq.gz


S078zr5677_170V1V3_R1.fastq.gzzr5677_170V1V3_R2.fastq.gz


S079zr5677_171V1V3_R1.fastq.gzzr5677_171V1V3_R2.fastq.gz


S080zr5677_172V1V3_R1.fastq.gzzr5677_172V1V3_R2.fastq.gz


S081zr5677_173V1V3_R1.fastq.gzzr5677_173V1V3_R2.fastq.gz


S082zr5677_174V1V3_R1.fastq.gzzr5677_174V1V3_R2.fastq.gz


S083zr5677_175V1V3_R1.fastq.gzzr5677_175V1V3_R2.fastq.gz


S084zr5677_176V1V3_R1.fastq.gzzr5677_176V1V3_R2.fastq.gz


S085zr5677_177V1V3_R1.fastq.gzzr5677_177V1V3_R2.fastq.gz


S086zr5677_178V1V3_R1.fastq.gzzr5677_178V1V3_R2.fastq.gz


S087zr5677_179V1V3_R1.fastq.gzzr5677_179V1V3_R2.fastq.gz


S088zr5677_17V1V3_R1.fastq.gzzr5677_17V1V3_R2.fastq.gz


S089zr5677_180V1V3_R1.fastq.gzzr5677_180V1V3_R2.fastq.gz


S090zr5677_181V1V3_R1.fastq.gzzr5677_181V1V3_R2.fastq.gz


S091zr5677_182V1V3_R1.fastq.gzzr5677_182V1V3_R2.fastq.gz


S092zr5677_183V1V3_R1.fastq.gzzr5677_183V1V3_R2.fastq.gz


S093zr5677_184V1V3_R1.fastq.gzzr5677_184V1V3_R2.fastq.gz


S094zr5677_185V1V3_R1.fastq.gzzr5677_185V1V3_R2.fastq.gz


S095zr5677_186V1V3_R1.fastq.gzzr5677_186V1V3_R2.fastq.gz


S096zr5677_187V1V3_R1.fastq.gzzr5677_187V1V3_R2.fastq.gz


S097zr5677_188V1V3_R1.fastq.gzzr5677_188V1V3_R2.fastq.gz


S098zr5677_189V1V3_R1.fastq.gzzr5677_189V1V3_R2.fastq.gz


S099zr5677_18V1V3_R1.fastq.gzzr5677_18V1V3_R2.fastq.gz


S100zr5677_190V1V3_R1.fastq.gzzr5677_190V1V3_R2.fastq.gz


S101zr5677_191V1V3_R1.fastq.gzzr5677_191V1V3_R2.fastq.gz


S102zr5677_192V1V3_R1.fastq.gzzr5677_192V1V3_R2.fastq.gz


S103zr5677_193V1V3_R1.fastq.gzzr5677_193V1V3_R2.fastq.gz


S104zr5677_194V1V3_R1.fastq.gzzr5677_194V1V3_R2.fastq.gz


S105zr5677_195V1V3_R1.fastq.gzzr5677_195V1V3_R2.fastq.gz


S106zr5677_196V1V3_R1.fastq.gzzr5677_196V1V3_R2.fastq.gz


S107zr5677_197V1V3_R1.fastq.gzzr5677_197V1V3_R2.fastq.gz


S108zr5677_198V1V3_R1.fastq.gzzr5677_198V1V3_R2.fastq.gz


S109zr5677_199V1V3_R1.fastq.gzzr5677_199V1V3_R2.fastq.gz


S110zr5677_19V1V3_R1.fastq.gzzr5677_19V1V3_R2.fastq.gz


S111zr5677_1V1V3_R1.fastq.gzzr5677_1V1V3_R2.fastq.gz


S112zr5677_200V1V3_R1.fastq.gzzr5677_200V1V3_R2.fastq.gz


S113zr5677_201V1V3_R1.fastq.gzzr5677_201V1V3_R2.fastq.gz


S114zr5677_202V1V3_R1.fastq.gzzr5677_202V1V3_R2.fastq.gz


S115zr5677_203V1V3_R1.fastq.gzzr5677_203V1V3_R2.fastq.gz


S116zr5677_204V1V3_R1.fastq.gzzr5677_204V1V3_R2.fastq.gz


S117zr5677_205V1V3_R1.fastq.gzzr5677_205V1V3_R2.fastq.gz


S118zr5677_206V1V3_R1.fastq.gzzr5677_206V1V3_R2.fastq.gz


S119zr5677_207V1V3_R1.fastq.gzzr5677_207V1V3_R2.fastq.gz


S120zr5677_208V1V3_R1.fastq.gzzr5677_208V1V3_R2.fastq.gz


S121zr5677_209V1V3_R1.fastq.gzzr5677_209V1V3_R2.fastq.gz


S122zr5677_20V1V3_R1.fastq.gzzr5677_20V1V3_R2.fastq.gz


S123zr5677_210V1V3_R1.fastq.gzzr5677_210V1V3_R2.fastq.gz


S124zr5677_211V1V3_R1.fastq.gzzr5677_211V1V3_R2.fastq.gz


S125zr5677_212V1V3_R1.fastq.gzzr5677_212V1V3_R2.fastq.gz


S126zr5677_213V1V3_R1.fastq.gzzr5677_213V1V3_R2.fastq.gz


S127zr5677_214V1V3_R1.fastq.gzzr5677_214V1V3_R2.fastq.gz


S128zr5677_215V1V3_R1.fastq.gzzr5677_215V1V3_R2.fastq.gz


S129zr5677_216V1V3_R1.fastq.gzzr5677_216V1V3_R2.fastq.gz


S130zr5677_217V1V3_R1.fastq.gzzr5677_217V1V3_R2.fastq.gz


S131zr5677_218V1V3_R1.fastq.gzzr5677_218V1V3_R2.fastq.gz


S132zr5677_219V1V3_R1.fastq.gzzr5677_219V1V3_R2.fastq.gz


S133zr5677_21V1V3_R1.fastq.gzzr5677_21V1V3_R2.fastq.gz


S134zr5677_220V1V3_R1.fastq.gzzr5677_220V1V3_R2.fastq.gz


S135zr5677_221V1V3_R1.fastq.gzzr5677_221V1V3_R2.fastq.gz


S136zr5677_222V1V3_R1.fastq.gzzr5677_222V1V3_R2.fastq.gz


S137zr5677_223V1V3_R1.fastq.gzzr5677_223V1V3_R2.fastq.gz


S138zr5677_224V1V3_R1.fastq.gzzr5677_224V1V3_R2.fastq.gz


S139zr5677_225V1V3_R1.fastq.gzzr5677_225V1V3_R2.fastq.gz


S140zr5677_226V1V3_R1.fastq.gzzr5677_226V1V3_R2.fastq.gz


S141zr5677_227V1V3_R1.fastq.gzzr5677_227V1V3_R2.fastq.gz


S142zr5677_228V1V3_R1.fastq.gzzr5677_228V1V3_R2.fastq.gz


S143zr5677_229V1V3_R1.fastq.gzzr5677_229V1V3_R2.fastq.gz


S144zr5677_22V1V3_R1.fastq.gzzr5677_22V1V3_R2.fastq.gz


S145zr5677_230V1V3_R1.fastq.gzzr5677_230V1V3_R2.fastq.gz


S146zr5677_231V1V3_R1.fastq.gzzr5677_231V1V3_R2.fastq.gz


S147zr5677_232V1V3_R1.fastq.gzzr5677_232V1V3_R2.fastq.gz


S148zr5677_233V1V3_R1.fastq.gzzr5677_233V1V3_R2.fastq.gz


S149zr5677_234V1V3_R1.fastq.gzzr5677_234V1V3_R2.fastq.gz


S150zr5677_235V1V3_R1.fastq.gzzr5677_235V1V3_R2.fastq.gz


S151zr5677_236V1V3_R1.fastq.gzzr5677_236V1V3_R2.fastq.gz


S152zr5677_237V1V3_R1.fastq.gzzr5677_237V1V3_R2.fastq.gz


S153zr5677_238V1V3_R1.fastq.gzzr5677_238V1V3_R2.fastq.gz


S154zr5677_239V1V3_R1.fastq.gzzr5677_239V1V3_R2.fastq.gz


S155zr5677_23V1V3_R1.fastq.gzzr5677_23V1V3_R2.fastq.gz


S156zr5677_240V1V3_R1.fastq.gzzr5677_240V1V3_R2.fastq.gz


S157zr5677_241V1V3_R1.fastq.gzzr5677_241V1V3_R2.fastq.gz


S158zr5677_242V1V3_R1.fastq.gzzr5677_242V1V3_R2.fastq.gz


S159zr5677_243V1V3_R1.fastq.gzzr5677_243V1V3_R2.fastq.gz


S160zr5677_244V1V3_R1.fastq.gzzr5677_244V1V3_R2.fastq.gz


S161zr5677_245V1V3_R1.fastq.gzzr5677_245V1V3_R2.fastq.gz


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Please download and save the file to your computer storage device. The download link will expire after 60 days upon your receiving of this report.

Raw sequence data download link:

 

VI. Analysis - DADA2 Read Processing

3. Error plots from learning the error rates After DADA2 building the error model for the set of data, it is always worthwhile, as a sanity check if nothing else, to visualize the estimated error rates. The error rates for each possible transition (A→C, A→G, …) are shown below. Points are the observed error rates for each consensus quality score. The black line shows the estimated error rates after convergence of the machine-learning algorithm. The red line shows the error rates expected under the nominal definition of the Q-score. The ideal result would be the estimated error rates (black line) are a good fit to the observed rates (points), and the error rates drop with increased quality as expected.

Forward Read R1 Error Plot


Reverse Read R2 Error Plot

The PDF version of these plots are available here:

What is DADA2?

DADA2 is a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. DADA2 identified more real variants and output fewer spurious sequences than other methods.

DADA2’s advantage is that it uses more of the data. The DADA2 error model incorporates quality information, which is ignored by all other methods after filtering. The DADA2 error model incorporates quantitative abundances, whereas most other methods use abundance ranks if they use abundance at all. The DADA2 error model identifies the differences between sequences, eg. A->C, whereas other methods merely count the mismatches. DADA2 can parameterize its error model from the data itself, rather than relying on previous datasets that may or may not reflect the PCR and sequencing protocols used in your study.

DADA2 Publication: Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23. PMID: 27214047; PMCID: PMC4927377.

DADA2 Software Package is available as an R package at : https://benjjneb.github.io/dada2/index.html

Analysis Procedures:

DADA2 pipeline includes several tools for read quality control, including quality filtering, trimming, denoising, pair merging and chimera filtering. Below are the major processing steps of DADA2:

Step 1. Read trimming based on sequence quality The quality of NGS Illumina sequences often decreases toward the end of the reads. DADA2 allows to trim off the poor quality read ends in order to improve the error model building and pair mergicing performance.

Step 2. Learn the Error Rates The DADA2 algorithm makes use of a parametric error model (err) and every amplicon dataset has a different set of error rates. The learnErrors method learns this error model from the data, by alternating estimation of the error rates and inference of sample composition until they converge on a jointly consistent solution. As in many machine-learning problems, the algorithm must begin with an initial guess, for which the maximum possible error rates in this data are used (the error rates if only the most abundant sequence is correct and all the rest are errors).

Step 3. Infer amplicon sequence variants (ASVs) based on the error model built in previous step. This step is also called sequence "denoising". The outcome of this step is a list of ASVs that are the equivalent of oligonucleotides.

Step 4. Merge paired reads. If the sequencing products are read pairs, DADA2 will merge the R1 and R2 ASVs into single sequences. Merging is performed by aligning the denoised forward reads with the reverse-complement of the corresponding denoised reverse reads, and then constructing the merged “contig” sequences. By default, merged sequences are only output if the forward and reverse reads overlap by at least 12 bases, and are identical to each other in the overlap region (but these conditions can be changed via function arguments).

Step 5. Remove chimera. The core dada method corrects substitution and indel errors, but chimeras remain. Fortunately, the accuracy of sequence variants after denoising makes identifying chimeric ASVs simpler than when dealing with fuzzy OTUs. Chimeric sequences are identified if they can be exactly reconstructed by combining a left-segment and a right-segment from two more abundant “parent” sequences. The frequency of chimeric sequences varies substantially from dataset to dataset, and depends on on factors including experimental procedures and sample complexity.

Results

1. Read Quality Plots NGS sequence analaysis starts with visualizing the quality of the sequencing. Below are the quality plots of the first sample for the R1 and R2 reads separately. In gray-scale is a heat map of the frequency of each quality score at each base position. The mean quality score at each position is shown by the green line, and the quartiles of the quality score distribution by the orange lines. The forward reads are usually of better quality. It is a common practice to trim the last few nucleotides to avoid less well-controlled errors that can arise there. The trimming affects the downstream steps including error model building, merging and chimera calling. FOMC uses an empirical approach to test many combinations of different trim length in order to achieve best final amplicon sequence variants (ASVs), see the next section “Optimal trim length for ASVs”.

Below is the link to a PDF file for viewing the quality plots for all samples:

2. Optimal trim length for ASVs The final number of merged and chimera-filtered ASVs depends on the quality filtering (hence trimming) in the very beginning of the DADA2 pipeline. In order to achieve highest number of ASVs, an empirical approach was used -

  1. Create a random subset of each sample consisting of 5,000 R1 and 5,000 R2 (to reduce computation time)
  2. Trim 10 bases at a time from the ends of both R1 and R2 up to 50 bases
  3. For each combination of trimmed length (e.g., 300x300, 300x290, 290x290 etc), the trimmed reads are subject to the entire DADA2 pipeline for chimera-filtered merged ASVs
  4. The combination with highest percentage of the input reads becoming final ASVs is selected for the complete set of data

Below is the result of such operation, showing ASV percentages of total reads for all trimming combinations (1st Column = R1 lengths in bases; 1st Row = R2 lengths in bases):

 
 

4. DADA2 Result Summary The table below shows the summary of the DADA2 analysis, tracking paired read counts of each samples for all the steps during DADA2 denoising process - including end-trimming (filtered), denoising (denoisedF, denoisedF), pair merging (merged) and chimera removal (nonchim).

Sample IDF5677.S101F5677.S102F5677.S103F5677.S104F5677.S105F5677.S106F5677.S107F5677.S108F5677.S109F5677.S110F5677.S111F5677.S112F5677.S113F5677.S114F5677.S115F5677.S116F5677.S117F5677.S118F5677.S119F5677.S120F5677.S121F5677.S122F5677.S123F5677.S124F5677.S125F5677.S126F5677.S127F5677.S128F5677.S129F5677.S130F5677.S131F5677.S132F5677.S133F5677.S134F5677.S135F5677.S136F5677.S137F5677.S138F5677.S139F5677.S140F5677.S141F5677.S142F5677.S143F5677.S144F5677.S145F5677.S146F5677.S147F5677.S148F5677.S149F5677.S150F5677.S001F5677.S002F5677.S003F5677.S004F5677.S005F5677.S006F5677.S007F5677.S008F5677.S009F5677.S010F5677.S011F5677.S012F5677.S013F5677.S014F5677.S015F5677.S016F5677.S017F5677.S018F5677.S019F5677.S020F5677.S021F5677.S022F5677.S023F5677.S024F5677.S025F5677.S026F5677.S027F5677.S028F5677.S029F5677.S030F5677.S031F5677.S032F5677.S033F5677.S034F5677.S035F5677.S036F5677.S037F5677.S038F5677.S039F5677.S040F5677.S041F5677.S042F5677.S043F5677.S044F5677.S045F5677.S046F5677.S047F5677.S048F5677.S049F5677.S050F5677.S151F5677.S152F5677.S153F5677.S154F5677.S155F5677.S156F5677.S157F5677.S158F5677.S159F5677.S160F5677.S161F5677.S162F5677.S163F5677.S164F5677.S165F5677.S166F5677.S167F5677.S168F5677.S169F5677.S170F5677.S171F5677.S172F5677.S173F5677.S174F5677.S175F5677.S176F5677.S177F5677.S178F5677.S179F5677.S180F5677.S181F5677.S182F5677.S183F5677.S184F5677.S185F5677.S186F5677.S187F5677.S188F5677.S189F5677.S190F5677.S191F5677.S192F5677.S193F5677.S194F5677.S195F5677.S196F5677.S197F5677.S198F5677.S199F5677.S200F5677.S201F5677.S202F5677.S203F5677.S204F5677.S205F5677.S206F5677.S207F5677.S208F5677.S209F5677.S210F5677.S211F5677.S212F5677.S213F5677.S214F5677.S215F5677.S216F5677.S217F5677.S218F5677.S219F5677.S220F5677.S221F5677.S222F5677.S223F5677.S224F5677.S225F5677.S226F5677.S227F5677.S228F5677.S229F5677.S230F5677.S231F5677.S232F5677.S233F5677.S234F5677.S235F5677.S236F5677.S237F5677.S238F5677.S239F5677.S240F5677.S241F5677.S242F5677.S243F5677.S244F5677.S245F5677.S246F5677.S247F5677.S248F5677.S249F5677.S250F5677.S251F5677.S252F5677.S253F5677.S254F5677.S255F5677.S256F5677.S257F5677.S258F5677.S259F5677.S260F5677.S261F5677.S262F5677.S263F5677.S264F5677.S265F5677.S266F5677.S267F5677.S268F5677.S269F5677.S270F5677.S271F5677.S272F5677.S273F5677.S274F5677.S275F5677.S276F5677.S277F5677.S278F5677.S279F5677.S280F5677.S281F5677.S282F5677.S283F5677.S284F5677.S285F5677.S286F5677.S287F5677.S288F5677.S289F5677.S290F5677.S291F5677.S292F5677.S293F5677.S294F5677.S295F5677.S296F5677.S297F5677.S298F5677.S299F5677.S300F5677.S301F5677.S302F5677.S303F5677.S304F5677.S305F5677.S306F5677.S307F5677.S308F5677.S309F5677.S310F5677.S311F5677.S312F5677.S313F5677.S314F5677.S315F5677.S316F5677.S317F5677.S318F5677.S319F5677.S320F5677.S321F5677.S322F5677.S323F5677.S324F5677.S325F5677.S326F5677.S327F5677.S328F5677.S329F5677.S330F5677.S331F5677.S332F5677.S333F5677.S334F5677.S335F5677.S336F5677.S337F5677.S338F5677.S339F5677.S340F5677.S341F5677.S342F5677.S343F5677.S344F5677.S345F5677.S346F5677.S347F5677.S348F5677.S349F5677.S350F5677.S351F5677.S352F5677.S353F5677.S354F5677.S355F5677.S356F5677.S357F5677.S358F5677.S359F5677.S360F5677.S361F5677.S362F5677.S363F5677.S364F5677.S365F5677.S366F5677.S367F5677.S368F5677.S369F5677.S370F5677.S371F5677.S372F5677.S373F5677.S374F5677.S375F5677.S376F5677.S377F5677.S378F5677.S379F5677.S380F5677.S381F5677.S382F5677.S383F5677.S384F5677.S385F5677.S386F5677.S387F5677.S388F5677.S389F5677.S390F5677.S391F5677.S392F5677.S393F5677.S394F5677.S395F5677.S396F5677.S397F5677.S398F5677.S399F5677.S400F5677.S401F5677.S402F5677.S403F5677.S404F5677.S405F5677.S406F5677.S407F5677.S408F5677.S409F5677.S410F5677.S411F5677.S412F5677.S413F5677.S414F5677.S415F5677.S416F5677.S417F5677.S418F5677.S419F5677.S420F5677.S421F5677.S422F5677.S423F5677.S424F5677.S425F5677.S426F5677.S427F5677.S428F5677.S429F5677.S430F5677.S431F5677.S432F5677.S433F5677.S434F5677.S435F5677.S436F5677.S437F5677.S438F5677.S439F5677.S440F5677.S441F5677.S442F5677.S443F5677.S444F5677.S445F5677.S446F5677.S447F5677.S448F5677.S449F5677.S450F5677.S451F5677.S452F5677.S453F5677.S454F5677.S455F5677.S456F5677.S457F5677.S458F5677.S459F5677.S460F5677.S461F5677.S462F5677.S463F5677.S464F5677.S465F5677.S466F5677.S467F5677.S468F5677.S469F5677.S470F5677.S471F5677.S472F5677.S473F5677.S474F5677.S475F5677.S476F5677.S477F5677.S478F5677.S479F5677.S480F5677.S481F5677.S482F5677.S483F5677.S484F5677.S485F5677.S486F5677.S487F5677.S488F5677.S489F5677.S490F5677.S491F5677.S492F5677.S493F5677.S494F5677.S495F5677.S496F5677.S497F5677.S498F5677.S499F5677.S500F5677.S501F5677.S502F5677.S503F5677.S504F5677.S505F5677.S506F5677.S507F5677.S508F5677.S509F5677.S510F5677.S511F5677.S512F5677.S513F5677.S514F5677.S515F5677.S516F5677.S517F5677.S518F5677.S519F5677.S520F5677.S521F5677.S522F5677.S523F5677.S524F5677.S525F5677.S526F5677.S527F5677.S528F5677.S529F5677.S530F5677.S531F5677.S532F5677.S533F5677.S534F5677.S535F5677.S536F5677.S537F5677.S538F5677.S539F5677.S540F5677.S541F5677.S542F5677.S543F5677.S544F5677.S545F5677.S546F5677.S547F5677.S548F5677.S549F5677.S550F5677.S051F5677.S052F5677.S053F5677.S054F5677.S055F5677.S056F5677.S057F5677.S058F5677.S059F5677.S060F5677.S061F5677.S062F5677.S063F5677.S064F5677.S065F5677.S066F5677.S067F5677.S068F5677.S069F5677.S070F5677.S071F5677.S072F5677.S073F5677.S074F5677.S075F5677.S076F5677.S077F5677.S078F5677.S079F5677.S080F5677.S081F5677.S082F5677.S083F5677.S084F5677.S085F5677.S086F5677.S087F5677.S088F5677.S089F5677.S090F5677.S091F5677.S092F5677.S093F5677.S094F5677.S095F5677.S096F5677.S097F5677.S098F5677.S099F5677.S100F5677.S551F5677.S552F5677.S553F5677.S554F5677.S555F5677.S556F5677.S557F5677.S558F5677.S559F5677.S560F5677.S561F5677.S562F5677.S563F5677.S564F5677.S565F5677.S566F5677.S567F5677.S568F5677.S569F5677.S570F5677.S571F5677.S572F5677.S573F5677.S574F5677.S575F5677.S576F5677.S577F5677.S578F5677.S579F5677.S580F5677.S581F5677.S582F5677.S583F5677.S584F5677.S585F5677.S586F5677.S587F5677.S588F5677.S589F5677.S590F5677.S591F5677.S592F5677.S593F5677.S594F5677.S595F5677.S596F5677.S597F5677.S598F5677.S599F5677.S600F5677.S601F5677.S602F5677.S603F5677.S604F5677.S605F5677.S606F5677.S607F5677.S608F5677.S609F5677.S610F5677.S611F5677.S612F5677.S613F5677.S614F5677.S615F5677.S616F5677.S617F5677.S618F5677.S619F5677.S620F5677.S621F5677.S622F5677.S623F5677.S624F5677.S625F5677.S626F5677.S627F5677.S628F5677.S629F5677.S630F5677.S631F5677.S632F5677.S633F5677.S634F5677.S635F5677.S636F5677.S637F5677.S638F5677.S639F5677.S640F5677.S641F5677.S642F5677.S643F5677.S644F5677.S645F5677.S646F5677.S647F5677.S648F5677.S649F5677.S650F5677.S651F5677.S652F5677.S653F5677.S654F5677.S655F5677.S656F5677.S657F5677.S658F5677.S659F5677.S660F5677.S661F5677.S662F5677.S663F5677.S664F5677.S665F5677.S666F5677.S667F5677.S668F5677.S669F5677.S670F5677.S671F5677.S672F5677.S673F5677.S674F5677.S675F5677.S676F5677.S677F5677.S678F5677.S679F5677.S680F5677.S681F5677.S682Row SumPercentage
input55,05162,59950,74451,39451,48555,93053,51763,81250,68744,67951,53460,41854,97155,32055,79758,63550,42763,99163,08854,19551,21458,55361,28266,21666,15243,86547,13754,02844,51046,17251,61951,10245,95247,94154,61452,96143,37048,75046,42061,00049,94156,43149,14247,82738,96959,99043,89354,09048,03957,77962,94771,41875,42046,49356,41755,34251,94155,66058,77659,24154,20066,82343,99557,57446,62143,33359,75257,37752,43654,74849,77946,67654,19451,72355,26957,67748,72156,73252,93765,17379,60261,63953,96252,68870,87354,80461,78264,23656,03753,67458,59664,19249,37551,52551,01658,35459,63738,45251,84250,08543,43540,45652,43246,61157,77950,52342,20352,75750,93638,80645,33040,35146,03947,09150,40563,80846,39140,45245,19242,35445,05743,40839,88650,23738,19942,58158,54746,17551,14344,94546,96355,26050,12851,06951,95141,57746,76151,93548,04243,81146,16160,08253,48249,58345,27041,94237,63047,00051,21939,49045,30244,94651,45845,56545,73450,67051,05244,86849,35749,08345,97952,04740,97343,00450,09253,20045,69156,09257,66647,40754,24361,93243,17142,77841,76144,54540,89344,41943,60539,31052,27749,02865,50445,99846,68652,52758,71052,54054,92138,78234,04939,32736,49361,01530,89248,51139,16858,49557,88049,50849,42851,98747,69564,01057,21539,39752,07749,38747,16546,49745,27148,37252,15842,07848,97349,71649,48642,80650,70136,04950,16343,45739,87244,15741,18746,79861,40438,25732,35639,02637,83951,69850,32447,37951,22248,29144,95849,45253,69453,99042,99142,96341,85944,27552,11339,93950,29449,76060,19838,22348,35947,50133,91945,06634,72639,09048,89446,87743,39354,18046,70546,14848,79755,48850,57943,34051,11240,46949,20346,45767,91845,24045,59043,32448,92837,80336,78534,14440,15338,76538,26464,14759,01443,56056,85646,62850,47151,58151,31753,88342,97949,14847,66960,50233,00832,23638,03938,38029,54333,49344,47249,71836,38637,39159,54342,32148,37841,05550,74040,74545,85041,84948,95645,91055,31563,84945,27155,98044,06345,59838,58352,09839,69639,83837,64443,10161,44534,64342,42533,13244,94637,78438,83246,08344,90445,58845,20183,91237,12637,24034,64851,17544,60623,97734,68129,38217,73845,16559,75125,84526,26732,04219,81018,45432,38630,84628,85932,83932,00167,16020,26837,19626,86623,50023,20027,26530,95239,74426,62223,24166,55522,00718,00732,45418,90937,21823,27339,02019,62118,98831,53454,99736,75012,03435,05524,41432,59838,41424,34724,92417,38830,25740,54064,32234,93030,73626,33531,44028,61916,16831,94828,91729,06330,31051,07737,89328,92124,20626,90634,67231,39332,02529,91230,86738,43755,92925,94134,54925,37622,16327,72531,95134,86534,94045,27625,30151,49021,95233,19329,15336,68625,32034,45648,03832,96629,16232,02352,28219,06417,10934,09442,66330,03627,11823,79022,20128,68724,80853,34628,55443,27235,30131,06023,74728,50828,22132,83738,29433,31152,50426,41745,36827,02025,07439,56233,49436,78027,81335,57224,79051,71340,30038,75137,38229,99427,11031,17141,24341,44432,20432,90858,89840,16138,23242,47629,49125,50220,51634,34034,13332,87243,21554,80236,05929,51839,03232,26533,10132,37340,58851,97250,49651,17756,85262,70157,13343,95059,99358,78557,20546,42159,10056,59167,47144,77660,85945,81867,42058,86755,14455,63062,15358,75352,29853,44642,07160,35237,61844,57757,14954,42461,67559,41177,51964,76753,11355,34548,94156,93759,73267,64745,91338,57240,47835,57737,26839,16050,77056,49654,77034,73636,51221,32060,67650,12434,94828,68426,19833,96529,63338,39233,37030,75826,20125,14856,84031,73433,98835,87237,13329,09832,59535,97038,01032,92238,97257,22427,38131,96133,80534,34945,98932,56823,19527,17330,92132,91268,36428,09357,05037,39735,39634,26931,16236,71940,36423,55930,37155,13728,73530,35431,24223,71443,00033,26324,92321,39833,70340,79755,55730,03126,33144,24035,98632,84630,45532,21515,94533,54737,71657,34427,97548,94930,06838,44841,04937,12336,89431,96728,46727,41950,17536,92433,68132,69527,78545,43620,30230,41234,34628,21528,77553,65822,85133,44041,94163,26749,32661,13458,20856,95659,92453,36747,38649,67950,73841,96456,72145,32654,37347,57453,98569,19160,45582,72956,09888,27059,81472,37548,26363,82347,73640,32445,02034,12640,64846,12782,97259,47956,03361,55652,77130,089,286100.00%
filtered54,26561,75250,02950,60150,70755,15252,72362,87949,95044,03350,79859,55654,21254,50754,94757,78249,69963,04662,20053,38250,47257,69560,38565,21365,24243,26546,48253,28843,90445,50750,84650,33445,32947,30953,85952,13542,76048,03845,74260,09249,23255,99448,75047,10238,68359,51743,61053,70247,69757,32262,00270,36774,32245,83855,56954,55751,15054,83857,88558,39453,44065,84543,35556,70845,92842,76758,96056,58751,72053,92449,13446,05653,40850,93854,52856,82347,99755,87552,15964,32378,42660,77853,21451,96569,81354,00260,89663,27555,24852,87157,68763,32248,66150,77550,30957,47158,81937,89251,07949,28943,08940,14552,06046,26456,94350,19441,84052,37150,55738,50544,98740,07145,63046,75350,04162,87046,04940,16944,85241,94644,74343,06339,63449,84537,93842,27257,72145,82850,75644,61546,53054,86249,72050,74851,60841,28146,43151,14847,71243,48345,82959,61253,10749,20944,89241,63837,39346,62850,50139,25344,96544,61851,10145,21745,37250,30450,63844,55848,97648,35745,68251,66140,63242,65649,73352,80745,38155,67357,29247,07253,48861,03842,85142,43541,48444,18940,64244,06543,26139,05851,90848,66964,49945,68546,30452,18658,24552,21854,53238,50533,76939,05336,19660,07930,69948,14438,86258,08657,40049,11849,07051,65847,31663,51256,33839,15251,67549,03146,79946,14545,00548,03751,79141,79248,59349,00649,10242,44350,34835,83149,77843,12139,56543,82140,85646,44060,47837,99432,18838,74837,54651,32549,96146,99250,84647,97544,65548,77953,31353,53042,67642,63741,55343,92251,76839,69349,92349,32859,29737,94948,02847,12533,68644,76834,49838,81648,51746,54343,06253,41346,34445,78048,45055,11950,17143,02250,73440,19548,82346,08166,90144,89445,28442,97848,56737,51136,51733,87339,82438,47538,03463,20358,19143,25056,38846,29450,09451,16050,89353,46842,71548,77147,29159,58432,78532,00137,76038,07429,33433,29144,16149,34936,11937,11058,71742,04848,00340,79850,34440,41945,47741,53948,57645,56954,90162,93344,94455,57243,74945,22138,34851,68139,42639,51937,40042,76060,56234,39342,09932,89244,61237,50338,48845,74044,54245,25744,84682,73036,87336,90034,40650,77444,28123,78134,38029,14917,59544,74758,89325,64126,06831,77419,64718,26732,14230,57128,65232,54731,74166,17120,11536,92326,63623,33523,03827,03230,71139,36126,36323,03365,51821,79917,83832,19118,77136,88423,09438,65819,42318,81331,24754,22736,40611,92734,75224,21832,29538,01024,13624,71717,25029,98439,94263,37634,56130,47126,08431,16728,38016,02731,69028,63328,79830,05350,33537,58128,65323,99526,67134,38831,12631,74129,66030,61138,11855,18025,71134,24825,17621,94627,49731,69034,52934,64844,89925,06450,72721,74932,93328,89336,35925,10834,15447,67732,65928,91031,71051,55518,90916,97633,80142,30229,75326,87323,62622,04628,41324,57452,61428,30442,92135,02730,76423,55128,24027,96832,55537,95233,01851,73126,17144,97326,78424,84039,21733,21936,47927,56135,27624,56150,96639,92738,44137,08629,73226,87830,88340,87841,08131,92632,62258,01039,81737,90842,13029,24525,29220,33534,04133,82032,57442,83853,95135,70029,25738,67231,99132,80732,11240,22551,13849,81650,47356,08561,78756,25243,38759,03957,93756,38945,78558,21855,73066,50744,14660,02845,18466,44958,02154,35254,78261,30057,90051,57152,63941,41559,43137,09243,94356,32253,70160,77458,49376,32063,82952,38654,57548,22856,12958,88166,61145,31237,96839,83335,05136,72638,55050,03355,61953,98434,47636,17721,14659,81549,40634,61028,45525,96833,72429,35438,06933,07430,45825,99024,95655,98731,44933,71735,53036,81928,83832,30535,65437,65232,60338,60656,43627,12831,69133,48034,09445,57732,29523,01026,94830,69132,65067,24727,84356,54137,04435,05233,98230,87136,41040,01123,33230,10554,32628,50030,08631,00023,47642,62132,95324,76521,24133,42640,47654,78029,77526,08143,87535,66532,60530,21031,94515,84333,24637,36756,57727,75348,49429,79138,12040,69536,81236,57631,71028,22427,14649,46736,55533,39632,41227,54545,08920,14630,15534,00927,95428,52852,92922,69133,14941,58062,34048,65060,28357,34756,15759,02852,58946,68248,99249,98441,35455,87744,61953,58546,87553,21168,18759,56981,44655,32187,01558,93771,24047,59762,94047,07539,66444,37033,69340,11445,51581,80758,56455,18960,67252,00629,768,43098.93%
denoisedF49,41657,15046,74446,51047,61750,72948,93159,07345,50239,75446,73155,39050,51750,41451,24154,65445,88159,18358,73049,72546,67053,44857,29561,94561,08239,63143,28049,42241,45141,85747,30447,13440,98544,56750,09248,15038,85544,90241,84156,99845,52753,68945,69743,19236,51956,41140,85251,30745,40954,17257,43166,09868,64341,67452,69250,67846,75250,78954,25054,58049,74561,30539,97951,78942,12938,49454,50753,75348,01349,70144,70842,26649,45046,43849,64152,24644,43852,37948,08359,53973,02856,20048,76946,87965,59550,40056,83257,79951,01848,42853,93858,71544,38846,92046,11653,34154,45234,14647,32145,53640,51537,86349,64743,76953,09547,47339,00649,62448,13035,77042,50037,30043,26943,99946,98358,83443,81637,97642,20439,42242,02940,32736,77947,16335,65539,62452,73843,02047,74641,64743,70451,96746,89347,82548,53838,63944,25247,50044,62040,89243,24456,19050,56546,62842,54539,11135,16244,36046,24836,91542,93842,52748,41341,94243,09147,64348,25541,68046,41844,34042,89348,42838,04040,37647,19349,80843,15253,55754,27744,29348,94155,94040,14840,09238,84342,62138,21341,78140,66437,11048,82446,12760,97543,10644,11148,82054,52348,83951,53836,30031,31636,84034,59255,83428,63345,88535,81954,32254,61046,20746,25348,89744,80560,11752,09636,74748,88946,68344,44144,11943,03345,57648,51539,14246,28443,84946,24539,09147,69033,88047,76440,17937,44641,25437,99343,27855,52835,75430,20336,35335,81448,08447,02043,86646,60744,98442,28244,00051,29950,30040,04040,72438,74641,40148,67637,56447,14846,03354,80335,57845,53845,21731,18642,55332,73636,54245,57843,97739,78249,21443,26442,75346,12852,25146,91140,00047,84037,60444,93442,63262,19742,45442,81340,31745,45335,32533,94131,43836,69536,40535,67357,87154,50040,68752,78643,59747,27948,21547,42550,73341,11045,49044,04754,73331,26529,87236,39535,51127,48931,61741,72447,09634,16134,52854,97339,61145,59137,99847,27437,91742,81638,92245,56642,92951,88059,15942,47252,36740,84842,87635,88249,57736,42137,71235,02640,28456,79432,15040,43230,57942,45535,64636,29843,42841,35542,41442,68777,91134,02235,46232,14048,23742,14122,70033,07628,47516,67143,88954,30224,86724,69231,02618,59217,32430,51629,46527,58331,29830,51661,89319,02035,86725,70522,26521,34725,74029,69938,25125,02321,85662,28320,72616,67830,91317,59935,91121,78937,53718,33717,85930,35650,06635,14410,94433,03723,00730,98536,60722,98223,55716,02428,42437,08159,20632,97829,07124,88230,01626,96114,87329,97226,89727,63428,63646,51735,87227,36222,49325,23733,75729,55830,59228,12729,13336,23251,40324,46332,96923,17921,19226,51930,11033,01232,76943,45724,03147,37820,31331,89027,30334,42523,98333,25146,57431,28527,77430,86148,42417,43116,28932,71440,66928,63025,57022,40621,10327,38723,29047,54027,04641,94033,52629,54122,21427,43626,68931,41136,75031,59548,62525,17243,63725,87323,69538,18731,68635,20826,66433,95123,55047,05038,31336,99135,82228,77525,62030,14840,25539,42530,71131,24853,41538,87336,55041,31727,52824,04519,29132,72732,51731,25840,72149,28634,09327,89137,22330,81631,19330,82138,62846,85945,89646,98052,16957,94852,79438,96154,22153,25251,68941,43155,43151,93762,99640,48856,13141,81363,37652,19050,08551,53457,29553,00448,28548,83937,61555,80032,99940,41753,38950,17457,43954,15072,20559,01747,33050,65643,96251,91555,41962,18341,91735,02437,06831,37434,07336,59845,69451,98550,53332,61834,86420,03754,82545,66733,47527,30325,03932,29527,87136,40132,00429,31424,75523,86551,68130,52632,14733,93235,21927,48130,86534,53236,32530,68037,47952,82226,11030,01432,50332,59644,86331,09321,68125,79929,36531,27362,40226,53455,20335,55433,79532,44329,71035,55238,49422,65829,23650,75127,62128,67030,14022,11841,33731,46723,04720,54331,94538,99451,21328,83125,12242,92233,67431,09028,72930,54014,87431,65336,28552,71326,90947,21028,87636,75139,56835,70735,01730,29426,35826,05045,33135,13631,68831,03325,81442,77818,99728,75732,64926,85827,02047,96521,67931,74539,32258,74944,98455,72253,31553,25555,00948,02543,14345,25346,68338,08851,98540,96349,72743,95349,45464,11355,64977,32651,02982,60354,59168,03143,87859,18744,02936,27541,13430,98237,40940,97276,59554,51348,97156,25847,02827,987,11693.01%
denoisedR51,79558,85747,88147,89048,30752,06250,44159,91447,42141,84548,15256,32451,99551,30852,55755,01947,18460,47559,81050,50848,36254,78557,95862,54261,70240,99843,99750,98341,99443,35948,11047,85543,17944,69951,54949,42540,48645,94043,68658,03946,52353,82046,11644,33536,48456,37641,20151,29045,56154,45358,61067,13770,68943,53053,52251,24348,91952,25855,15355,34950,62162,64641,39153,45943,40140,87056,15954,23848,98451,17346,58643,52650,21548,10251,97953,51545,38353,20749,23061,95674,95957,93749,95749,54267,06651,39858,06059,99352,68450,17854,95060,96846,14148,22947,91254,42656,11135,69848,13046,31340,79537,79549,47743,62654,03247,88039,48349,82748,14136,19742,74737,77543,39644,47347,25859,70443,62338,13942,81439,55242,39340,80837,50647,60935,86340,00854,81943,85048,39441,97543,91952,58147,41548,34448,69439,13244,14448,59245,01541,08743,86256,98650,40547,03242,41038,93234,92743,44447,80037,17542,58042,49347,94842,36143,20447,55948,15142,30446,76445,78242,87148,70438,47540,41247,32749,89243,54653,45354,29444,40551,05057,77540,24840,13139,09442,11838,66441,68540,92637,29349,03946,04062,09843,37143,87449,45054,98549,16851,31336,58131,70037,15234,56956,76229,05346,00836,93754,99554,65847,29246,27848,97744,76860,55453,64637,02948,97546,67344,91143,91342,93845,59349,03839,97446,20146,31746,37439,90647,67033,71347,23440,76237,89041,56238,37443,97357,13235,57730,33136,06435,95749,02947,53244,19248,12545,49042,22746,31551,06050,92040,26540,82539,06842,05048,99537,75547,19046,89356,41835,49045,41844,95731,91442,72232,19535,90445,42744,53840,28451,22843,63443,67045,97552,02347,17940,70848,26938,01145,93043,66163,78242,39142,75140,27646,43335,79634,36331,66337,73336,47435,38559,70355,73140,51153,29444,27147,38048,42248,46550,83040,72645,47244,68656,44631,33629,82636,33336,50227,78831,85542,14947,08634,29634,92456,30740,13445,84338,14447,81638,17143,01139,18945,55443,54652,13960,21242,44252,58041,50443,42236,18049,54737,23637,89435,26740,41658,25032,48040,16030,79342,36336,04236,43143,34241,74042,93742,55579,26834,62535,31732,69448,58442,03922,93333,14628,42016,60843,62456,48924,95425,09631,00118,67617,40730,76729,72827,67431,32230,82362,84319,28635,85025,74322,46822,06326,05429,80738,26725,20822,07962,81321,02717,11731,16817,96335,84322,19837,59318,49818,00130,47551,41935,23811,36933,46223,28130,95636,44623,09423,71316,47328,81738,13760,59233,19529,39025,10630,08127,31215,23630,53827,48927,95628,82147,39235,96927,64222,93725,63933,46829,98630,76628,71529,41336,58452,66024,76733,24724,20221,32926,50430,21632,95733,73943,56324,13247,68720,85032,17527,57034,67024,19333,19546,35031,64227,80330,86249,30618,19116,35632,59640,81328,80925,60722,95021,33527,42623,42249,35227,40441,81433,69329,57922,72627,28526,90431,62336,69232,00149,30625,18343,74026,08123,79737,84632,13534,99026,55633,93123,75647,69238,71937,19335,80628,66425,93629,76339,98939,84030,80731,40755,21838,59536,38141,08827,72924,37919,44133,02632,43931,41441,17750,64634,47228,20437,17730,70531,54230,90138,81548,75547,15047,88552,70158,84653,96141,29856,11054,92654,11142,88755,93052,80363,99941,99357,28343,13964,11055,63451,47652,40058,17054,98249,32249,72638,97356,94134,97441,49853,93450,69758,11655,73473,15260,29849,77951,36645,61153,13556,28763,57442,96536,02437,92633,15235,03137,10147,45752,80551,72833,00134,96920,48356,83947,16133,53727,49325,03632,32428,16736,60132,07229,34724,97024,18053,00430,46132,58734,39535,44727,59831,07534,51636,64131,33137,39054,46526,11430,57032,22433,16044,55731,23922,13725,94129,38831,43264,08526,79155,09635,80634,00032,97829,71735,46638,80822,65829,18651,59927,49629,26129,99222,55141,35531,55923,89020,58932,20739,29651,77228,79825,25142,94633,97631,21529,17830,98615,03131,70736,32554,05426,86147,29728,80037,04139,61335,70034,98030,40927,06026,30746,73735,31632,08331,12026,53343,79819,53928,97532,76026,98227,11650,09922,04731,83639,43559,85846,82856,57354,30353,97556,22150,02344,08946,53147,29139,52453,20342,06750,94044,87050,70265,16257,13378,26752,77283,45655,40068,36745,08560,18944,80337,81642,20532,19337,98843,57678,36555,85952,24757,92049,23628,383,86794.33%
merged47,84255,37045,34344,72546,12448,75947,59357,17344,03538,49145,23253,38749,11448,42349,72852,97044,49457,53557,27248,01145,40451,68755,78360,25958,77138,29541,79348,07640,25140,50545,54545,53439,74742,88848,62546,52137,48843,54540,60555,71243,78052,32143,87041,42735,20454,18539,20749,60243,96152,18455,14864,05666,40540,41051,37248,52145,65649,19152,33652,55947,90559,37138,96049,86840,63937,58752,84952,20146,29447,97843,20540,75747,51044,80848,19150,18842,66750,68546,41358,12770,99854,49246,65345,60264,01948,82555,02955,80249,44346,80752,17257,35542,86345,29744,57651,32852,74433,00245,51043,73939,00636,19647,91841,90051,17145,87737,32547,78646,41034,30441,10535,83041,73442,51245,00356,80942,18036,63040,88237,77940,59038,79135,39745,71534,29638,08351,15441,81146,14739,96141,85750,48645,30646,16446,59337,17742,58845,96542,72739,10441,88254,33848,64545,10240,77237,15233,41241,91144,63635,52441,34740,96746,13140,05941,71745,81646,59040,22644,93242,78740,88146,34736,65338,81945,56047,60041,93051,97552,07642,46847,51953,97238,36838,50737,23641,14636,84740,18439,02735,91546,95944,32559,46341,64842,34947,01052,24946,65449,26734,96729,82135,56333,43453,68027,46644,38434,50052,28952,69545,11244,34346,89443,12858,26650,47635,29047,10845,04343,27642,57841,50543,84046,58638,01844,76342,34644,48537,48445,88832,23846,00838,68536,40539,72636,36741,65753,38034,05628,83334,44534,84546,55945,46342,00344,84343,28940,55842,62149,78648,50538,34339,56836,98540,15746,62736,10345,16544,45153,08433,77843,73943,70830,05041,09830,93034,38643,46042,78437,91447,90941,47041,42844,43649,88844,88738,52546,08436,19942,95541,09260,25040,64640,79438,40144,02834,26332,57129,95635,42935,07933,66455,63153,02138,69850,68142,35445,43146,40745,92748,84439,66943,16542,27552,99130,25628,31135,39734,47226,37130,54340,45145,55332,91933,00353,56838,27844,02836,04445,48636,48741,10737,40543,49841,57050,01757,42140,72750,22439,34441,68234,56348,09734,94836,58233,51938,64355,30730,81539,07029,14740,83634,67234,92441,66239,39940,92141,06975,64932,57134,39731,01546,71940,58821,99132,07527,87815,85942,95152,83824,31123,89630,36917,82816,62429,38128,77926,88730,27229,85059,66318,37634,95324,94221,60920,61024,94828,94337,33624,06321,09360,52020,10216,08830,08816,90835,05021,03536,66917,64117,20429,68448,24834,18410,55432,00222,24129,88435,35022,13622,77815,39427,46636,08557,55131,94828,18724,09529,12226,09914,23329,03525,98126,97227,59744,79234,55726,54921,64924,39632,98328,64229,82127,36728,13834,94549,77823,69732,18122,43220,71725,68328,85631,68732,02142,34123,23845,36119,57631,26426,17733,03623,24232,41945,45130,47826,87030,16846,99416,84615,79631,71539,40327,84624,55421,88220,54626,55122,33745,51126,33041,01532,41028,51121,56726,65525,81230,69635,70030,75546,99924,39542,65225,29722,85937,10930,85833,95025,79732,85922,88644,94337,30135,93934,74127,88724,84329,21939,47338,38229,78730,24551,84637,90635,25640,46526,25923,29118,53031,88431,34630,26139,35147,11533,13027,02436,01029,73630,11929,75137,47845,70344,36545,28550,08756,05751,38237,84552,46551,54950,36739,64953,91250,01161,50239,16554,27940,54161,86450,93948,32049,84555,10551,19046,96947,02536,11354,33231,77538,98651,68948,09755,67452,44770,21656,82845,80548,57542,34149,94053,81860,30240,34233,80035,96330,28032,98635,61844,05250,21049,06831,38233,83619,51653,23044,45732,61626,50224,24931,14426,90235,17631,20528,35423,92723,23749,91629,72331,20932,95534,09226,42229,86333,55935,47529,62036,44751,69225,28029,13131,40831,84243,97030,22820,96924,99328,29830,28360,36525,74053,96634,56632,95531,61928,73834,77537,47322,12028,47849,07326,85328,02229,25421,34940,26230,32722,33519,99830,92938,05349,52128,01224,39942,20632,26029,93027,89229,76414,20230,35435,37851,25526,18846,21828,04435,85638,64234,79133,69829,22725,45725,42143,58634,10430,57529,94324,98841,73418,51927,73831,60826,06925,80946,32621,21230,63737,49857,11543,92853,29151,31151,76553,30146,54841,56243,69044,92836,90550,26439,23948,18842,66948,07762,22554,20475,26949,53280,30652,25266,21142,36457,44342,59535,14339,72230,08036,09139,79574,54052,97747,27754,54745,44327,046,30489.89%
nonchim23,32724,10820,26820,34323,15620,46023,32727,28221,78719,27328,98624,22926,18823,50919,65325,46018,99330,04036,92622,28722,86023,30129,67630,35423,48922,99920,68321,07016,50618,01020,83720,58617,75121,20224,23520,47918,95721,31423,43118,69217,02131,73421,20619,91216,11724,43922,97119,55116,72422,00125,87532,67928,48125,48923,45120,71522,82621,52422,31324,35323,36527,78319,93324,30717,92818,30125,59828,59921,48318,13423,54621,74824,47421,24922,85925,92920,58118,71018,82626,13932,76922,28322,56721,03727,75323,68123,52425,92024,20721,68623,41631,39520,33020,82320,64324,11421,16523,80626,00922,41017,80116,15419,63719,63819,57719,62917,94719,00520,16316,66116,13717,67717,21820,48223,70126,18618,46912,92514,08415,71320,76616,98218,24319,14816,24616,93624,48015,87319,76923,66021,75524,56817,73920,66222,78021,48918,29820,21821,47618,07516,90624,79019,61317,38117,21117,36617,62815,58621,00316,30118,84717,85920,21318,36820,44425,66217,70918,42722,51417,09822,22222,40516,67716,16219,66922,54115,40424,73223,97719,79725,57627,42219,19517,80717,56024,07017,20819,83316,59414,69319,63321,74925,42620,10220,45020,26026,40022,23623,86215,41815,50214,71612,71222,06313,58220,47317,99722,33123,26821,14423,83520,40517,61226,53525,92616,21918,79421,52423,00624,44720,86522,11221,42717,57320,09720,31018,85519,32422,70317,07322,52919,29816,76617,27415,01820,62824,42517,23113,19215,17619,39421,03617,83919,01724,41220,74120,18920,35327,77422,87719,83814,34619,38220,29120,67216,57019,39421,74227,08716,10419,99016,92613,87016,24115,11615,92418,23220,79717,84718,86621,25617,43317,49626,41419,68216,81319,65218,10221,53220,44128,47316,88920,09618,44120,46214,97113,37016,97216,93017,21720,13325,24622,28220,45025,42918,63221,00421,61022,03118,13023,03123,95620,06221,45213,00814,52115,74413,94911,77911,75420,66620,90014,40317,94026,39317,90318,46117,07419,97717,52018,74915,34122,14017,31022,60830,06517,73822,05217,74227,90916,70827,65218,57722,96515,09316,51225,72215,35821,02914,48218,11621,55220,26522,80518,79417,52618,19346,64216,14624,27720,82222,73819,67410,05013,82818,2718,21130,57123,90812,41911,98412,7198,9908,10915,23013,2929,05514,56615,58430,8109,25418,1288,35012,18811,87711,34112,00016,84011,7389,21626,6017,8678,35012,5469,00317,98911,71116,0057,5027,14611,80621,87414,7715,74414,02010,15816,79314,8498,6469,0328,16012,40814,01822,77711,80111,1749,84211,60912,1407,67113,09510,83412,09113,80424,06415,06311,37211,68012,26817,60913,57012,22012,98612,27216,96323,19310,15613,03410,7428,93312,98313,90414,93613,44118,7939,87321,04810,15616,30412,42013,2209,72515,38817,49113,11413,43511,10325,1348,0915,84815,43916,48810,71612,6698,0218,14411,23311,02124,56811,62416,31814,44614,3889,47313,30710,92410,03014,16513,31319,08412,69618,98711,94711,25616,48112,43013,49310,52412,4968,50119,29114,30914,38515,4819,52211,43212,98716,42316,53311,70213,08525,71818,57915,51117,74213,5229,8559,20512,13319,61113,01719,83325,99714,76312,34317,11211,77013,71112,93817,85718,10919,45819,62721,57723,32628,38721,44323,51223,58822,32322,00925,92124,40929,41019,76530,13719,45326,69927,27125,14221,91225,24324,51424,36121,34616,99825,72416,40120,49623,72425,16226,55221,54634,44026,66022,44224,93523,89825,19921,81724,72119,06415,05017,12515,65315,16718,40223,20719,01422,21217,14016,4618,68922,62021,89211,95411,38911,76512,71613,50416,05514,57313,56410,05310,11920,27317,27812,24714,26014,47510,79012,71017,08917,63415,15813,83627,41612,82212,96712,68612,82821,42113,3399,37110,78515,12113,40426,24911,24820,79613,91713,98815,43611,37518,08915,2367,68915,91116,38014,92610,74212,78511,23017,82214,67112,9268,58215,33323,01027,48112,13911,19230,03416,26016,05813,33913,6117,92513,46118,19321,69013,24620,35212,71016,22820,36617,88416,70515,75112,9179,16022,89914,75914,69015,54813,31521,95610,48012,64716,10411,75912,64926,9547,84414,50018,92123,84323,99831,03328,35027,64123,92920,06821,37526,84427,19516,69925,45621,96122,52817,03928,91333,91824,80144,84024,79646,38525,66933,13924,28428,34718,67616,74619,27319,85816,46622,22235,85523,46827,08727,90122,45612,764,16642.42%

This table can be downloaded as an Excel table below:

 

5. DADA2 Amplicon Sequence Variants (ASVs). A total of 56023 unique merged and chimera-free ASV sequences were identified, and their corresponding read counts for each sample are available in the "ASV Read Count Table" with rows for the ASV sequences and columns for sample. This read count table can be used for microbial profile comparison among different samples and the sequences provided in the table can be used to taxonomy assignment.

 

The table can be downloaded from this link:

 
 

Sample Meta Information

#SampleIDSamplesVisitWeekSubjectPlaque NoTobacco KeyGroup
F5677.S157F5677.S157Visit 912 WeeksSubject 26001Plaque 1A12 Weeks.A.Plaque 1
F5677.S161F5677.S161Visit 912 WeeksSubject 26008Plaque 1A12 Weeks.A.Plaque 1
F5677.S164F5677.S164Visit 912 WeeksSubject 26013Plaque 1A12 Weeks.A.Plaque 1
F5677.S165F5677.S165Visit 912 WeeksSubject 26014Plaque 1A12 Weeks.A.Plaque 1
F5677.S166F5677.S166Visit 912 WeeksSubject 26015Plaque 1A12 Weeks.A.Plaque 1
F5677.S167F5677.S167Visit 912 WeeksSubject 26016Plaque 1A12 Weeks.A.Plaque 1
F5677.S168F5677.S168Visit 912 WeeksSubject 26018Plaque 1A12 Weeks.A.Plaque 1
F5677.S169F5677.S169Visit 912 WeeksSubject 26019Plaque 1A12 Weeks.A.Plaque 1
F5677.S170F5677.S170Visit 912 WeeksSubject 26020Plaque 1A12 Weeks.A.Plaque 1
F5677.S174F5677.S174Visit 912 WeeksSubject 26030Plaque 1A12 Weeks.A.Plaque 1
F5677.S177F5677.S177Visit 912 WeeksSubject 26033Plaque 1A12 Weeks.A.Plaque 1
F5677.S178F5677.S178Visit 912 WeeksSubject 26037Plaque 1A12 Weeks.A.Plaque 1
F5677.S179F5677.S179Visit 912 WeeksSubject 26040Plaque 1A12 Weeks.A.Plaque 1
F5677.S180F5677.S180Visit 912 WeeksSubject 26042Plaque 1A12 Weeks.A.Plaque 1
F5677.S181F5677.S181Visit 912 WeeksSubject 26044Plaque 1A12 Weeks.A.Plaque 1
F5677.S183F5677.S183Visit 912 WeeksSubject 26048Plaque 1A12 Weeks.A.Plaque 1
F5677.S187F5677.S187Visit 912 WeeksSubject 26055Plaque 1A12 Weeks.A.Plaque 1
F5677.S188F5677.S188Visit 912 WeeksSubject 26059Plaque 1A12 Weeks.A.Plaque 1
F5677.S189F5677.S189Visit 912 WeeksSubject 26061Plaque 1A12 Weeks.A.Plaque 1
F5677.S190F5677.S190Visit 912 WeeksSubject 26062Plaque 1A12 Weeks.A.Plaque 1
F5677.S193F5677.S193Visit 912 WeeksSubject 26067Plaque 1A12 Weeks.A.Plaque 1
F5677.S201F5677.S201Visit 912 WeeksSubject 26085Plaque 1A12 Weeks.A.Plaque 1
F5677.S203F5677.S203Visit 912 WeeksSubject 26087Plaque 1A12 Weeks.A.Plaque 1
F5677.S207F5677.S207Visit 912 WeeksSubject 26093Plaque 1A12 Weeks.A.Plaque 1
F5677.S208F5677.S208Visit 912 WeeksSubject 26094Plaque 1A12 Weeks.A.Plaque 1
F5677.S209F5677.S209Visit 912 WeeksSubject 26095Plaque 1A12 Weeks.A.Plaque 1
F5677.S210F5677.S210Visit 912 WeeksSubject 26097Plaque 1A12 Weeks.A.Plaque 1
F5677.S211F5677.S211Visit 912 WeeksSubject 26099Plaque 1A12 Weeks.A.Plaque 1
F5677.S215F5677.S215Visit 912 WeeksSubject 26105Plaque 1A12 Weeks.A.Plaque 1
F5677.S216F5677.S216Visit 912 WeeksSubject 26106Plaque 1A12 Weeks.A.Plaque 1
F5677.S219F5677.S219Visit 912 WeeksSubject 26114Plaque 1A12 Weeks.A.Plaque 1
F5677.S220F5677.S220Visit 912 WeeksSubject 26115Plaque 1A12 Weeks.A.Plaque 1
F5677.S221F5677.S221Visit 912 WeeksSubject 26116Plaque 1A12 Weeks.A.Plaque 1
F5677.S226F5677.S226Visit 912 WeeksSubject 26125Plaque 1A12 Weeks.A.Plaque 1
F5677.S227F5677.S227Visit 912 WeeksSubject 26126Plaque 1A12 Weeks.A.Plaque 1
F5677.S229F5677.S229Visit 912 WeeksSubject 26131Plaque 1A12 Weeks.A.Plaque 1
F5677.S231F5677.S231Visit 912 WeeksSubject 26140Plaque 1A12 Weeks.A.Plaque 1
F5677.S232F5677.S232Visit 912 WeeksSubject 26142Plaque 1A12 Weeks.A.Plaque 1
F5677.S236F5677.S236Visit 912 WeeksSubject 26147Plaque 1A12 Weeks.A.Plaque 1
F5677.S243F5677.S243Visit 912 WeeksSubject 26157Plaque 1A12 Weeks.A.Plaque 1
F5677.S244F5677.S244Visit 912 WeeksSubject 26160Plaque 1A12 Weeks.A.Plaque 1
F5677.S245F5677.S245Visit 912 WeeksSubject 26161Plaque 1A12 Weeks.A.Plaque 1
F5677.S246F5677.S246Visit 912 WeeksSubject 26162Plaque 1A12 Weeks.A.Plaque 1
F5677.S247F5677.S247Visit 912 WeeksSubject 26163Plaque 1A12 Weeks.A.Plaque 1
F5677.S249F5677.S249Visit 912 WeeksSubject 26165Plaque 1A12 Weeks.A.Plaque 1
F5677.S250F5677.S250Visit 912 WeeksSubject 26167Plaque 1A12 Weeks.A.Plaque 1
F5677.S253F5677.S253Visit 912 WeeksSubject 26173Plaque 1A12 Weeks.A.Plaque 1
F5677.S256F5677.S256Visit 912 WeeksSubject 26177Plaque 1A12 Weeks.A.Plaque 1
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F5677.S682F5677.S682Visit 1524 WeeksSubject 26177Plaque 2A24 Weeks.A.Plaque 2
F5677.S514F5677.S514Visit 1524 WeeksSubject 26003Plaque 1B24 Weeks.B.Plaque 1
F5677.S515F5677.S515Visit 1524 WeeksSubject 26005Plaque 1B24 Weeks.B.Plaque 1
F5677.S516F5677.S516Visit 1524 WeeksSubject 26006Plaque 1B24 Weeks.B.Plaque 1
F5677.S518F5677.S518Visit 1524 WeeksSubject 26009Plaque 1B24 Weeks.B.Plaque 1
F5677.S519F5677.S519Visit 1524 WeeksSubject 26012Plaque 1B24 Weeks.B.Plaque 1
F5677.S527F5677.S527Visit 1524 WeeksSubject 26027Plaque 1B24 Weeks.B.Plaque 1
F5677.S528F5677.S528Visit 1524 WeeksSubject 26029Plaque 1B24 Weeks.B.Plaque 1
F5677.S530F5677.S530Visit 1524 WeeksSubject 26031Plaque 1B24 Weeks.B.Plaque 1
F5677.S531F5677.S531Visit 1524 WeeksSubject 26032Plaque 1B24 Weeks.B.Plaque 1
F5677.S536F5677.S536Visit 1524 WeeksSubject 26046Plaque 1B24 Weeks.B.Plaque 1
F5677.S538F5677.S538Visit 1524 WeeksSubject 26050Plaque 1B24 Weeks.B.Plaque 1
F5677.S539F5677.S539Visit 1524 WeeksSubject 26052Plaque 1B24 Weeks.B.Plaque 1
F5677.S540F5677.S540Visit 1524 WeeksSubject 26054Plaque 1B24 Weeks.B.Plaque 1
F5677.S545F5677.S545Visit 1524 WeeksSubject 26066Plaque 1B24 Weeks.B.Plaque 1
F5677.S547F5677.S547Visit 1524 WeeksSubject 26072Plaque 1B24 Weeks.B.Plaque 1
F5677.S548F5677.S548Visit 1524 WeeksSubject 26073Plaque 1B24 Weeks.B.Plaque 1
F5677.S549F5677.S549Visit 1524 WeeksSubject 26079Plaque 1B24 Weeks.B.Plaque 1
F5677.S550F5677.S550Visit 1524 WeeksSubject 26080Plaque 1B24 Weeks.B.Plaque 1
F5677.S551F5677.S551Visit 1524 WeeksSubject 26081Plaque 1B24 Weeks.B.Plaque 1
F5677.S552F5677.S552Visit 1524 WeeksSubject 26083Plaque 1B24 Weeks.B.Plaque 1
F5677.S553F5677.S553Visit 1524 WeeksSubject 26084Plaque 1B24 Weeks.B.Plaque 1
F5677.S555F5677.S555Visit 1524 WeeksSubject 26086Plaque 1B24 Weeks.B.Plaque 1
F5677.S557F5677.S557Visit 1524 WeeksSubject 26089Plaque 1B24 Weeks.B.Plaque 1
F5677.S558F5677.S558Visit 1524 WeeksSubject 26090Plaque 1B24 Weeks.B.Plaque 1
F5677.S559F5677.S559Visit 1524 WeeksSubject 26091Plaque 1B24 Weeks.B.Plaque 1
F5677.S563F5677.S563Visit 1524 WeeksSubject 26102Plaque 1B24 Weeks.B.Plaque 1
F5677.S564F5677.S564Visit 1524 WeeksSubject 26103Plaque 1B24 Weeks.B.Plaque 1
F5677.S567F5677.S567Visit 1524 WeeksSubject 26109Plaque 1B24 Weeks.B.Plaque 1
F5677.S568F5677.S568Visit 1524 WeeksSubject 26111Plaque 1B24 Weeks.B.Plaque 1
F5677.S570F5677.S570Visit 1524 WeeksSubject 26118Plaque 1B24 Weeks.B.Plaque 1
F5677.S571F5677.S571Visit 1524 WeeksSubject 26121Plaque 1B24 Weeks.B.Plaque 1
F5677.S572F5677.S572Visit 1524 WeeksSubject 26123Plaque 1B24 Weeks.B.Plaque 1
F5677.S575F5677.S575Visit 1524 WeeksSubject 26132Plaque 1B24 Weeks.B.Plaque 1
F5677.S577F5677.S577Visit 1524 WeeksSubject 26143Plaque 1B24 Weeks.B.Plaque 1
F5677.S578F5677.S578Visit 1524 WeeksSubject 26144Plaque 1B24 Weeks.B.Plaque 1
F5677.S579F5677.S579Visit 1524 WeeksSubject 26146Plaque 1B24 Weeks.B.Plaque 1
F5677.S581F5677.S581Visit 1524 WeeksSubject 26148Plaque 1B24 Weeks.B.Plaque 1
F5677.S582F5677.S582Visit 1524 WeeksSubject 26149Plaque 1B24 Weeks.B.Plaque 1
F5677.S583F5677.S583Visit 1524 WeeksSubject 26151Plaque 1B24 Weeks.B.Plaque 1
F5677.S584F5677.S584Visit 1524 WeeksSubject 26152Plaque 1B24 Weeks.B.Plaque 1
F5677.S585F5677.S585Visit 1524 WeeksSubject 26154Plaque 1B24 Weeks.B.Plaque 1
F5677.S586F5677.S586Visit 1524 WeeksSubject 26155Plaque 1B24 Weeks.B.Plaque 1
F5677.S594F5677.S594Visit 1524 WeeksSubject 26168Plaque 1B24 Weeks.B.Plaque 1
F5677.S595F5677.S595Visit 1524 WeeksSubject 26170Plaque 1B24 Weeks.B.Plaque 1
F5677.S596F5677.S596Visit 1524 WeeksSubject 26175Plaque 1B24 Weeks.B.Plaque 1
F5677.S599F5677.S599Visit 1524 WeeksSubject 26003Plaque 2B24 Weeks.B.Plaque 2
F5677.S600F5677.S600Visit 1524 WeeksSubject 26005Plaque 2B24 Weeks.B.Plaque 2
F5677.S601F5677.S601Visit 1524 WeeksSubject 26006Plaque 2B24 Weeks.B.Plaque 2
F5677.S603F5677.S603Visit 1524 WeeksSubject 26009Plaque 2B24 Weeks.B.Plaque 2
F5677.S604F5677.S604Visit 1524 WeeksSubject 26012Plaque 2B24 Weeks.B.Plaque 2
F5677.S612F5677.S612Visit 1524 WeeksSubject 26027Plaque 2B24 Weeks.B.Plaque 2
F5677.S613F5677.S613Visit 1524 WeeksSubject 26029Plaque 2B24 Weeks.B.Plaque 2
F5677.S615F5677.S615Visit 1524 WeeksSubject 26031Plaque 2B24 Weeks.B.Plaque 2
F5677.S616F5677.S616Visit 1524 WeeksSubject 26032Plaque 2B24 Weeks.B.Plaque 2
F5677.S621F5677.S621Visit 1524 WeeksSubject 26046Plaque 2B24 Weeks.B.Plaque 2
F5677.S623F5677.S623Visit 1524 WeeksSubject 26050Plaque 2B24 Weeks.B.Plaque 2
F5677.S624F5677.S624Visit 1524 WeeksSubject 26052Plaque 2B24 Weeks.B.Plaque 2
F5677.S625F5677.S625Visit 1524 WeeksSubject 26054Plaque 2B24 Weeks.B.Plaque 2
F5677.S630F5677.S630Visit 1524 WeeksSubject 26066Plaque 2B24 Weeks.B.Plaque 2
F5677.S632F5677.S632Visit 1524 WeeksSubject 26072Plaque 2B24 Weeks.B.Plaque 2
F5677.S633F5677.S633Visit 1524 WeeksSubject 26073Plaque 2B24 Weeks.B.Plaque 2
F5677.S634F5677.S634Visit 1524 WeeksSubject 26079Plaque 2B24 Weeks.B.Plaque 2
F5677.S635F5677.S635Visit 1524 WeeksSubject 26080Plaque 2B24 Weeks.B.Plaque 2
F5677.S636F5677.S636Visit 1524 WeeksSubject 26081Plaque 2B24 Weeks.B.Plaque 2
F5677.S637F5677.S637Visit 1524 WeeksSubject 26083Plaque 2B24 Weeks.B.Plaque 2
F5677.S638F5677.S638Visit 1524 WeeksSubject 26084Plaque 2B24 Weeks.B.Plaque 2
F5677.S640F5677.S640Visit 1524 WeeksSubject 26086Plaque 2B24 Weeks.B.Plaque 2
F5677.S642F5677.S642Visit 1524 WeeksSubject 26089Plaque 2B24 Weeks.B.Plaque 2
F5677.S643F5677.S643Visit 1524 WeeksSubject 26090Plaque 2B24 Weeks.B.Plaque 2
F5677.S644F5677.S644Visit 1524 WeeksSubject 26091Plaque 2B24 Weeks.B.Plaque 2
F5677.S648F5677.S648Visit 1524 WeeksSubject 26102Plaque 2B24 Weeks.B.Plaque 2
F5677.S649F5677.S649Visit 1524 WeeksSubject 26103Plaque 2B24 Weeks.B.Plaque 2
F5677.S652F5677.S652Visit 1524 WeeksSubject 26109Plaque 2B24 Weeks.B.Plaque 2
F5677.S653F5677.S653Visit 1524 WeeksSubject 26111Plaque 2B24 Weeks.B.Plaque 2
F5677.S655F5677.S655Visit 1524 WeeksSubject 26118Plaque 2B24 Weeks.B.Plaque 2
F5677.S656F5677.S656Visit 1524 WeeksSubject 26121Plaque 2B24 Weeks.B.Plaque 2
F5677.S657F5677.S657Visit 1524 WeeksSubject 26123Plaque 2B24 Weeks.B.Plaque 2
F5677.S660F5677.S660Visit 1524 WeeksSubject 26132Plaque 2B24 Weeks.B.Plaque 2
F5677.S662F5677.S662Visit 1524 WeeksSubject 26143Plaque 2B24 Weeks.B.Plaque 2
F5677.S663F5677.S663Visit 1524 WeeksSubject 26144Plaque 2B24 Weeks.B.Plaque 2
F5677.S664F5677.S664Visit 1524 WeeksSubject 26146Plaque 2B24 Weeks.B.Plaque 2
F5677.S666F5677.S666Visit 1524 WeeksSubject 26148Plaque 2B24 Weeks.B.Plaque 2
F5677.S667F5677.S667Visit 1524 WeeksSubject 26149Plaque 2B24 Weeks.B.Plaque 2
F5677.S668F5677.S668Visit 1524 WeeksSubject 26151Plaque 2B24 Weeks.B.Plaque 2
F5677.S669F5677.S669Visit 1524 WeeksSubject 26152Plaque 2B24 Weeks.B.Plaque 2
F5677.S670F5677.S670Visit 1524 WeeksSubject 26154Plaque 2B24 Weeks.B.Plaque 2
F5677.S671F5677.S671Visit 1524 WeeksSubject 26155Plaque 2B24 Weeks.B.Plaque 2
F5677.S679F5677.S679Visit 1524 WeeksSubject 26168Plaque 2B24 Weeks.B.Plaque 2
F5677.S680F5677.S680Visit 1524 WeeksSubject 26170Plaque 2B24 Weeks.B.Plaque 2
F5677.S681F5677.S681Visit 1524 WeeksSubject 26175Plaque 2B24 Weeks.B.Plaque 2
F5677.S001F5677.S001Visit 3BaselineSubject 26001Plaque 1ABaseline.A.Plaque 1
F5677.S002F5677.S002Visit 3BaselineSubject 26002Plaque 1ABaseline.A.Plaque 1
F5677.S007F5677.S007Visit 3BaselineSubject 26007Plaque 1ABaseline.A.Plaque 1
F5677.S008F5677.S008Visit 3BaselineSubject 26008Plaque 1ABaseline.A.Plaque 1
F5677.S010F5677.S010Visit 3BaselineSubject 26010Plaque 1ABaseline.A.Plaque 1
F5677.S011F5677.S011Visit 3BaselineSubject 26011Plaque 1ABaseline.A.Plaque 1
F5677.S013F5677.S013Visit 3BaselineSubject 26013Plaque 1ABaseline.A.Plaque 1
F5677.S014F5677.S014Visit 3BaselineSubject 26014Plaque 1ABaseline.A.Plaque 1
F5677.S015F5677.S015Visit 3BaselineSubject 26015Plaque 1ABaseline.A.Plaque 1
F5677.S016F5677.S016Visit 3BaselineSubject 26016Plaque 1ABaseline.A.Plaque 1
F5677.S017F5677.S017Visit 3BaselineSubject 26017Plaque 1ABaseline.A.Plaque 1
F5677.S018F5677.S018Visit 3BaselineSubject 26018Plaque 1ABaseline.A.Plaque 1
F5677.S019F5677.S019Visit 3BaselineSubject 26019Plaque 1ABaseline.A.Plaque 1
F5677.S020F5677.S020Visit 3BaselineSubject 26020Plaque 1ABaseline.A.Plaque 1
F5677.S022F5677.S022Visit 3BaselineSubject 26022Plaque 1ABaseline.A.Plaque 1
F5677.S023F5677.S023Visit 3BaselineSubject 26023Plaque 1ABaseline.A.Plaque 1
F5677.S024F5677.S024Visit 3BaselineSubject 26024Plaque 1ABaseline.A.Plaque 1
F5677.S026F5677.S026Visit 3BaselineSubject 26028Plaque 1ABaseline.A.Plaque 1
F5677.S028F5677.S028Visit 3BaselineSubject 26030Plaque 1ABaseline.A.Plaque 1
F5677.S031F5677.S031Visit 3BaselineSubject 26033Plaque 1ABaseline.A.Plaque 1
F5677.S032F5677.S032Visit 3BaselineSubject 26034Plaque 1ABaseline.A.Plaque 1
F5677.S033F5677.S033Visit 3BaselineSubject 26035Plaque 1ABaseline.A.Plaque 1
F5677.S034F5677.S034Visit 3BaselineSubject 26036Plaque 1ABaseline.A.Plaque 1
F5677.S035F5677.S035Visit 3BaselineSubject 26037Plaque 1ABaseline.A.Plaque 1
F5677.S036F5677.S036Visit 3BaselineSubject 26038Plaque 1ABaseline.A.Plaque 1
F5677.S037F5677.S037Visit 3BaselineSubject 26039Plaque 1ABaseline.A.Plaque 1
F5677.S038F5677.S038Visit 3BaselineSubject 26040Plaque 1ABaseline.A.Plaque 1
F5677.S039F5677.S039Visit 3BaselineSubject 26042Plaque 1ABaseline.A.Plaque 1
F5677.S040F5677.S040Visit 3BaselineSubject 26043Plaque 1ABaseline.A.Plaque 1
F5677.S041F5677.S041Visit 3BaselineSubject 26044Plaque 1ABaseline.A.Plaque 1
F5677.S042F5677.S042Visit 3BaselineSubject 26045Plaque 1ABaseline.A.Plaque 1
F5677.S045F5677.S045Visit 3BaselineSubject 26048Plaque 1ABaseline.A.Plaque 1
F5677.S049F5677.S049Visit 3BaselineSubject 26055Plaque 1ABaseline.A.Plaque 1
F5677.S050F5677.S050Visit 3BaselineSubject 26056Plaque 1ABaseline.A.Plaque 1
F5677.S053F5677.S053Visit 3BaselineSubject 26059Plaque 1ABaseline.A.Plaque 1
F5677.S054F5677.S054Visit 3BaselineSubject 26061Plaque 1ABaseline.A.Plaque 1
F5677.S055F5677.S055Visit 3BaselineSubject 26062Plaque 1ABaseline.A.Plaque 1
F5677.S056F5677.S056Visit 3BaselineSubject 26063Plaque 1ABaseline.A.Plaque 1
F5677.S057F5677.S057Visit 3BaselineSubject 26064Plaque 1ABaseline.A.Plaque 1
F5677.S060F5677.S060Visit 3BaselineSubject 26067Plaque 1ABaseline.A.Plaque 1
F5677.S061F5677.S061Visit 3BaselineSubject 26068Plaque 1ABaseline.A.Plaque 1
F5677.S062F5677.S062Visit 3BaselineSubject 26070Plaque 1ABaseline.A.Plaque 1
F5677.S063F5677.S063Visit 3BaselineSubject 26071Plaque 1ABaseline.A.Plaque 1
F5677.S066F5677.S066Visit 3BaselineSubject 26075Plaque 1ABaseline.A.Plaque 1
F5677.S068F5677.S068Visit 3BaselineSubject 26077Plaque 1ABaseline.A.Plaque 1
F5677.S073F5677.S073Visit 3BaselineSubject 26082Plaque 1ABaseline.A.Plaque 1
F5677.S076F5677.S076Visit 3BaselineSubject 26085Plaque 1ABaseline.A.Plaque 1
F5677.S078F5677.S078Visit 3BaselineSubject 26087Plaque 1ABaseline.A.Plaque 1
F5677.S079F5677.S079Visit 3BaselineSubject 26088Plaque 1ABaseline.A.Plaque 1
F5677.S083F5677.S083Visit 3BaselineSubject 26092Plaque 1ABaseline.A.Plaque 1
F5677.S084F5677.S084Visit 3BaselineSubject 26093Plaque 1ABaseline.A.Plaque 1
F5677.S085F5677.S085Visit 3BaselineSubject 26094Plaque 1ABaseline.A.Plaque 1
F5677.S086F5677.S086Visit 3BaselineSubject 26095Plaque 1ABaseline.A.Plaque 1
F5677.S087F5677.S087Visit 3BaselineSubject 26096Plaque 1ABaseline.A.Plaque 1
F5677.S088F5677.S088Visit 3BaselineSubject 26097Plaque 1ABaseline.A.Plaque 1
F5677.S089F5677.S089Visit 3BaselineSubject 26098Plaque 1ABaseline.A.Plaque 1
F5677.S090F5677.S090Visit 3BaselineSubject 26099Plaque 1ABaseline.A.Plaque 1
F5677.S095F5677.S095Visit 3BaselineSubject 26104Plaque 1ABaseline.A.Plaque 1
F5677.S096F5677.S096Visit 3BaselineSubject 26105Plaque 1ABaseline.A.Plaque 1
F5677.S097F5677.S097Visit 3BaselineSubject 26106Plaque 1ABaseline.A.Plaque 1
F5677.S098F5677.S098Visit 3BaselineSubject 26108Plaque 1ABaseline.A.Plaque 1
F5677.S102F5677.S102Visit 3BaselineSubject 26113Plaque 1ABaseline.A.Plaque 1
F5677.S103F5677.S103Visit 3BaselineSubject 26114Plaque 1ABaseline.A.Plaque 1
F5677.S104F5677.S104Visit 3BaselineSubject 26115Plaque 1ABaseline.A.Plaque 1
F5677.S105F5677.S105Visit 3BaselineSubject 26116Plaque 1ABaseline.A.Plaque 1
F5677.S107F5677.S107Visit 3BaselineSubject 26119Plaque 1ABaseline.A.Plaque 1
F5677.S110F5677.S110Visit 3BaselineSubject 26122Plaque 1ABaseline.A.Plaque 1
F5677.S113F5677.S113Visit 3BaselineSubject 26125Plaque 1ABaseline.A.Plaque 1
F5677.S114F5677.S114Visit 3BaselineSubject 26126Plaque 1ABaseline.A.Plaque 1
F5677.S115F5677.S115Visit 3BaselineSubject 26127Plaque 1ABaseline.A.Plaque 1
F5677.S117F5677.S117Visit 3BaselineSubject 26131Plaque 1ABaseline.A.Plaque 1
F5677.S119F5677.S119Visit 3BaselineSubject 26134Plaque 1ABaseline.A.Plaque 1
F5677.S120F5677.S120Visit 3BaselineSubject 26135Plaque 1ABaseline.A.Plaque 1
F5677.S121F5677.S121Visit 3BaselineSubject 26136Plaque 1ABaseline.A.Plaque 1
F5677.S122F5677.S122Visit 3BaselineSubject 26140Plaque 1ABaseline.A.Plaque 1
F5677.S123F5677.S123Visit 3BaselineSubject 26141Plaque 1ABaseline.A.Plaque 1
F5677.S124F5677.S124Visit 3BaselineSubject 26142Plaque 1ABaseline.A.Plaque 1
F5677.S127F5677.S127Visit 3BaselineSubject 26145Plaque 1ABaseline.A.Plaque 1
F5677.S129F5677.S129Visit 3BaselineSubject 26147Plaque 1ABaseline.A.Plaque 1
F5677.S137F5677.S137Visit 3BaselineSubject 26157Plaque 1ABaseline.A.Plaque 1
F5677.S138F5677.S138Visit 3BaselineSubject 26158Plaque 1ABaseline.A.Plaque 1
F5677.S139F5677.S139Visit 3BaselineSubject 26159Plaque 1ABaseline.A.Plaque 1
F5677.S140F5677.S140Visit 3BaselineSubject 26160Plaque 1ABaseline.A.Plaque 1
F5677.S141F5677.S141Visit 3BaselineSubject 26161Plaque 1ABaseline.A.Plaque 1
F5677.S142F5677.S142Visit 3BaselineSubject 26162Plaque 1ABaseline.A.Plaque 1
F5677.S143F5677.S143Visit 3BaselineSubject 26163Plaque 1ABaseline.A.Plaque 1
F5677.S145F5677.S145Visit 3BaselineSubject 26165Plaque 1ABaseline.A.Plaque 1
F5677.S146F5677.S146Visit 3BaselineSubject 26166Plaque 1ABaseline.A.Plaque 1
F5677.S147F5677.S147Visit 3BaselineSubject 26167Plaque 1ABaseline.A.Plaque 1
F5677.S151F5677.S151Visit 3BaselineSubject 26173Plaque 1ABaseline.A.Plaque 1
F5677.S155F5677.S155Visit 3BaselineSubject 26177Plaque 1ABaseline.A.Plaque 1
F5677.S156F5677.S156Visit 3BaselineSubject 26178Plaque 1ABaseline.A.Plaque 1
F5677.S257F5677.S257Visit 3BaselineSubject 26001Plaque 2ABaseline.A.Plaque 2
F5677.S258F5677.S258Visit 3BaselineSubject 26002Plaque 2ABaseline.A.Plaque 2
F5677.S263F5677.S263Visit 3BaselineSubject 26007Plaque 2ABaseline.A.Plaque 2
F5677.S264F5677.S264Visit 3BaselineSubject 26008Plaque 2ABaseline.A.Plaque 2
F5677.S266F5677.S266Visit 3BaselineSubject 26010Plaque 2ABaseline.A.Plaque 2
F5677.S267F5677.S267Visit 3BaselineSubject 26011Plaque 2ABaseline.A.Plaque 2
F5677.S269F5677.S269Visit 3BaselineSubject 26013Plaque 2ABaseline.A.Plaque 2
F5677.S270F5677.S270Visit 3BaselineSubject 26014Plaque 2ABaseline.A.Plaque 2
F5677.S271F5677.S271Visit 3BaselineSubject 26015Plaque 2ABaseline.A.Plaque 2
F5677.S272F5677.S272Visit 3BaselineSubject 26016Plaque 2ABaseline.A.Plaque 2
F5677.S273F5677.S273Visit 3BaselineSubject 26017Plaque 2ABaseline.A.Plaque 2
F5677.S274F5677.S274Visit 3BaselineSubject 26018Plaque 2ABaseline.A.Plaque 2
F5677.S275F5677.S275Visit 3BaselineSubject 26019Plaque 2ABaseline.A.Plaque 2
F5677.S276F5677.S276Visit 3BaselineSubject 26020Plaque 2ABaseline.A.Plaque 2
F5677.S278F5677.S278Visit 3BaselineSubject 26022Plaque 2ABaseline.A.Plaque 2
F5677.S279F5677.S279Visit 3BaselineSubject 26023Plaque 2ABaseline.A.Plaque 2
F5677.S280F5677.S280Visit 3BaselineSubject 26024Plaque 2ABaseline.A.Plaque 2
F5677.S282F5677.S282Visit 3BaselineSubject 26028Plaque 2ABaseline.A.Plaque 2
F5677.S284F5677.S284Visit 3BaselineSubject 26030Plaque 2ABaseline.A.Plaque 2
F5677.S287F5677.S287Visit 3BaselineSubject 26033Plaque 2ABaseline.A.Plaque 2
F5677.S288F5677.S288Visit 3BaselineSubject 26034Plaque 2ABaseline.A.Plaque 2
F5677.S289F5677.S289Visit 3BaselineSubject 26035Plaque 2ABaseline.A.Plaque 2
F5677.S290F5677.S290Visit 3BaselineSubject 26036Plaque 2ABaseline.A.Plaque 2
F5677.S291F5677.S291Visit 3BaselineSubject 26037Plaque 2ABaseline.A.Plaque 2
F5677.S292F5677.S292Visit 3BaselineSubject 26038Plaque 2ABaseline.A.Plaque 2
F5677.S293F5677.S293Visit 3BaselineSubject 26039Plaque 2ABaseline.A.Plaque 2
F5677.S294F5677.S294Visit 3BaselineSubject 26040Plaque 2ABaseline.A.Plaque 2
F5677.S295F5677.S295Visit 3BaselineSubject 26042Plaque 2ABaseline.A.Plaque 2
F5677.S296F5677.S296Visit 3BaselineSubject 26043Plaque 2ABaseline.A.Plaque 2
F5677.S297F5677.S297Visit 3BaselineSubject 26044Plaque 2ABaseline.A.Plaque 2
F5677.S298F5677.S298Visit 3BaselineSubject 26045Plaque 2ABaseline.A.Plaque 2
F5677.S301F5677.S301Visit 3BaselineSubject 26048Plaque 2ABaseline.A.Plaque 2
F5677.S305F5677.S305Visit 3BaselineSubject 26055Plaque 2ABaseline.A.Plaque 2
F5677.S306F5677.S306Visit 3BaselineSubject 26056Plaque 2ABaseline.A.Plaque 2
F5677.S309F5677.S309Visit 3BaselineSubject 26059Plaque 2ABaseline.A.Plaque 2
F5677.S310F5677.S310Visit 3BaselineSubject 26061Plaque 2ABaseline.A.Plaque 2
F5677.S311F5677.S311Visit 3BaselineSubject 26062Plaque 2ABaseline.A.Plaque 2
F5677.S312F5677.S312Visit 3BaselineSubject 26063Plaque 2ABaseline.A.Plaque 2
F5677.S313F5677.S313Visit 3BaselineSubject 26064Plaque 2ABaseline.A.Plaque 2
F5677.S316F5677.S316Visit 3BaselineSubject 26067Plaque 2ABaseline.A.Plaque 2
F5677.S317F5677.S317Visit 3BaselineSubject 26068Plaque 2ABaseline.A.Plaque 2
F5677.S318F5677.S318Visit 3BaselineSubject 26070Plaque 2ABaseline.A.Plaque 2
F5677.S319F5677.S319Visit 3BaselineSubject 26071Plaque 2ABaseline.A.Plaque 2
F5677.S322F5677.S322Visit 3BaselineSubject 26075Plaque 2ABaseline.A.Plaque 2
F5677.S324F5677.S324Visit 3BaselineSubject 26077Plaque 2ABaseline.A.Plaque 2
F5677.S329F5677.S329Visit 3BaselineSubject 26082Plaque 2ABaseline.A.Plaque 2
F5677.S332F5677.S332Visit 3BaselineSubject 26085Plaque 2ABaseline.A.Plaque 2
F5677.S334F5677.S334Visit 3BaselineSubject 26087Plaque 2ABaseline.A.Plaque 2
F5677.S335F5677.S335Visit 3BaselineSubject 26088Plaque 2ABaseline.A.Plaque 2
F5677.S339F5677.S339Visit 3BaselineSubject 26092Plaque 2ABaseline.A.Plaque 2
F5677.S340F5677.S340Visit 3BaselineSubject 26093Plaque 2ABaseline.A.Plaque 2
F5677.S341F5677.S341Visit 3BaselineSubject 26094Plaque 2ABaseline.A.Plaque 2
F5677.S342F5677.S342Visit 3BaselineSubject 26095Plaque 2ABaseline.A.Plaque 2
F5677.S343F5677.S343Visit 3BaselineSubject 26096Plaque 2ABaseline.A.Plaque 2
F5677.S344F5677.S344Visit 3BaselineSubject 26097Plaque 2ABaseline.A.Plaque 2
F5677.S345F5677.S345Visit 3BaselineSubject 26098Plaque 2ABaseline.A.Plaque 2
F5677.S346F5677.S346Visit 3BaselineSubject 26099Plaque 2ABaseline.A.Plaque 2
F5677.S351F5677.S351Visit 3BaselineSubject 26104Plaque 2ABaseline.A.Plaque 2
F5677.S352F5677.S352Visit 3BaselineSubject 26105Plaque 2ABaseline.A.Plaque 2
F5677.S353F5677.S353Visit 3BaselineSubject 26106Plaque 2ABaseline.A.Plaque 2
F5677.S354F5677.S354Visit 3BaselineSubject 26108Plaque 2ABaseline.A.Plaque 2
F5677.S358F5677.S358Visit 3BaselineSubject 26113Plaque 2ABaseline.A.Plaque 2
F5677.S359F5677.S359Visit 3BaselineSubject 26114Plaque 2ABaseline.A.Plaque 2
F5677.S360F5677.S360Visit 3BaselineSubject 26115Plaque 2ABaseline.A.Plaque 2
F5677.S361F5677.S361Visit 3BaselineSubject 26116Plaque 2ABaseline.A.Plaque 2
F5677.S363F5677.S363Visit 3BaselineSubject 26119Plaque 2ABaseline.A.Plaque 2
F5677.S366F5677.S366Visit 3BaselineSubject 26122Plaque 2ABaseline.A.Plaque 2
F5677.S369F5677.S369Visit 3BaselineSubject 26125Plaque 2ABaseline.A.Plaque 2
F5677.S370F5677.S370Visit 3BaselineSubject 26126Plaque 2ABaseline.A.Plaque 2
F5677.S371F5677.S371Visit 3BaselineSubject 26127Plaque 2ABaseline.A.Plaque 2
F5677.S373F5677.S373Visit 3BaselineSubject 26131Plaque 2ABaseline.A.Plaque 2
F5677.S375F5677.S375Visit 3BaselineSubject 26134Plaque 2ABaseline.A.Plaque 2
F5677.S376F5677.S376Visit 3BaselineSubject 26135Plaque 2ABaseline.A.Plaque 2
F5677.S377F5677.S377Visit 3BaselineSubject 26136Plaque 2ABaseline.A.Plaque 2
F5677.S378F5677.S378Visit 3BaselineSubject 26140Plaque 2ABaseline.A.Plaque 2
F5677.S379F5677.S379Visit 3BaselineSubject 26141Plaque 2ABaseline.A.Plaque 2
F5677.S380F5677.S380Visit 3BaselineSubject 26142Plaque 2ABaseline.A.Plaque 2
F5677.S383F5677.S383Visit 3BaselineSubject 26145Plaque 2ABaseline.A.Plaque 2
F5677.S385F5677.S385Visit 3BaselineSubject 26147Plaque 2ABaseline.A.Plaque 2
F5677.S393F5677.S393Visit 3BaselineSubject 26157Plaque 2ABaseline.A.Plaque 2
F5677.S394F5677.S394Visit 3BaselineSubject 26158Plaque 2ABaseline.A.Plaque 2
F5677.S395F5677.S395Visit 3BaselineSubject 26159Plaque 2ABaseline.A.Plaque 2
F5677.S396F5677.S396Visit 3BaselineSubject 26160Plaque 2ABaseline.A.Plaque 2
F5677.S397F5677.S397Visit 3BaselineSubject 26161Plaque 2ABaseline.A.Plaque 2
F5677.S398F5677.S398Visit 3BaselineSubject 26162Plaque 2ABaseline.A.Plaque 2
F5677.S399F5677.S399Visit 3BaselineSubject 26163Plaque 2ABaseline.A.Plaque 2
F5677.S401F5677.S401Visit 3BaselineSubject 26165Plaque 2ABaseline.A.Plaque 2
F5677.S402F5677.S402Visit 3BaselineSubject 26166Plaque 2ABaseline.A.Plaque 2
F5677.S403F5677.S403Visit 3BaselineSubject 26167Plaque 2ABaseline.A.Plaque 2
F5677.S407F5677.S407Visit 3BaselineSubject 26173Plaque 2ABaseline.A.Plaque 2
F5677.S411F5677.S411Visit 3BaselineSubject 26177Plaque 2ABaseline.A.Plaque 2
F5677.S412F5677.S412Visit 3BaselineSubject 26178Plaque 2ABaseline.A.Plaque 2
F5677.S003F5677.S003Visit 3BaselineSubject 26003Plaque 1BBaseline.B.Plaque 1
F5677.S004F5677.S004Visit 3BaselineSubject 26004Plaque 1BBaseline.B.Plaque 1
F5677.S005F5677.S005Visit 3BaselineSubject 26005Plaque 1BBaseline.B.Plaque 1
F5677.S006F5677.S006Visit 3BaselineSubject 26006Plaque 1BBaseline.B.Plaque 1
F5677.S009F5677.S009Visit 3BaselineSubject 26009Plaque 1BBaseline.B.Plaque 1
F5677.S012F5677.S012Visit 3BaselineSubject 26012Plaque 1BBaseline.B.Plaque 1
F5677.S021F5677.S021Visit 3BaselineSubject 26021Plaque 1BBaseline.B.Plaque 1
F5677.S025F5677.S025Visit 3BaselineSubject 26027Plaque 1BBaseline.B.Plaque 1
F5677.S027F5677.S027Visit 3BaselineSubject 26029Plaque 1BBaseline.B.Plaque 1
F5677.S029F5677.S029Visit 3BaselineSubject 26031Plaque 1BBaseline.B.Plaque 1
F5677.S030F5677.S030Visit 3BaselineSubject 26032Plaque 1BBaseline.B.Plaque 1
F5677.S043F5677.S043Visit 3BaselineSubject 26046Plaque 1BBaseline.B.Plaque 1
F5677.S044F5677.S044Visit 3BaselineSubject 26047Plaque 1BBaseline.B.Plaque 1
F5677.S046F5677.S046Visit 3BaselineSubject 26050Plaque 1BBaseline.B.Plaque 1
F5677.S047F5677.S047Visit 3BaselineSubject 26052Plaque 1BBaseline.B.Plaque 1
F5677.S048F5677.S048Visit 3BaselineSubject 26054Plaque 1BBaseline.B.Plaque 1
F5677.S051F5677.S051Visit 3BaselineSubject 26057Plaque 1BBaseline.B.Plaque 1
F5677.S052F5677.S052Visit 3BaselineSubject 26058Plaque 1BBaseline.B.Plaque 1
F5677.S058F5677.S058Visit 3BaselineSubject 26065Plaque 1BBaseline.B.Plaque 1
F5677.S059F5677.S059Visit 3BaselineSubject 26066Plaque 1BBaseline.B.Plaque 1
F5677.S064F5677.S064Visit 3BaselineSubject 26072Plaque 1BBaseline.B.Plaque 1
F5677.S065F5677.S065Visit 3BaselineSubject 26073Plaque 1BBaseline.B.Plaque 1
F5677.S067F5677.S067Visit 3BaselineSubject 26076Plaque 1BBaseline.B.Plaque 1
F5677.S070F5677.S070Visit 3BaselineSubject 26079Plaque 1BBaseline.B.Plaque 1
F5677.S071F5677.S071Visit 3BaselineSubject 26080Plaque 1BBaseline.B.Plaque 1
F5677.S072F5677.S072Visit 3BaselineSubject 26081Plaque 1BBaseline.B.Plaque 1
F5677.S074F5677.S074Visit 3BaselineSubject 26083Plaque 1BBaseline.B.Plaque 1
F5677.S075F5677.S075Visit 3BaselineSubject 26084Plaque 1BBaseline.B.Plaque 1
F5677.S077F5677.S077Visit 3BaselineSubject 26086Plaque 1BBaseline.B.Plaque 1
F5677.S080F5677.S080Visit 3BaselineSubject 26089Plaque 1BBaseline.B.Plaque 1
F5677.S081F5677.S081Visit 3BaselineSubject 26090Plaque 1BBaseline.B.Plaque 1
F5677.S082F5677.S082Visit 3BaselineSubject 26091Plaque 1BBaseline.B.Plaque 1
F5677.S091F5677.S091Visit 3BaselineSubject 26100Plaque 1BBaseline.B.Plaque 1
F5677.S092F5677.S092Visit 3BaselineSubject 26101Plaque 1BBaseline.B.Plaque 1
F5677.S093F5677.S093Visit 3BaselineSubject 26102Plaque 1BBaseline.B.Plaque 1
F5677.S094F5677.S094Visit 3BaselineSubject 26103Plaque 1BBaseline.B.Plaque 1
F5677.S099F5677.S099Visit 3BaselineSubject 26109Plaque 1BBaseline.B.Plaque 1
F5677.S100F5677.S100Visit 3BaselineSubject 26110Plaque 1BBaseline.B.Plaque 1
F5677.S101F5677.S101Visit 3BaselineSubject 26111Plaque 1BBaseline.B.Plaque 1
F5677.S106F5677.S106Visit 3BaselineSubject 26118Plaque 1BBaseline.B.Plaque 1
F5677.S108F5677.S108Visit 3BaselineSubject 26120Plaque 1BBaseline.B.Plaque 1
F5677.S109F5677.S109Visit 3BaselineSubject 26121Plaque 1BBaseline.B.Plaque 1
F5677.S111F5677.S111Visit 3BaselineSubject 26123Plaque 1BBaseline.B.Plaque 1
F5677.S112F5677.S112Visit 3BaselineSubject 26124Plaque 1BBaseline.B.Plaque 1
F5677.S116F5677.S116Visit 3BaselineSubject 26129Plaque 1BBaseline.B.Plaque 1
F5677.S118F5677.S118Visit 3BaselineSubject 26132Plaque 1BBaseline.B.Plaque 1
F5677.S125F5677.S125Visit 3BaselineSubject 26143Plaque 1BBaseline.B.Plaque 1
F5677.S126F5677.S126Visit 3BaselineSubject 26144Plaque 1BBaseline.B.Plaque 1
F5677.S128F5677.S128Visit 3BaselineSubject 26146Plaque 1BBaseline.B.Plaque 1
F5677.S130F5677.S130Visit 3BaselineSubject 26148Plaque 1BBaseline.B.Plaque 1
F5677.S131F5677.S131Visit 3BaselineSubject 26149Plaque 1BBaseline.B.Plaque 1
F5677.S132F5677.S132Visit 3BaselineSubject 26151Plaque 1BBaseline.B.Plaque 1
F5677.S133F5677.S133Visit 3BaselineSubject 26152Plaque 1BBaseline.B.Plaque 1
F5677.S134F5677.S134Visit 3BaselineSubject 26154Plaque 1BBaseline.B.Plaque 1
F5677.S135F5677.S135Visit 3BaselineSubject 26155Plaque 1BBaseline.B.Plaque 1
F5677.S136F5677.S136Visit 3BaselineSubject 26156Plaque 1BBaseline.B.Plaque 1
F5677.S144F5677.S144Visit 3BaselineSubject 26164Plaque 1BBaseline.B.Plaque 1
F5677.S148F5677.S148Visit 3BaselineSubject 26168Plaque 1BBaseline.B.Plaque 1
F5677.S149F5677.S149Visit 3BaselineSubject 26170Plaque 1BBaseline.B.Plaque 1
F5677.S150F5677.S150Visit 3BaselineSubject 26171Plaque 1BBaseline.B.Plaque 1
F5677.S152F5677.S152Visit 3BaselineSubject 26174Plaque 1BBaseline.B.Plaque 1
F5677.S153F5677.S153Visit 3BaselineSubject 26175Plaque 1BBaseline.B.Plaque 1
F5677.S154F5677.S154Visit 3BaselineSubject 26176Plaque 1BBaseline.B.Plaque 1
F5677.S259F5677.S259Visit 3BaselineSubject 26003Plaque 2BBaseline.B.Plaque 2
F5677.S260F5677.S260Visit 3BaselineSubject 26004Plaque 2BBaseline.B.Plaque 2
F5677.S261F5677.S261Visit 3BaselineSubject 26005Plaque 2BBaseline.B.Plaque 2
F5677.S262F5677.S262Visit 3BaselineSubject 26006Plaque 2BBaseline.B.Plaque 2
F5677.S265F5677.S265Visit 3BaselineSubject 26009Plaque 2BBaseline.B.Plaque 2
F5677.S268F5677.S268Visit 3BaselineSubject 26012Plaque 2BBaseline.B.Plaque 2
F5677.S277F5677.S277Visit 3BaselineSubject 26021Plaque 2BBaseline.B.Plaque 2
F5677.S281F5677.S281Visit 3BaselineSubject 26027Plaque 2BBaseline.B.Plaque 2
F5677.S283F5677.S283Visit 3BaselineSubject 26029Plaque 2BBaseline.B.Plaque 2
F5677.S285F5677.S285Visit 3BaselineSubject 26031Plaque 2BBaseline.B.Plaque 2
F5677.S286F5677.S286Visit 3BaselineSubject 26032Plaque 2BBaseline.B.Plaque 2
F5677.S299F5677.S299Visit 3BaselineSubject 26046Plaque 2BBaseline.B.Plaque 2
F5677.S300F5677.S300Visit 3BaselineSubject 26047Plaque 2BBaseline.B.Plaque 2
F5677.S302F5677.S302Visit 3BaselineSubject 26050Plaque 2BBaseline.B.Plaque 2
F5677.S303F5677.S303Visit 3BaselineSubject 26052Plaque 2BBaseline.B.Plaque 2
F5677.S304F5677.S304Visit 3BaselineSubject 26054Plaque 2BBaseline.B.Plaque 2
F5677.S307F5677.S307Visit 3BaselineSubject 26057Plaque 2BBaseline.B.Plaque 2
F5677.S308F5677.S308Visit 3BaselineSubject 26058Plaque 2BBaseline.B.Plaque 2
F5677.S314F5677.S314Visit 3BaselineSubject 26065Plaque 2BBaseline.B.Plaque 2
F5677.S315F5677.S315Visit 3BaselineSubject 26066Plaque 2BBaseline.B.Plaque 2
F5677.S320F5677.S320Visit 3BaselineSubject 26072Plaque 2BBaseline.B.Plaque 2
F5677.S321F5677.S321Visit 3BaselineSubject 26073Plaque 2BBaseline.B.Plaque 2
F5677.S323F5677.S323Visit 3BaselineSubject 26076Plaque 2BBaseline.B.Plaque 2
F5677.S326F5677.S326Visit 3BaselineSubject 26079Plaque 2BBaseline.B.Plaque 2
F5677.S327F5677.S327Visit 3BaselineSubject 26080Plaque 2BBaseline.B.Plaque 2
F5677.S328F5677.S328Visit 3BaselineSubject 26081Plaque 2BBaseline.B.Plaque 2
F5677.S330F5677.S330Visit 3BaselineSubject 26083Plaque 2BBaseline.B.Plaque 2
F5677.S331F5677.S331Visit 3BaselineSubject 26084Plaque 2BBaseline.B.Plaque 2
F5677.S333F5677.S333Visit 3BaselineSubject 26086Plaque 2BBaseline.B.Plaque 2
F5677.S336F5677.S336Visit 3BaselineSubject 26089Plaque 2BBaseline.B.Plaque 2
F5677.S337F5677.S337Visit 3BaselineSubject 26090Plaque 2BBaseline.B.Plaque 2
F5677.S338F5677.S338Visit 3BaselineSubject 26091Plaque 2BBaseline.B.Plaque 2
F5677.S347F5677.S347Visit 3BaselineSubject 26100Plaque 2BBaseline.B.Plaque 2
F5677.S348F5677.S348Visit 3BaselineSubject 26101Plaque 2BBaseline.B.Plaque 2
F5677.S349F5677.S349Visit 3BaselineSubject 26102Plaque 2BBaseline.B.Plaque 2
F5677.S350F5677.S350Visit 3BaselineSubject 26103Plaque 2BBaseline.B.Plaque 2
F5677.S355F5677.S355Visit 3BaselineSubject 26109Plaque 2BBaseline.B.Plaque 2
F5677.S356F5677.S356Visit 3BaselineSubject 26110Plaque 2BBaseline.B.Plaque 2
F5677.S357F5677.S357Visit 3BaselineSubject 26111Plaque 2BBaseline.B.Plaque 2
F5677.S362F5677.S362Visit 3BaselineSubject 26118Plaque 2BBaseline.B.Plaque 2
F5677.S364F5677.S364Visit 3BaselineSubject 26120Plaque 2BBaseline.B.Plaque 2
F5677.S365F5677.S365Visit 3BaselineSubject 26121Plaque 2BBaseline.B.Plaque 2
F5677.S367F5677.S367Visit 3BaselineSubject 26123Plaque 2BBaseline.B.Plaque 2
F5677.S368F5677.S368Visit 3BaselineSubject 26124Plaque 2BBaseline.B.Plaque 2
F5677.S372F5677.S372Visit 3BaselineSubject 26129Plaque 2BBaseline.B.Plaque 2
F5677.S374F5677.S374Visit 3BaselineSubject 26132Plaque 2BBaseline.B.Plaque 2
F5677.S381F5677.S381Visit 3BaselineSubject 26143Plaque 2BBaseline.B.Plaque 2
F5677.S382F5677.S382Visit 3BaselineSubject 26144Plaque 2BBaseline.B.Plaque 2
F5677.S384F5677.S384Visit 3BaselineSubject 26146Plaque 2BBaseline.B.Plaque 2
F5677.S386F5677.S386Visit 3BaselineSubject 26148Plaque 2BBaseline.B.Plaque 2
F5677.S387F5677.S387Visit 3BaselineSubject 26149Plaque 2BBaseline.B.Plaque 2
F5677.S388F5677.S388Visit 3BaselineSubject 26151Plaque 2BBaseline.B.Plaque 2
F5677.S389F5677.S389Visit 3BaselineSubject 26152Plaque 2BBaseline.B.Plaque 2
F5677.S390F5677.S390Visit 3BaselineSubject 26154Plaque 2BBaseline.B.Plaque 2
F5677.S391F5677.S391Visit 3BaselineSubject 26155Plaque 2BBaseline.B.Plaque 2
F5677.S392F5677.S392Visit 3BaselineSubject 26156Plaque 2BBaseline.B.Plaque 2
F5677.S400F5677.S400Visit 3BaselineSubject 26164Plaque 2BBaseline.B.Plaque 2
F5677.S404F5677.S404Visit 3BaselineSubject 26168Plaque 2BBaseline.B.Plaque 2
F5677.S405F5677.S405Visit 3BaselineSubject 26170Plaque 2BBaseline.B.Plaque 2
F5677.S406F5677.S406Visit 3BaselineSubject 26171Plaque 2BBaseline.B.Plaque 2
F5677.S408F5677.S408Visit 3BaselineSubject 26174Plaque 2BBaseline.B.Plaque 2
F5677.S409F5677.S409Visit 3BaselineSubject 26175Plaque 2BBaseline.B.Plaque 2
F5677.S410F5677.S410Visit 3BaselineSubject 26176Plaque 2BBaseline.B.Plaque 2
F5677.S069F5677.S069Visit 3BaselineSubject 26078Plaque 1NABaseline.NA.Plaque 1
F5677.S325F5677.S325Visit 3BaselineSubject 26078Plaque 2NABaseline.NA.Plaque 2
 
 

ASV Read Counts by Samples

#Sample IDRead Count
F5677.S4342,863
F5677.S4902,911
F5677.S4303,840
F5677.S4964,396
F5677.S4954,488
F5677.S4044,498
F5677.S6444,513
F5677.S5974,535
F5677.S4134,542
F5677.S4294,834
F5677.S4504,923
F5677.S5204,930
F5677.S4894,968
F5677.S6184,999
F5677.S3975,071
F5677.S4415,133
F5677.S5385,152
F5677.S4225,233
F5677.S4825,274
F5677.S4255,297
F5677.S6075,315
F5677.S4395,316
F5677.S4235,341
F5677.S4765,372
F5677.S5645,419
F5677.S5375,476
F5677.S6315,483
F5677.S4405,502
F5677.S5845,676
F5677.S5075,710
F5677.S4075,732
F5677.S4475,769
F5677.S4365,924
F5677.S3945,997
F5677.S4036,031
F5677.S5256,047
F5677.S4166,057
F5677.S4676,105
F5677.S4786,117
F5677.S5186,121
F5677.S4206,186
F5677.S4706,238
F5677.S6386,264
F5677.S4586,275
F5677.S5006,281
F5677.S4016,354
F5677.S5536,398
F5677.S5476,438
F5677.S4486,520
F5677.S5946,522
F5677.S4526,536
F5677.S5066,561
F5677.S4196,577
F5677.S5586,632
F5677.S5716,635
F5677.S4456,649
F5677.S2436,684
F5677.S5896,693
F5677.S4936,720
F5677.S4696,769
F5677.S5806,772
F5677.S5396,774
F5677.S4576,785
F5677.S5486,851
F5677.S4116,861
F5677.S5656,879
F5677.S6016,950
F5677.S5496,978
F5677.S5046,978
F5677.S3957,098
F5677.S5687,111
F5677.S4627,124
F5677.S4537,144
F5677.S5597,159
F5677.S4177,211
F5677.S5857,237
F5677.S6037,238
F5677.S5567,270
F5677.S4007,291
F5677.S4977,322
F5677.S4987,331
F5677.S4877,354
F5677.S3507,373
F5677.S4467,401
F5677.S5137,420
F5677.S5457,422
F5677.S4687,443
F5677.S5197,511
F5677.S4497,512
F5677.S4807,585
F5677.S5267,587
F5677.S1687,591
F5677.S4817,598
F5677.S4857,599
F5677.S5577,611
F5677.S5147,626
F5677.S3537,659
F5677.S4647,671
F5677.S5627,707
F5677.S5177,721
F5677.S5167,722
F5677.S5817,729
F5677.S5307,742
F5677.S3497,752
F5677.S6417,757
F5677.S6197,761
F5677.S5037,779
F5677.S6067,817
F5677.S4427,848
F5677.S4317,852
F5677.S6307,874
F5677.S6127,887
F5677.S4337,897
F5677.S4027,916
F5677.S4247,916
F5677.S5837,922
F5677.S5637,945
F5677.S2427,953
F5677.S6397,983
F5677.S6427,988
F5677.S2927,989
F5677.S6117,990
F5677.S5797,993
F5677.S6027,996
F5677.S6178,001
F5677.S6168,010
F5677.S4948,073
F5677.S5418,075
F5677.S2798,117
F5677.S4518,120
F5677.S4718,144
F5677.S4088,145
F5677.S5368,191
F5677.S6338,243
F5677.S5938,257
F5677.S5728,258
F5677.S4158,263
F5677.S6458,333
F5677.S4748,344
F5677.S3058,407
F5677.S5608,449
F5677.S5928,454
F5677.S1948,455
F5677.S6368,464
F5677.S1608,469
F5677.S5768,503
F5677.S4388,515
F5677.S6248,517
F5677.S4548,542
F5677.S4598,548
F5677.S4618,573
F5677.S4278,590
F5677.S1698,634
F5677.S5028,648
F5677.S5228,660
F5677.S3758,669
F5677.S4358,688
F5677.S5318,706
F5677.S5618,732
F5677.S4728,744
F5677.S5878,777
F5677.S5098,795
F5677.S2738,859
F5677.S5298,903
F5677.S5238,927
F5677.S5018,931
F5677.S4568,949
F5677.S2408,959
F5677.S1709,000
F5677.S5089,026
F5677.S2759,027
F5677.S5349,042
F5677.S3809,079
F5677.S5759,093
F5677.S6349,096
F5677.S5919,106
F5677.S1459,108
F5677.S5709,109
F5677.S5059,117
F5677.S3489,124
F5677.S5699,127
F5677.S3789,151
F5677.S4069,178
F5677.S5969,200
F5677.S4929,208
F5677.S4439,215
F5677.S4739,255
F5677.S3309,263
F5677.S5789,307
F5677.S3459,312
F5677.S4639,316
F5677.S3279,328
F5677.S6059,352
F5677.S6229,356
F5677.S3229,394
F5677.S3269,414
F5677.S5999,427
F5677.S3139,441
F5677.S5529,451
F5677.S5739,466
F5677.S2459,487
F5677.S1529,490
F5677.S5119,510
F5677.S2569,542
F5677.S4919,564
F5677.S4189,574
F5677.S3469,590
F5677.S5449,644
F5677.S3629,654
F5677.S4839,655
F5677.S6289,693
F5677.S4149,694
F5677.S2309,696
F5677.S3479,707
F5677.S4869,718
F5677.S3649,735
F5677.S2019,746
F5677.S3039,829
F5677.S1619,842
F5677.S4659,884
F5677.S4059,908
F5677.S1989,920
F5677.S6299,943
F5677.S2299,954
F5677.S5959,989
F5677.S22710,019
F5677.S09610,025
F5677.S52710,036
F5677.S62510,051
F5677.S37610,065
F5677.S60810,081
F5677.S30910,094
F5677.S14110,101
F5677.S25710,127
F5677.S35810,156
F5677.S55110,183
F5677.S17510,207
F5677.S18310,223
F5677.S15710,237
F5677.S47910,245
F5677.S37110,250
F5677.S38610,282
F5677.S31510,303
F5677.S63510,315
F5677.S28310,337
F5677.S35610,351
F5677.S29610,362
F5677.S52410,383
F5677.S32810,390
F5677.S38910,405
F5677.S09310,408
F5677.S24110,409
F5677.S28010,429
F5677.S19110,458
F5677.S09510,476
F5677.S30710,486
F5677.S59810,523
F5677.S17810,601
F5677.S15810,603
F5677.S48410,632
F5677.S54610,653
F5677.S17910,662
F5677.S30010,676
F5677.S31610,728
F5677.S40910,732
F5677.S14910,752
F5677.S17610,754
F5677.S19610,767
F5677.S61510,778
F5677.S09410,781
F5677.S30410,784
F5677.S30610,821
F5677.S58610,830
F5677.S61410,842
F5677.S35710,893
F5677.S15610,923
F5677.S20010,932
F5677.S32411,022
F5677.S21311,039
F5677.S19311,057
F5677.S17411,083
F5677.S17211,094
F5677.S06511,094
F5677.S38111,101
F5677.S12911,110
F5677.S07611,117
F5677.S18711,172
F5677.S36011,179
F5677.S66111,187
F5677.S32511,192
F5677.S27811,194
F5677.S55011,194
F5677.S22411,202
F5677.S21411,230
F5677.S19011,264
F5677.S42811,265
F5677.S33611,273
F5677.S26311,278
F5677.S21711,284
F5677.S39611,288
F5677.S56711,343
F5677.S19511,374
F5677.S13011,376
F5677.S65711,434
F5677.S17311,445
F5677.S21011,454
F5677.S28211,456
F5677.S32911,471
F5677.S36111,590
F5677.S22511,599
F5677.S27411,642
F5677.S51511,643
F5677.S64011,668
F5677.S16311,675
F5677.S28111,713
F5677.S14811,753
F5677.S38511,783
F5677.S20211,821
F5677.S31211,822
F5677.S21511,824
F5677.S22311,825
F5677.S38711,913
F5677.S27011,943
F5677.S30211,962
F5677.S36911,980
F5677.S24711,987
F5677.S25311,996
F5677.S28412,012
F5677.S29312,030
F5677.S60012,031
F5677.S57412,037
F5677.S02012,044
F5677.S36712,089
F5677.S37312,116
F5677.S16212,151
F5677.S52812,157
F5677.S60412,170
F5677.S01612,220
F5677.S43712,226
F5677.S47712,263
F5677.S25212,276
F5677.S32312,279
F5677.S23112,287
F5677.S15412,297
F5677.S30812,319
F5677.S26412,322
F5677.S67312,323
F5677.S26812,327
F5677.S07812,335
F5677.S54212,335
F5677.S29112,379
F5677.S59012,390
F5677.S62712,397
F5677.S02812,402
F5677.S01512,442
F5677.S26512,473
F5677.S53512,490
F5677.S18412,515
F5677.S19712,538
F5677.S31812,547
F5677.S42612,589
F5677.S31712,592
F5677.S36512,606
F5677.S15112,615
F5677.S23212,635
F5677.S35912,644
F5677.S67612,657
F5677.S20712,658
F5677.S23612,673
F5677.S10312,710
F5677.S55412,712
F5677.S51212,721
F5677.S09212,725
F5677.S02912,735
F5677.S64612,744
F5677.S15312,744
F5677.S31912,769
F5677.S31112,773
F5677.S07912,799
F5677.S21612,804
F5677.S35412,806
F5677.S47512,834
F5677.S13712,842
F5677.S26012,855
F5677.S26712,885
F5677.S14412,894
F5677.S09912,900
F5677.S33812,946
F5677.S03412,981
F5677.S67212,995
F5677.S13313,001
F5677.S20413,009
F5677.S62013,034
F5677.S30113,060
F5677.S34013,072
F5677.S29413,121
F5677.S13613,131
F5677.S56613,143
F5677.S11013,149
F5677.S15513,167
F5677.S22813,174
F5677.S20513,256
F5677.S20813,259
F5677.S67413,259
F5677.S20313,259
F5677.S14313,280
F5677.S06713,286
F5677.S22013,307
F5677.S27113,317
F5677.S33913,415
F5677.S29513,415
F5677.S36813,416
F5677.S52113,420
F5677.S53313,463
F5677.S27213,463
F5677.S13813,471
F5677.S04713,536
F5677.S18813,540
F5677.S14013,556
F5677.S14713,557
F5677.S26113,599
F5677.S29713,613
F5677.S34313,629
F5677.S46013,640
F5677.S31013,703
F5677.S12113,713
F5677.S13113,725
F5677.S18113,757
F5677.S41213,777
F5677.S10413,786
F5677.S39213,799
F5677.S05313,817
F5677.S34413,826
F5677.S65313,829
F5677.S10113,829
F5677.S04413,845
F5677.S16413,872
F5677.S21213,884
F5677.S15013,923
F5677.S65913,924
F5677.S37713,927
F5677.S24413,946
F5677.S15913,946
F5677.S29813,954
F5677.S26213,996
F5677.S16713,999
F5677.S28614,032
F5677.S23414,102
F5677.S51014,104
F5677.S62614,118
F5677.S11514,129
F5677.S28814,137
F5677.S12814,165
F5677.S28714,171
F5677.S05214,302
F5677.S43214,313
F5677.S27614,327
F5677.S24614,335
F5677.S35214,342
F5677.S09714,359
F5677.S33714,372
F5677.S39314,382
F5677.S32014,404
F5677.S03614,412
F5677.S10614,466
F5677.S03214,469
F5677.S25814,470
F5677.S33414,473
F5677.S23814,482
F5677.S11714,518
F5677.S37414,553
F5677.S13214,556
F5677.S10014,558
F5677.S00814,575
F5677.S12714,615
F5677.S05514,619
F5677.S02714,629
F5677.S27714,643
F5677.S12514,719
F5677.S04314,733
F5677.S05914,735
F5677.S62314,747
F5677.S24914,779
F5677.S00614,779
F5677.S19914,819
F5677.S18914,857
F5677.S10914,859
F5677.S36314,872
F5677.S65414,879
F5677.S34114,887
F5677.S04514,889
F5677.S05115,020
F5677.S14615,025
F5677.S38415,049
F5677.S33515,066
F5677.S65215,138
F5677.S54015,187
F5677.S04615,213
F5677.S17115,223
F5677.S23515,226
F5677.S07115,232
F5677.S06115,236
F5677.S05715,238
F5677.S07515,320
F5677.S63715,345
F5677.S03315,358
F5677.S25015,371
F5677.S24815,391
F5677.S38315,440
F5677.S33115,467
F5677.S01415,482
F5677.S04015,491
F5677.S05415,509
F5677.S02215,513
F5677.S29015,559
F5677.S03715,559
F5677.S02415,568
F5677.S21115,599
F5677.S02515,619
F5677.S11215,625
F5677.S20915,639
F5677.S18615,659
F5677.S35115,680
F5677.S23915,695
F5677.S17715,744
F5677.S67715,744
F5677.S00915,778
F5677.S39915,812
F5677.S07315,815
F5677.S01915,839
F5677.S04115,870
F5677.S37915,943
F5677.S34216,020
F5677.S01316,046
F5677.S44416,082
F5677.S21916,127
F5677.S13516,129
F5677.S16516,134
F5677.S08316,148
F5677.S13416,172
F5677.S26616,184
F5677.S09816,215
F5677.S07216,238
F5677.S64716,238
F5677.S67916,242
F5677.S39116,244
F5677.S01116,248
F5677.S06016,251
F5677.S62116,255
F5677.S05016,258
F5677.S08016,270
F5677.S66016,272
F5677.S08516,282
F5677.S68216,299
F5677.S25916,310
F5677.S38216,362
F5677.S05816,436
F5677.S08616,447
F5677.S67516,459
F5677.S10716,468
F5677.S63216,490
F5677.S02316,495
F5677.S03816,498
F5677.S11416,504
F5677.S09016,520
F5677.S01016,669
F5677.S18216,685
F5677.S07716,703
F5677.S06316,739
F5677.S01716,785
F5677.S00716,825
F5677.S05616,847
F5677.S28516,854
F5677.S06216,886
F5677.S26916,901
F5677.S06916,908
F5677.S09116,951
F5677.S12016,990
F5677.S66417,017
F5677.S58217,040
F5677.S11617,058
F5677.S21817,069
F5677.S00117,099
F5677.S28917,151
F5677.S55517,221
F5677.S33217,226
F5677.S18517,237
F5677.S02117,247
F5677.S25117,345
F5677.S65517,348
F5677.S58817,443
F5677.S12617,459
F5677.S02617,485
F5677.S19217,564
F5677.S12217,608
F5677.S46617,709
F5677.S68117,713
F5677.S25417,722
F5677.S60917,733
F5677.S68017,743
F5677.S03917,760
F5677.S08817,775
F5677.S10217,810
F5677.S18017,856
F5677.S66817,864
F5677.S29917,872
F5677.S13917,904
F5677.S08917,908
F5677.S64817,915
F5677.S07417,927
F5677.S49917,932
F5677.S23717,933
F5677.S06617,947
F5677.S10818,047
F5677.S25518,055
F5677.S22118,061
F5677.S31418,132
F5677.S65118,173
F5677.S65818,230
F5677.S33318,241
F5677.S66618,282
F5677.S11318,291
F5677.S20618,358
F5677.S00318,399
F5677.S08218,405
F5677.S67018,421
F5677.S08118,456
F5677.S16618,465
F5677.S57718,555
F5677.S00518,625
F5677.S23318,672
F5677.S03018,679
F5677.S10518,763
F5677.S22618,788
F5677.S64318,939
F5677.S07019,034
F5677.S39019,052
F5677.S53219,058
F5677.S08719,119
F5677.S48819,123
F5677.S37019,191
F5677.S03519,308
F5677.S35519,456
F5677.S45519,565
F5677.S11819,617
F5677.S54319,791
F5677.S42120,247
F5677.S67120,285
F5677.S65620,408
F5677.S04920,727
F5677.S03120,758
F5677.S04820,929
F5677.S37221,162
F5677.S06821,200
F5677.S65021,326
F5677.S32121,478
F5677.S66921,490
F5677.S00421,634
F5677.S00221,698
F5677.S61021,710
F5677.S22221,846
F5677.S08421,943
F5677.S01222,242
F5677.S64922,350
F5677.S67822,698
F5677.S61323,119
F5677.S66223,177
F5677.S36623,599
F5677.S41023,665
F5677.S12323,809
F5677.S06424,131
F5677.S39824,163
F5677.S01824,309
F5677.S11124,487
F5677.S12424,798
F5677.S66326,350
F5677.S04226,803
F5677.S14227,521
F5677.S38830,039
F5677.S11931,622
F5677.S66535,476
F5677.S66735,993
 
 
 

VII. Analysis - Read Taxonomy Assignment

Read Taxonomy Assignment - Methods

 

The species-level, open-reference 16S rRNA NGS reads taxonomy assignment pipeline

Version 20210310
 

1. Raw sequences reads in FASTA format were BLASTN-searched against a combined set of 16S rRNA reference sequences. It consists of MOMD (version 0.1), the HOMD (version 15.2 http://www.homd.org/index.php?name=seqDownload&file&type=R ), HOMD 16S rRNA RefSeq Extended Version 1.1 (EXT), GreenGene Gold (GG) (http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/gold_strains_gg16S_aligned.fasta.gz) , and the NCBI 16S rRNA reference sequence set (https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz). These sequences were screened and combined to remove short sequences (<1000nt), chimera, duplicated and sub-sequences, as well as sequences with poor taxonomy annotation (e.g., without species information). This process resulted in 1,015 from HOMD V15.22, 495 from EXT, 3,940 from GG and 18,044 from NCBI, a total of 25,120 sequences. Altogether these sequence represent a total of 15,601 oral and non-oral microbial species.

The NCBI BLASTN version 2.7.1+ (Zhang et al, 2000) was used with the default parameters. Reads with ≥ 98% sequence identity to the matched reference and ≥ 90% alignment length (i.e., ≥ 90% of the read length that was aligned to the reference and was used to calculate the sequence percent identity) were classified based on the taxonomy of the reference sequence with highest sequence identity. If a read matched with reference sequences representing more than one species with equal percent identity and alignment length, it was subject to chimera checking with USEARCH program version v8.1.1861 (Edgar 2010). Non-chimeric reads with multi-species best hits were considered valid and were assigned with a unique species notation (e.g., spp) denoting unresolvable multiple species.

2. Unassigned reads (i.e., reads with < 98% identity or < 90% alignment length) were pooled together and reads < 200 bases were removed. The remaining reads were subject to the de novo operational taxonomy unit (OTU) calling and chimera checking using the USEARCH program version v8.1.1861 (Edgar 2010). The de novo OTU calling and chimera checking was done using 98% as the sequence identity cutoff, i.e., the species-level OTU. The output of this step produced species-level de novo clustered OTUs with 98% identity. Representative reads from each of the OTUs/species were then BLASTN-searched against the same reference sequence set again to determine the closest species for these potential novel species. These potential novel species were pooled together with the reads that were signed to specie-level in the previous step, for down-stream analyses.

Reference:
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12. PubMed PMID: 20709691.

3. Designations used in the taxonomy:

	1) Taxonomy levels are indicated by these prefixes:
	
	   k__: domain/kingdom
	   p__: phylum
	   c__: class
	   o__: order
	   f__: family
	   g__: genus  
	   s__: species
	
	   Example: 
	
	   k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__faecis
		
	2) Unique level identified – known species:
	   
	   k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis
	
	   The above example shows some reads match to a single species (all levels are unique)
	
	3) Non-unique level identified – known species:

	   k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__multispecies_spp123_3
	   
	   The above example “s__multispecies_spp123_3” indicates certain reads equally match to 3 species of the 
	   genus Roseburia; the “spp123” is a temporally assigned species ID.
	
	   k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__multigenus;s__multispecies_spp234_5
	   
	   The above example indicates certain reads match equally to 5 different species, which belong to multiple genera.; 
	   the “spp234” is a temporally assigned species ID.
	
	4) Unique level identified – unknown species, potential novel species:
	   
	   k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ hominis_nov_97%
	   
	   The above example indicates that some reads have no match to any of the reference sequences with 
	   sequence identity ≥ 98% and percent coverage (alignment length)  ≥ 98% as well. However this groups 
	   of reads (actually the representative read from a de novo  OTU) has 96% percent identity to 
	   Roseburia hominis, thus this is a potential novel species, closest to Roseburia hominis. 
	   (But they are not the same species).
	
	5) Multiple level identified – unknown species, potential novel species:
	   k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ multispecies_sppn123_3_nov_96%
	
	   The above example indicates that some reads have no match to any of the reference sequences 
	   with sequence identity ≥ 98% and percent coverage (alignment length)  ≥ 98% as well. 
	   However this groups of reads (actually the representative read from a de novo  OTU) 
	   has 96% percent identity equally to 3 species in Roseburia. Thus this is no single 
	   closest species, instead this group of reads match equally to multiple species at 96%. 
	   Since they have passed chimera check so they represent a novel species. “sppn123” is a 
	   temporary ID for this potential novel species.

 
4. The taxonomy assignment algorithm is illustrated in this flow char below:
 
 
 
 

Read Taxonomy Assignment - Result Summary *

CodeCategoryMPC=0% (>=1 read)MPC=0.1%(>=5154 reads)
ATotal reads8,525,3728,525,372
BTotal assigned reads5,154,7945,154,794
CAssigned reads in species with read count < MPC0416,942
DAssigned reads in samples with read count < 50000
ETotal samples682682
FSamples with reads >= 500682682
GSamples with reads < 50000
HTotal assigned reads used for analysis (B-C-D)5,154,7944,737,852
IReads assigned to single species1,515,8941,411,778
JReads assigned to multiple species13,84510,824
KReads assigned to novel species3,625,0553,315,250
LTotal number of species1,003140
MNumber of single species17637
NNumber of multi-species221
ONumber of novel species805102
PTotal unassigned reads3,370,5783,370,578
QChimeric reads120,840120,840
RReads without BLASTN hits2,823,7992,823,799
SOthers: short, low quality, singletons, etc.425,939425,939
A=B+P=C+D+H+Q+R+S
E=F+G
B=C+D+H
H=I+J+K
L=M+N+O
P=Q+R+S
* MPC = Minimal percent (of all assigned reads) read count per species, species with read count < MPC were removed.
* Samples with reads < 500 were removed from downstream analyses.
* The assignment result from MPC=0.1% was used in the downstream analyses.
 
 
 

Read Taxonomy Assignment - ASV Species-Level Read Counts Table

This table shows the read counts for each sample (columns) and each species identified based on the ASV sequences. The downstream analyses were based on this table.
SPIDTaxonomyF5677.S001F5677.S002F5677.S003F5677.S004F5677.S005F5677.S006F5677.S007F5677.S008F5677.S009F5677.S010F5677.S011F5677.S012F5677.S013F5677.S014F5677.S015F5677.S016F5677.S017F5677.S018F5677.S019F5677.S020F5677.S021F5677.S022F5677.S023F5677.S024F5677.S025F5677.S026F5677.S027F5677.S028F5677.S029F5677.S030F5677.S031F5677.S032F5677.S033F5677.S034F5677.S035F5677.S036F5677.S037F5677.S038F5677.S039F5677.S040F5677.S041F5677.S042F5677.S043F5677.S044F5677.S045F5677.S046F5677.S047F5677.S048F5677.S049F5677.S050F5677.S051F5677.S052F5677.S053F5677.S054F5677.S055F5677.S056F5677.S057F5677.S058F5677.S059F5677.S060F5677.S061F5677.S062F5677.S063F5677.S064F5677.S065F5677.S066F5677.S067F5677.S068F5677.S069F5677.S070F5677.S071F5677.S072F5677.S073F5677.S074F5677.S075F5677.S076F5677.S077F5677.S078F5677.S079F5677.S080F5677.S081F5677.S082F5677.S083F5677.S084F5677.S085F5677.S086F5677.S087F5677.S088F5677.S089F5677.S090F5677.S091F5677.S092F5677.S093F5677.S094F5677.S095F5677.S096F5677.S097F5677.S098F5677.S099F5677.S100F5677.S101F5677.S102F5677.S103F5677.S104F5677.S105F5677.S106F5677.S107F5677.S108F5677.S109F5677.S110F5677.S111F5677.S112F5677.S113F5677.S114F5677.S115F5677.S116F5677.S117F5677.S118F5677.S119F5677.S120F5677.S121F5677.S122F5677.S123F5677.S124F5677.S125F5677.S126F5677.S127F5677.S128F5677.S129F5677.S130F5677.S131F5677.S132F5677.S133F5677.S134F5677.S135F5677.S136F5677.S137F5677.S138F5677.S139F5677.S140F5677.S141F5677.S142F5677.S143F5677.S144F5677.S145F5677.S146F5677.S147F5677.S148F5677.S149F5677.S150F5677.S151F5677.S152F5677.S153F5677.S154F5677.S155F5677.S156F5677.S157F5677.S158F5677.S159F5677.S160F5677.S161F5677.S162F5677.S163F5677.S164F5677.S165F5677.S166F5677.S167F5677.S168F5677.S169F5677.S170F5677.S171F5677.S172F5677.S173F5677.S174F5677.S175F5677.S176F5677.S177F5677.S178F5677.S179F5677.S180F5677.S181F5677.S182F5677.S183F5677.S184F5677.S185F5677.S186F5677.S187F5677.S188F5677.S189F5677.S190F5677.S191F5677.S192F5677.S193F5677.S194F5677.S195F5677.S196F5677.S197F5677.S198F5677.S199F5677.S200F5677.S201F5677.S202F5677.S203F5677.S204F5677.S205F5677.S206F5677.S207F5677.S208F5677.S209F5677.S210F5677.S211F5677.S212F5677.S213F5677.S214F5677.S215F5677.S216F5677.S217F5677.S218F5677.S219F5677.S220F5677.S221F5677.S222F5677.S223F5677.S224F5677.S225F5677.S226F5677.S227F5677.S228F5677.S229F5677.S230F5677.S231F5677.S232F5677.S233F5677.S234F5677.S235F5677.S236F5677.S237F5677.S238F5677.S239F5677.S240F5677.S241F5677.S242F5677.S243F5677.S244F5677.S245F5677.S246F5677.S247F5677.S248F5677.S249F5677.S250F5677.S251F5677.S252F5677.S253F5677.S254F5677.S255F5677.S256F5677.S257F5677.S258F5677.S259F5677.S260F5677.S261F5677.S262F5677.S263F5677.S264F5677.S265F5677.S266F5677.S267F5677.S268F5677.S269F5677.S270F5677.S271F5677.S272F5677.S273F5677.S274F5677.S275F5677.S276F5677.S277F5677.S278F5677.S279F5677.S280F5677.S281F5677.S282F5677.S283F5677.S284F5677.S285F5677.S286F5677.S287F5677.S288F5677.S289F5677.S290F5677.S291F5677.S292F5677.S293F5677.S294F5677.S295F5677.S296F5677.S297F5677.S298F5677.S299F5677.S300F5677.S301F5677.S302F5677.S303F5677.S304F5677.S305F5677.S306F5677.S307F5677.S308F5677.S309F5677.S310F5677.S311F5677.S312F5677.S313F5677.S314F5677.S315F5677.S316F5677.S317F5677.S318F5677.S319F5677.S320F5677.S321F5677.S322F5677.S323F5677.S324F5677.S325F5677.S326F5677.S327F5677.S328F5677.S329F5677.S330F5677.S331F5677.S332F5677.S333F5677.S334F5677.S335F5677.S336F5677.S337F5677.S338F5677.S339F5677.S340F5677.S341F5677.S342F5677.S343F5677.S344F5677.S345F5677.S346F5677.S347F5677.S348F5677.S349F5677.S350F5677.S351F5677.S352F5677.S353F5677.S354F5677.S355F5677.S356F5677.S357F5677.S358F5677.S359F5677.S360F5677.S361F5677.S362F5677.S363F5677.S364F5677.S365F5677.S366F5677.S367F5677.S368F5677.S369F5677.S370F5677.S371F5677.S372F5677.S373F5677.S374F5677.S375F5677.S376F5677.S377F5677.S378F5677.S379F5677.S380F5677.S381F5677.S382F5677.S383F5677.S384F5677.S385F5677.S386F5677.S387F5677.S388F5677.S389F5677.S390F5677.S391F5677.S392F5677.S393F5677.S394F5677.S395F5677.S396F5677.S397F5677.S398F5677.S399F5677.S400F5677.S401F5677.S402F5677.S403F5677.S404F5677.S405F5677.S406F5677.S407F5677.S408F5677.S409F5677.S410F5677.S411F5677.S412F5677.S413F5677.S414F5677.S415F5677.S416F5677.S417F5677.S418F5677.S419F5677.S420F5677.S421F5677.S422F5677.S423F5677.S424F5677.S425F5677.S426F5677.S427F5677.S428F5677.S429F5677.S430F5677.S431F5677.S432F5677.S433F5677.S434F5677.S435F5677.S436F5677.S437F5677.S438F5677.S439F5677.S440F5677.S441F5677.S442F5677.S443F5677.S444F5677.S445F5677.S446F5677.S447F5677.S448F5677.S449F5677.S450F5677.S451F5677.S452F5677.S453F5677.S454F5677.S455F5677.S456F5677.S457F5677.S458F5677.S459F5677.S460F5677.S461F5677.S462F5677.S463F5677.S464F5677.S465F5677.S466F5677.S467F5677.S468F5677.S469F5677.S470F5677.S471F5677.S472F5677.S473F5677.S474F5677.S475F5677.S476F5677.S477F5677.S478F5677.S479F5677.S480F5677.S481F5677.S482F5677.S483F5677.S484F5677.S485F5677.S486F5677.S487F5677.S488F5677.S489F5677.S490F5677.S491F5677.S492F5677.S493F5677.S494F5677.S495F5677.S496F5677.S497F5677.S498F5677.S499F5677.S500F5677.S501F5677.S502F5677.S503F5677.S504F5677.S505F5677.S506F5677.S507F5677.S508F5677.S509F5677.S510F5677.S511F5677.S512F5677.S513F5677.S514F5677.S515F5677.S516F5677.S517F5677.S518F5677.S519F5677.S520F5677.S521F5677.S522F5677.S523F5677.S524F5677.S525F5677.S526F5677.S527F5677.S528F5677.S529F5677.S530F5677.S531F5677.S532F5677.S533F5677.S534F5677.S535F5677.S536F5677.S537F5677.S538F5677.S539F5677.S540F5677.S541F5677.S542F5677.S543F5677.S544F5677.S545F5677.S546F5677.S547F5677.S548F5677.S549F5677.S550F5677.S551F5677.S552F5677.S553F5677.S554F5677.S555F5677.S556F5677.S557F5677.S558F5677.S559F5677.S560F5677.S561F5677.S562F5677.S563F5677.S564F5677.S565F5677.S566F5677.S567F5677.S568F5677.S569F5677.S570F5677.S571F5677.S572F5677.S573F5677.S574F5677.S575F5677.S576F5677.S577F5677.S578F5677.S579F5677.S580F5677.S581F5677.S582F5677.S583F5677.S584F5677.S585F5677.S586F5677.S587F5677.S588F5677.S589F5677.S590F5677.S591F5677.S592F5677.S593F5677.S594F5677.S595F5677.S596F5677.S597F5677.S598F5677.S599F5677.S600F5677.S601F5677.S602F5677.S603F5677.S604F5677.S605F5677.S606F5677.S607F5677.S608F5677.S609F5677.S610F5677.S611F5677.S612F5677.S613F5677.S614F5677.S615F5677.S616F5677.S617F5677.S618F5677.S619F5677.S620F5677.S621F5677.S622F5677.S623F5677.S624F5677.S625F5677.S626F5677.S627F5677.S628F5677.S629F5677.S630F5677.S631F5677.S632F5677.S633F5677.S634F5677.S635F5677.S636F5677.S637F5677.S638F5677.S639F5677.S640F5677.S641F5677.S642F5677.S643F5677.S644F5677.S645F5677.S646F5677.S647F5677.S648F5677.S649F5677.S650F5677.S651F5677.S652F5677.S653F5677.S654F5677.S655F5677.S656F5677.S657F5677.S658F5677.S659F5677.S660F5677.S661F5677.S662F5677.S663F5677.S664F5677.S665F5677.S666F5677.S667F5677.S668F5677.S669F5677.S670F5677.S671F5677.S672F5677.S673F5677.S674F5677.S675F5677.S676F5677.S677F5677.S678F5677.S679F5677.S680F5677.S681F5677.S682
SP1Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;gordonii4123315017555965518832640993692184647364800424480001860322173045473615000313003327100544450007880031002400338230005363076360108108207331100006731981020000018900133000550923022530490507067018402722490460567074930100111338892029300000605116001361540248410615500006440506189012700046120130914644000117052021602838658359085001313390007310120811531151400057992014614423810806970065600007570559321163002785402517200383181155527615723002811472041480951002510550380730024625402297692314700467831891040054115510301611039293702190224057304201260001340022001260440010407000990212002699816016587083273272005151160093011658107616196211319614010000219594022134330093770600112342890015200165625021601931198025800005664518121010452203015021622800001491457422529401820560220115179116006414300704379665142041600111067001250040065110774108400010207202630013329087119120180012000002702190240080012304630386000490305018000018913962800102959200020930000121755803800000000031600042270592853005920046301120013543542700034316014215536065304380072001040017001140013400590099015604205500048736022501441050932455054601575335816112317600004362055010200013710144556154028841189003702321272615484503600260016324805200635066106000062605000161046310007321000611631047729852162052047045935032301443160052000003711855722588264001250
SP11Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;vaginalis00001670000158009800000042000000000000000000000038200027400003100000000000002830282410000000000000000000000000000000000000000000000000000000003560013800002190000000000341000000000000000000000197000000000000000000000000000000003420002320000000003900582000000000017300000015000010700000000000032808400019700000000000000516000000034002500000278000000001350000000000023690000000015100000000026400000081017426000212000000000000000000000055000000000000000000000000012200180000000000224000001500011100000083000140600000000126000000003900000000000000000000000000000256000000000680000000001350000000000001910000003731300000000000000000000000000000720000003020000000000000000000000000000320000000000127000000000003300000000000000000000000000000000000000000003080000000000000000000021000000020000
SP13Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;sp. HMT170000000000000000080000000002280000123715100000000001340000000000000000000023700004600000053000000110700000000000000000000000000000000000000000123000001530000035700000000000015715200000000000000000001845300008729000000032000006741701840000000000000000460000000123019300000000034141000000000001640000000000001110000000009088000000000000011600000217000015100677014600000000178000000000370000001130000000160430000000001800000038002070000001701470000139002760000000000003600000000000000260153000580000000000000000114005521200000000001531730000000001120000060000000520000912700000035000035850003500000000000000000000000000000000010100273500200000003805721000000000000000000510000000000000690000000000870000000002240001270000000000880000000440730000111022000009203200280071250670082051000000000000000000000007600000000000211000183
SP14Bacteria;Synergistetes;Synergistia;Synergistales;Synergistaceae;Fretibacterium;fastidiosum46827100000106001139309800140170500426660016500014402820000015700010242212000027400013100850007207100000000183485019002367014703600000360211410000000043227000188000011400189000000000019100000117082002330000000740411510000007011359590000400020100008100001602200063000000001720870000000000280000110210018716911497770070001820000191000210003000720133000000021355000960034116566000007600102421810580280000000000000450000000011243870103150040010163000270001050000124061177101000028800267183074120011254930001220000000000335000300000380000128000000000000000002590219690028001505405706100000078054000000007200019058045075000000001061701000009304200001330102000488501490010600000000017137000035000078000000620400001500026116121075000000000000015104883000000000000019400072121666306592001416917003000620061056000000470000600037000000000300000000000000025700000600000189910720000000008615105086173683242940013507612000390010685000325168000790000000048000026000000510159
SP15Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;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
SP17Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Colibacter;massiliensis000310199000033000000000000000700000115000006500001521800000000003635800000001190000010301130000018400000000923100000000000000000002500570000000000000000000016700000200000053000000000000000001220000193000000000000001100000004000000110000000013200000970000039000000000003200055000055018000000001170000000056000042880000000000048000083000070890054000004400000000000000000000000000000000715985990000720126000105000000000015020103500004100020100000104000000012100000000001700000000107000000000000000000000000000000000000000000000138000158000000000000000230000065000000000000000000000000000006300000000000000000000000000000000000000400000000000037000000630650000000000000000000000000000000000000000000000000000000000000000000000980000044000000000000003800047000000000000009100000000
SP18Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;intermedius0000010111200590000014481897352402210328542000004300550011800012917000027395150056400000001740018300107000067001310141000137184000045000016359190016300640088015162484273650007453159750146529400155533008846391850983201228120000504010300781440047822200000721205700038200908860145077028021600139029306773091840001418732547417992000047701659144685000056075026044140125064302026404598000000840930024086003130590213017410050311205536771520002218151955209800608701820000005630000801100017700092000079001230025860332000483350027000039055950157165002522603000480130229098002457239018230800000047600017800000001511260924545256012508700293480000075600001641010914272161829118250005570012100118558000259570015602500002000132000000009014100002170105860100290000195003810770042022212561015400008800119000037013206004041300514040064117460003000521135015444402365077928650545950409094101250130071073092000009900019152000000470037231120001187300233960075003100061424106900001449115417112101761515120133001140018218001390145583560002737840020100368570599001050282040000783310530000008000208910001379200442235402310646900057400096365183624173001639729010563
SP19Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-2];Saccharibacteria_(TM7)_[G-5];bacterium HMT356225340670001070084440180006200057629616121000000003587204601041280009230927200123000000001702970011202980630000262071659300383001058000007190288116720014800218009700421082136800820012123793625906490000000359001141372630003060279000180601550670278796000000000110000000620400020100180026601040000390401274746001365200002100030129001943500075165367582400714800532001012988089000001160002417141118852220820001090289150013400209108000000072002732514502100320000398949007802926009613600667027700124020701051100015428413105203100005100456689921508660000415073139208058640902180003872122802520160000243900704014400625127500016632100201505700274021509724000194194018300143005375000330155000850000141000083680055000690211032000010701900381625001970002351421700154870000002186005300590068011900540000029014000001100047001490372033018921300262191019000004500065571470308702257002180690000198000023900047104886202452086201220012200310038051182631013800229448000750006500000000000180681810600610000000000029200055000017902260133122000000004903671031054511580801016502160371645087640010872270001277150990135000000001908017080004332737000663084
SP2Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;sp. HMT20400000260205000000000000000662730000000000000000000123000000001300000000000000002900000000000000002400000000000000235000250000000000000000000000000000018920600000000374000004417800000040000000000001950000000490000000000107000000000000000000034001638900000000000000000000000000000000000000000000000000740000000028000000000000001630012000000000000000000000000000014700023000000000000000000002500000000000053000000000059000000000000000940000164000000000006700002105100000000149800000000049000000000000000270210000000980000000000222000000057000004606400000000000000000000000000000000000000011700000000000000000060000000000330000000000000000000000001370000000900000000000000000000000000000006730000000000500015700000061000500000017000000000000000000000000001791900000000
SP20Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum002580000025302100010500000000002331303881370127000070031404861551240000290000000026900284023200000000060307100021400033246094053204440450093121001450031601210000121002021150160000000561730006000000029500000010601250000237452441381860047014902171953768000005800488111021271000173000003160003650470175563134438000326000000372134000524700003070000168002703470000000102004102120000008771026600000000010000024552141000011800000196222018400104001913000593900054980000000166750057850072026349169914000002371351860001130144650101002740000731740017900000037632600861332313366323001410032600001910149960640000007400000000013400021901742310228112000019129000059560673300000161000000000012493000181004101340000002661150145000000000001920002740310890156006300107132000020107400000000000570000000000150002000000000189000010800043950920116760010234006423700000095156290057000471501216319467980000136229004600022700980010097000000960070020627300640010311800850000010900000001628700151017107702440886700000108380201000700000017300260000000036500017000
SP21Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;infelix000000000000010100000046007200820000048004200275870000227000000000670000011400000000106004100000000275000006082000000000008600000000000005100000000000000000000034000000067139000000000023138000000000075000000063000000516900013100440058000310000000000834002100870000005806500000079000034000000000736500000053107000040640940046000000003300000000214000000000004305100004351000003814000000860001771491130058111001360580000000390000000000010000006800000213000970004000004800000000000000000000003500000000137000000000000000043000000000027009200048000000180006300000000000000036000880044062000023000012480000000000000000000000000000000310000680000004704400045730000025002700000000000000000021065025000000000062020600000000000000004338038000009200003000000000770510078159465200107000380410000000010400046000000011900000000000000096
SP22Bacteria;Firmicutes;Clostridia;Clostridiales;Peptococcaceae;Peptococcus;sp._Oral_Taxon_1670159025000000024003800000048001298700008001320000000000000038000001340190000000000000111006400000008400000067220000000000044000000000000911940000000001070000081000000000000710032001820002452159000005500000000000000480000000057004000000270000000300000000000000000000000000000000001206021540008000000074000000050037000000113000350240000000062707700000440420000000000000000009400000000390000000165002900005700000000000000000000000025000000000003000000000441154706000470000468000000000000000000200000000000000000000000700000033000005957000000000046300056000000770000000000000000000000022000001100000000000001250000000000027000024000130072000023670000000008000310015000320000000000000000000026000000000000000054000000000000000000000000299002500000150000000003000001260000000000000210000000138083
SP25Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;invisus124426017302360002480001911171314020065013324300012000050196174106043801990117008010020800134056706700023525300020902820000014027221602308296130391531940273041501793061481780210227650156001413500560141562231102130022613101981610207000000074105104001092490121098111294000110091144022130002911411756700000931210980029603490028011511301291510769621286222019013993271220291176088009631221022622000195000002560263115750091106258002741362001927176220151080007822280002961121713904801688801437650815502299402400156851110145021800016300000510161008828908394284012000026909108393671039800015219400101024102564040127009515788950127142001282705621718710914213001720480074339215713400234012710802200174302132400751284512800221132075352171560892140105369774000920000003900160991432190655144250000561080000860197130440966893400290000261231070058550594415800691325800721520010915200062002414860111057011603643161000086001561180088000000142114500430136006415600166015426001929200005514152013661136009900000005900510046431701991717038025068001140000133315511300161311330421170230850161106000058002504345690027995812000002420001092016929068000001388387173333460119000000000028100114476846094032114001000015426900011700114222014901414300727512601262330135576800282090180156
SP27Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Veillonella;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
SP28Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;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
SP29Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT957000000013511600005006711901100031081351350000002000210083200000000082000028000052510000000000063002505602800068000018307600000000010800004300000166089100000004300001510000000000022086000002011705700000005000000722900070490650001207307600000601071280700060022005000000000002137000018000007835000000000000140580000000000005100024000000000000000000000002827000000000000000024000141008830001100000004433000001840001023006626000060460000000006029000005700500031077000000009700052650000300182000000000430000000000000065220000000820000000000044520220710000310000310759012000026002700000208650000000210000000000000140041000000212400013000000000000000000000000075041000000721000571030000000400000000037000410045006028012000250000000010800000000000000260000822000000600000027047019000000158000210964500003700005500000022391500002900000000050000775500040
SP3Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;anginosus1092490101000000495100010219986067230727750723023121009200067197013256736090402816050182002540150901728402910000690003810043117012600000018525000000013242171001211783014411000013941370388125235290006319687376005000790006900512112012439600016185154980459522828660000170127080042127014005401900446160531012118042440004642771239700019817001170230005162800000043700048527011401376530707765011019328102101190365026100050669001758690004380078429548603160097002729269111117002103171400010060048509800240297034611911610176524210090351922271244386166211002130019029024314121200381070941241020405001282005681580000134780001512971394063387000054687109014000001160000744000760005420923801420001306003100660172290010000061064060048232200190102003240400048530820447346000006725085018219433710000800030005619125053023021017170732400008700058001410000015500001660000000104001870051004611690001401130402801995052070028330029800020000010991000082028561270142970460151125273350490048029400445033005814003199011330000000310156029360544902400000088094370000018403090136990291485210904900225084000133400067000040101922219462470009901537008700500000107019815211162282700077200105
SP31Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;mutans09415301171560004289001900314212141702474440071000004910486000011800000646000001489003024033300100730620000109026508726003000157000339000000005500731700050980083521070081618140031920007910350102571583920001100245000001294000000143109004293006670183204370000045000000013530023800260011500000022790000021117670045760000000450000473009752670014906000244100001711520016004403110930360142000200762000359000001292310000035713100009210336633605484000016432000000001918440000025506150019169050290401190821299057561120017800014373090105000002880000020300372900000110400334503400010900074228147002197209000116001090000000000953700006910249500003200664307236500762098454056830000000003220000000536200710440664000120000000000000119000014600000000000084765117335100000002911011100047000043736440001500238002202741171230015510002830557975001319400049725180006600104208961032453001040000043000216000179002001700001383633224602086000000222000004570000160114800013036300580638104930019110004473047914224166000036908754525133390075016630030215700000000000000002430000000000660010736000084517469143175714233500028000005390135401923000000
SP32Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT34700000099289470398901051240000000000157008300000000001870137000869900000000001170000000000000000001980000390000000126175547000237000000000018000890027725511100000031800000000000000000000000000230000000000047149146000029000000143040000000004430001320016446000005928055000000000000540720000000177000000015200000000003380000000000000018026900000000000006130001020660048000670000992430000000007522900000113000000000053000014407700013522000310000000012700096000000001050000000000000000011600000000000000000000143021415000002190014044001200000410001020010600000000113000450048703726901440082292600000000000000035000000000000400000000018200000560620330000006912901050000058000000000102000085151000000000000000000001481440001050000061000000059000000070590009900006500001420000169288840000007404096980420000007307400124000000026000000052016330800049009600001729300661310000000035001877200000010390
SP33Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Megasphaera;micronuciformis00864400000010435002500057000047250560014400009104100000096001800000113000000000000003000217500018350014804000419790899200012500004356000018707000014414271000032400015000013969000473092140000000000000000090177000000000580000360000000000000000000000000178001832800008500070000000000000100000000120000000001610069000000000058000000000000006300000000000000000047318887000013700000000710031016206205902040034551496000119013000177630000135000102008455000002600000019101100000178068190000198012800000000015601880001410000000000000000000058000007900000000000006800002004135011900000000073000000183000000000000000000009001620000000000002602200000017700160260000074000000550000000000007008552300055000380000000000000057000050095000000116000000019002000310000220000000000000000000610000000000154000000000000021700000000020000000007806900000057000000065118000000
SP34Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;sp. HMT17100000006400064700000000057835000000000033800000000230000000000000000000000002401170000284009100000000190000000001940000000000219006600000000000000000000010900000000000012000000009100163009400000003600000000000000790000000008300000000004200399007800004600000048003100000000000000450690020000000006020000520000000000000000000000000000000000000000380108000000118000000000010400000740008300000000000008600600000000000078009200000000000000000000270000790000000000850000000000000000000000000000000000087440000087000072100000000000000000000000007500000000005200000000000001990071074000440490810000550000026009800000000000880000850001730000000000000001702700008460000000000004500000000001190900001705623261121000003300000160000000000000000000000000073000001100099900017600203970490000000000000000000190087
SP36Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;artemidis000000000000001800004100000000124028000007401200000001070000032007105900000000000127000000000000000000045000810000000000000018102001080138212600000023000000000000100047000000000045000174800460000000003600000000002300003800002100000540031000004160001702170000000000123000570000000000031000000182000115000030000000000141000000000012102079000000000000000000890006600000000000214960440021000018700000940000000770000025000000430000000000014500000740000540760071000000000000000048000000000000009100000000000023039000000000011305000000000006700009700000000000000000003800000000049000330000000003202200000000000000000000081000000000000320000370000550000000000019000000000270000000000011603100390000000000000004000570600000024000115000000000032001200073000000044000000151017002910009000000000000000000000
SP37Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;massiliensis00103000006270044000000000002871940118207005355010000000000000000001490000003576622100000000032800000000000000000064100000000000000000000000000000000000000000000003850000000000000194612000000000000000000002340000164871900620110000000000365000000001151870088950001120000000137022800000000000012306700000204000000044000000000000076253011300000000126000002641640000000000000000000000000000000277151011300000000000000000000001470021700228001900000000217592000000070000520000012000000000360000000000001490000000000011000000001340000000000000000460000630037200000000000000000001100000000102035200000094009844000000000085000002400000000000006100059003900000097011600019700000850033800000000000000960000052000049000000000033700000016300000001120000009200000024700000104000000000058718877000000000050000000000001854551200000000168069900000000000000071960
SP38Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;gerencseriae018900001460035070030501254001642670064890000000170015600632000320084087077500180000000151000026025000000640001470000000002527275316650000000153000000002150000000000000001325674333101414670000000000032504790670128834500000007500000693300000000210000000000000003688198003200000000022020000002431930000038400071000000126000011200073000011000007500001040000000005500007514620017546233007008801700004295054326122000006505167890000015300208000081000020000164000000000000003709500064018000000000000300000000720002313900000000040000830000000000000000000065722250000126000000000092000078480000000089240008700240028000006031100000490000000011600000310000001050000000000000000352000000000066007023949000870000007150000011000011100013587074017900000000000000012900087940068000000000000000029400000000000000990000981710068000061000085071571600001290011000504001360000000020300030129000170001710000000000000001399780460000
SP4Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;periodonticum000000000000000000001000012706500000022000000279410000000015200000000000395000000000000000000104015800642000000000000323034274000000000000000009081000000000002770017900000000000597000028500161002910000000000730000000000000000000000133000000000000000000000002420000242000000000000000023200000578000000000000000000099000000000000000001840000000000000000000000000670000000019100000510000011200000001650000000038400000000001990000000000001380000000000000000000000000000000860000000000000000000000000000000000000017700008603300003400000000000139000000003210000034700000000002961100000001620000000000000000000019400000000000009711000011500301840000000333000000003450850000000087001695100000000000640000000000000000112000000000000000000000000010400000087000000003970000000000000000008600000000000109200000
SP41Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT349013600000750002909500000011104910006300012607200002346292230012922817495009611800016900000023401280825800234601527000105000005615022137920148001320014000000871541021110094000770000000007700188820009816000042920620002611780163730000006801480570000084003602118100000000000000057001064712600041510001320009000000202482175047000000026002601230750990007100020214800005009918500013600161048000053416200001000000120007200006005503819104582000827601420105000001710001090002240000622310831503069300232210015323605000410000125272000000000014800388264078660000562327003170000005200000001552700078000000023808504100007404800000000000055083000000280000229102650000170005000000076007905000550000000789104458053000000000000000103000109200360890021005524000000061870930926501750000775800066990870471931154086642014300002880000911910011031015500081002011800044000440000037100584400650000000088000000001962512213800019000000000630001189937910967646109224801000130780007016814001192680000000023403004201210000000246
SP47Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;sp._Oral_Taxon_17100000000025600000029102033420000000013370000000000000000075000001140000003840004560151018630005640000002351164000322000000000000000000003041021174346000297000001039000012350000001120142003653921760259000133242049300030300000000000015404311111502800000892222370000010100000264000000000000000000046273000017300000004893740000000000670000000580000000001950000000026571000000000760054910000860000000002610011400052261000000000022470000135000024000000000061300000000050000550000541032700000000000000000000000000000000005840129700241000000000000000000000265000110701320013401032000006800304006000000000002380038010500000022707516200017000048004040005040000000000000000000873000000202000284000000003740015701002210011700027601580000000000000001400002070250050000000000000000000000000006900001410000330000102900000003310052000000740022858000077300000410000001800148021300000267980800000000010700763000000000000000440000
SP48Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT3462694344920007000000652170127000728173141180233215000520000021211632630001833150694199000650193290000143000018500250007108115302301750013375000440158001590012000137000175240087006611239113098140000000117000460000032196000920000037854114000530049680010884012701000620179041018000159008574590470007400000610000234005806600000007301041400104000002262845665000001930000000143012147000000116932105901088007100000640067198325702220000086108156355005909800050000049001052581590001101972482060000124365900043014205421112650031139032621026000250560269125005400380091000105014499017628175121005394300001165705400056121000011212500000000003330607602600000083000009200876201110013100000071048103466700000000000890761000001367687000005000009400000014900033000081000121000060000046000370501590000000000000000085000026011500003216800085196060002286509193001040000004501010003198740877500109003500001800000000000039000000918400028000005095105006300000640050709462154049072890000641700046001321908934010334106166067000000022001840021920000026500
SP5Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum_ss_polymorphum0020000000640910016000000018300060000004620580343000126189000007945000000170002560058975784000000002845630130000570002191041811963451611832203430001900010505521200002210001806786602990000000018900000192640000002270000000000960205102283020711002010472330001050008000608216011034000583000003207802790011601231359523313400240166000000021600381470000208000862640040276006812000010200430403000108243295003355150000008700221000047256810000590000039032900002380010852000120000011800000000044000000001762330215600000120363700025400341005291310012900151000000000000006700438018906310900152267047032001611562700000004100000000341330001120163000160002300000084052580000000000000420121840000000100045001110000001590000000097008604020125002883000000001016200017013901970000398232094013900000086760000000000000000870750000014013918706104810001950227004302005200999800000000236043531480100000105000000020600000005800000042591751070146700000760001810000380001042570005212121001320670880690860000830176593003400000003300380000000086000000
SP52Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;gasseri00001990000000000010300000000000000210000000000000000000132000211000000000044600000000000000000000000000000000000016000000000005400000007300000000057600000000000000000000000000000000000000000000000000000000000000000800000000000000520247470000000000000000034700025000000000000197430000507001300000000000195600000000001270000784000000004886031400000000190000000000000000000000000000088000000000000000000000000000000000000000000000000000132500000000000000199900000000041300000000000000000000000000000000000000000000000000000000000000000000000000000006400000000002750000000000000000000000000000000000000000000000000000000000000000000000000000000000000057001500000000109000000000000000000000000000000000000000000010200000000006000000000149200000064000
SP53Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Anaeroglobus;geminatus86500920103000219000490000000087243000000734800012500000057011000057001300400000430007130009201940166001290018019041000001480097000000001290000220095105309102043800000000000850002350022703601731290000105319005900000000212270000000007300000000169000007100000010412900000000000010200000000000079001035502584001200053022500000000000000006000102000221100000000000009000000000000000020234395900013707595000066631200000118014670001063824000059180000059100087004208468000975800002130001410198018904116009309900001140000134073107000000000002045903900121800711420002302800010112300002300000001020000017000000134300007002133000006873000040000000003900007900000002500001170000000020400076000000610007100000000000206191370000000000002800093020900063002618000000032990009795000000043000000000000000059000000000000000440015000000125640060000000000000121006289000005141005600401110002143360013100007800006601620018700000089173106
SP6Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;fermentum000026328300000000008300000000000000000000000002170000000000009800000000000000000025000000000000000000000000000000000000000003810000000000000000487000006100000000000000000000000000000000000000000000000000000003000000000000000000000000000000000016000000000000000000000760000000001000000000004300000000000001402760000000000055632000000015800000000000000001440000000000027214000000000000000000000000000000000000000000000000000015100000000000001240000000008600000000000000000000000000000000000000000000000000000000000000000000000000000000000000000022700000000000000000000000000000000000006000000007900000000000000000000160000000000000000001040000000080000000000000000000000000000000000000000000000485000000000000000000002860000000000
SP60Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;naeslundii3180000000162000000000005460000042700000010730000000000914000000129000000653020922700000004310000202300000000000003500000000086800000000222000027700000078600000015700000000000000000011701811620039000001820011990000000000970000000144000000006200005190002831380012174000014500016200003900000000000000000008503400000000000000000000000000000000000001101120000810002340000005400000000000470090000297810003510000000218000000002420000000015515901880000000000000691000980314000000109000000000001590000000000000000000000000180000000000000000013402180980021100000158003760003300000076057000000190000009100000000040079000000000000000218000017900000075000000000000000028000001603005521000323000000006300000000288700001610004400000186000009300000000000000000000000182000000000000011300003185400263600000119000000000681200034006450940000053000224023800000000088000000
SP61Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;sp._str._2136FAA0062083008200000001700003501820002500000000000000025300000330760840000000993440003782225740000001360000000000054014900000840067000106000300029376000001500013900000000000133000000000000000136000000000170004800536900000000000060000010705501050000250000000001190456580000039800000000210000000004193335000822423033800155000000000000000360000009000230245000059033300000014550190000000000069000000122085000072000000190000000022000012400119000000000008400001146507000000000000000001260500000030000036383000000014012900000000000015000500051227900000000004606500000051000000609800065000000000000214700001450000000000000000000000000049000006635390001800100120272800413000660000000215040000011130000000000000000000000012548000000007300000048212900151000000000113035213000731080000000000019800350270350000000390000270000006200051000000001230001064100000001200254296007500000017600000248000
SP64Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;constellatus000000061077000000009100000000000000000050116000029000000005366003984000000178000108095088073047000000000000000000000000000000082006900000000000000000000146004386801404900000050000000320018314300000106094001775208002290007255000001023500012409100403000000000000000076000000000900005400000000002000000000640480030708401451040000000000000015950003513000000010000001362902050012700839600850000000640000000000157200000000000000000000004000000000000000000000000000530000074000046001195302300000001970000986900000000044003608505300000043001260000000057000000642603510906000000023051560837400056006700650000000000000000000000000000110000000000000000000000000000000270048000000270117000000062000043246400000004500007600000000054000005300006000000106304200000271000055430000000000010966891905715100610180078000109000420138135012873040000000018200000005500055
SP67Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;pneumosintes13900000003600107000000000001020028000331721620000000000290860390020000000116280000000920000116013200108059048900550010973873600119000000000000000033000050000000000029000003709000370076000831270000000001720010700001120041010000011800237110283063012800001092500125000230016003000197406063000183996500000193900000000092002401061302800000009493010800160000124610000000011089064000033007800000632511912920308031063019712300007200009900841030098220440001206000260001700466400130319211100023000071135057204046013801338004901340008876710850001700105054400027000005058000001712000000000005300005900233800044000130520000000027000000800330006800524000056067003600000008759340076000600008000000000000260320003400800000000000025000070000000340001510000000055000067003600001900108002600000000000000000026000000000000000000023000000000038710057740000000000133021300070001900162700110002250000099136200630000000000210008100000770102
SP7Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Veillonella;parvula073127811643075321316506876713668256556899151895692166111421560361286116562444134639103592908134940409760414186640806133561036633132291741165459784505115931054291031306281102112829382371263931550467153992065312014241254352627158649405471111670420214373865419063548132891078366118501803267229032201010187400128150491910591044303261261704401865337350359883260140211171141362652300193206229888961072196155269569116110352617348734106312081786373720411964417593251910374010102537477535281254407150010348513243048100107750064729210181583917268304361489871952811417582434206329116506442493217197444311481720251611438210844495314981742223734626996011008517073965953777042185554833193561305656455205431650607589178997137123928440820746229123229598144114662083116281532164525138318166102438945821052156122253390535620684274316351130722836557017533674069210371400272592185313249038018506055873863875585218315751759281698509641445360309415165394101190534982662811008771558441841221107913179863032738598361461911935259268560510386378373306850712281585560191453215823491109277200172129751310285706089747510022113759066432901162760167122126938928069142613420103663256581068000066602539010161864314781473140330018646574243553826246373691610134851212317444081106732821314569543122318924283537117338750841424441151293162120504351520760864225029739350247062032642348381133812232664331583357962791781709514963151331134123612330272038011923204863072264104390831232632431356152390042239643212610550018530878233051330640610456503983137811071869725841144028230034670930178336845700157124356819937910079381239027208309881181383613082163365849842348601743374381722422735378047468992000237845371338924014137618783451142293282602323681004586441962931353157131428373443060494282043473119623226166649915665817754051884630269365553716011161135002832154575537116376621071513442523360553471036954303874574232131241758728283144382125695602697214758881549668283040861158603113351011122992301273101024365941286963773013838991045204
SPN110Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;pyogenes_nov_91.53%071153028441811610034622604860007066761232110000015030000930000000000176401000118002210081511000002532620001864189563619509000000006949650000000000012410085132001350066000221544024811400296001050117500951640963036304380074000000700178076073641201823600000006000000045160407251725000370990018100113014281800900119508713900000048004387800031082731420072062000001511180027520003960001200152200091003501111624000011102592001262820158167317607616600053248038012940500690008242900000218000000010512106970479078000011041580000114003231710000762670075950000013357505944500142816030925900106012800171805982184035521004127000000245000220200057075350002580551388000003335102411794100000200006000000000188050017300199126104604200000000000002070092000241794100239000204037000308164900329000000000351000135000002510008100000000066000000068010352502120091000102002890551515960000090030300000000000124000000001390332015210900000000000450002300000001681230000000194620750000460065600009900330002200400076856000108000000000000030020115000039357700582000032591400096687022049507902440211146071026208991279000
SPN123Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Geosporobacter;subterraneus_nov_88.43%198000000004400000000002907700480000009900006406300096000000000260000000000000005900000132004203300002428000000200000000980000017011437096000000000000640058007600000000001190043000000006575015000008406200000008700010775000035770018000000350000004700000018010717000000001391080000000560000980320592200000820003600560000000000000000000000000740005463013513400630800031000000002059710650000140000263600150000780048000111000000140004100000390122013108242049000360000010102120000000000014100000000000032000052026000016000000000000002100001700000000000000000002500000000000008102500190000000000160000000000080000000510002000000000000000000104027000001400000067000530029007700000000009000001900721701800031000000000000340025000000000000000180000000064114000270000000075000000218102007900170000006500007300081000430000116015000300000012800
SPN128Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerocolumna;xylanovorans_nov_86.91%00000000000000000000103000220000000041000000000000000000000187097000720000000000000000000000039000000000000293001150000000175000000000000000003100000000000000000079044011106000500088000000010100000136970000000008314700005700083171140000000000350000129000094000000000000000000000147001500440001800000000000000000440011101040000000000010900098000000000000000000000000000150000000001790107001500011700000000045000102000000097008800001330000000000000000000000000000000000000000000000000000000000000053000000000000000000008000000003008102347000001360000008000000005700004700000049000000226000000000000000000000000000000000000027000002300000000011600000008000000000000042000000010000042080000000000000000013012400000000042000000000004500006297001040000036037720000000000000000000920000000000135000088
SPN146Bacteria;Bacteroidetes;Cytophagia;Cytophagales;[Amoebophilaceae];Candidatus_Amoebophilus;asiaticus_nov_80.21%000000000046000000000000000000000160000012000030158154000000000005500000000170000250161000054600000000049001440000000000000000000000000000004300153044000004900015600000000063000000152098000300194101770000178035570000007000000200013900006500000000000088005716977000001063100650000000108000157000000000006600000007500000000000000420000000132000560038760000000000006700000000000000000012087006600028140008300492500000000000000000000410116000001900008800000220000000000000000000000000003800000001000000000000017000000037002700065049000970000000051550009200005700008300007200000340000000090000000000000000000000000680005600000000000033000164600000680051000000000000000000000000000005400038000000058000900000000000000005800000000000000000002646430990580176050000000000590000000000000000112000001851000000000077
SPN152Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;hwasookii_nov_87.47%00224426030920900019000025800012769000000001420020404190147092612100008311143027701000072250643200000011901130023710354216010200001000223146000000040715335231001740118200210590002782250012943003580765816800000254000000000218002830180800291057408100175013412812960000372811855840000371860105910003730000051151038201252510013011000990142758919746000815937300033105531120225013100001331380035903460001234000000129609918920317007351920558000300380000000383119345011003320021901520650035806380000049885232001724850870002980127126244600970014820320073426216901581741182697401391030644410020102597001250001505930479490132147002850027431241617000147002922546036000603010417600106097278868280129013918009900000213000007400027000907112800000000130106034122271004819006800680222916705108101770108000007144028127900200320468052001400000000850265001000005143901030028812502101450019000134002060780252030922200170004400187085001260007721400023004910610000141015800631089944003911061424380056000056010422700023369298288871010620091000047960150045011600000000005100188000067092000339000062000187001840165140143160650019219207815620039029700255000012106128911710646528416802470002540196000000423011316700
SPN156Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Thermotalea;metallivorans_nov_88.34%117180000000080000000000002110010200006900000056500000102340000000401280001500210470055000002585000000000000048310009700000000000000000000011700000000000000000000067000000000039009000164067000004300110014000660000000006700043000000000000032000000000000235480045000003200000000630000000700000062042290066001200000000000024780002601810000000000335700000000000023310000014400100000040000001170044000006331008500822100455700007000000730000001090002900997900049045000017000001350053087000003106200000000004400003100000000014049000020000002209000023017000000170000115000000000008340024001600000000002700001500057000079000000000003000000000000000071000000300560053000010113000000000042000000017000005000000000003700310154000000000230000300000043000000000000000070033086683800007200050000150004506600000000000000000670000000068
SPN163Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Bacteroides;capillosus_nov_81.31%105600000000001520000000066322951802760000001180000732023600009400000000146000000004200119000000490000000840000000000000000000017100064000000014500000000006900000900000000000028003200000000158000000001700000000000000000000440000950003100000000000000000263078000000009300012000000000000228000000000000000001360000000025008400000000000000009000000006300026000000121000000000000000880000000073000500004400000000000000000000077000000321350000000000000000198000000000054000000000000000004400000000000900000590000280020000000000310000000084016000000000100005007900000000000000068000440000002000000000000007000002000000000000000000000000011500000000000082000047009000095000950000000000000740000000007002210900000007600000000000002900017300058000250000000003100001190000000000000000004600000000
SPN175Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_90.02%0361760023300000000000000000000000371000000000000000000880000000004806000000000092000000017200000004300000000520160000000000000000001231286100000000000000139200000708400000080360720000000000000000000000000016000000000001033100000013022000000000000000000000000000000222439360000000000000000000002800000000000000000000300000000000123000000000000000000000600000220000000000000090000000000000060390000000046000000005000000000000100049130000000000000022000280000000000000001160000000117070000430031000000066000000000000000000000001600000800000000000000390000000000000000000000044000124000270001700000000006100000000000000000000000000000000000000000000000011702000000007001900000029000000000033000000020640500000000000000000000000000000000000006353400000001104202702240000
SPN180Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;hwasookii_nov_88.45%03700000000140000000000000000000000000055304600000155000000000000000610000000000000000000000000016747000000000005800000000000000000000000000000000000000000202000000000000031300000000000000000000000860033300000000000000000000000000890000000000020200000000000000000000000143000000000000000000003320000000000000000750000000000000000000000000000152000000020401350005300210000000000471030000000000275000000000000000000127000000000000001490000000000000000000000140000000000000002200000000000000000226000000680000000000047000000051000000000000000000000000001460000000000000000000000000000000000000000480632780000380000000000049000000000000000000000000083000000000000000000000000000820000000000000090051200834500000190001290000000000000000000000000000000000055
SPN202Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Winogradskyella;eckloniae_nov_83.62%000000008100000000000000000160000000002285000350000000000000111000014900000000001343006000000152013700000085000000000000000000115086660000000000000016000000000000000000003008400198093000000077800006800001290123013500005500012603300420114000972500000951240000730000000000000017000000710000980000000000000000000000002400000000000000000071000009400000000000000000000000000001610250000041000000550129000059000000000000051100000024000010600006500011000190690000000000000000000009100000000000000000720000000000000000000000003170136000000000000000000000530000000630012500000000029000000000000001400000002300000000000000006300000060000005800000420010400000000000000000057000000000109000006000100000000000000630000000000000000000091000001100089008000000101000000000054000000000000170000000000006200
SPN209Bacteria;Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Vagococcus;lutrae_nov_87.66%002873200031326531160017402165800232564000033014404072192694698102670055031003361340003741090449240436000019923630628100911090185451421650110674943162580222000393205137300010829423248400022804616502993200002533130000013465037054274210721386987449022700272000002100072197029165027891000037244337035800097048000030677241037501837200700390000410891583537312419400764132771570292861290010244904026335612612617456256137036781120001263501464021829646014437602910100283001164891182211392815129724171271048100070430161290613810540012727318349018400091147000220159225133051010536615706348080000170149068100001452610651355721100431201020025811301041112627494140303280701870104015800029230227514431306008328003941441628810301430411200001780320400148002220128480074068135061146252960440030122917614315025802676010404001040070031401601600054370115952607712400002150015600166228138019621615901040036157820708056100020820200011032002210100004600985511841021301380125119107000004801115002460079541940021505019601470013263027260326712300001803085540005118847017122388124154850082104812340311039840029200000310017693000079009212286195116105380013554025224745128830092608000007079015032500169230651250039017300740340007001294715515525417915542989865853001651460020908168774700610407289661230242179000044032287175018949703899620492020139165196000001780
SPN210Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;riegelii_nov_90.36%0000000000037000000000000005400880014000000000000000000000000000057000000003100000000000000000004100480060005200224009500000000000000000000000000000000000000000000008200000008100000000000000000000000008900000000000000000000000000000000000001700000000000012343000000027900000000000001400000000000000000006402500530000000000000912000000000000000004240900000000260000001300144400000000000000000142000000000000000000000001600740133000000000005400000000000000000000000000000000000000000000000000000004600000000000000000000000000000001730000000000000004000005300000000000000000000000000000140000000530038000000000000000000000000000000000414621000180000000000000000000000000000000000001380000002239000001340000006400000000001090000000000000000000000000000033
SPN212Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;periodonticum_nov_86.34%0000000000960044000000000025181500006707300000063000000000000000740047270000000109000140000000000000006800013200000180000000009000000000000000000072000012700189000000000087000219622130050000000001500000000090000000000000062001380000014641000000000001613000000183500004700000000000000008705500000000008000000005900000000000090000134170000000007106705600000001080053600000089001030060000008900630034021100000000000000090002501020000152500000006505603800000008300000000000000015830003100019053000000000000000007000160000000000005600000000049008000000250001750030000000000130730190000000000091000000000003700000240177000000037000005200000000000000003480000000000013400000000000000009100009301500000000000000383604200614400000000000000003500000104000310000000180410000158014000000002000000000000085000000
SPN213Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Arenibacter;algicola_nov_84.04%000000000000000000000000420000000000001240037000000001280000104000000000000009600000000000000000031000480000000000000000000059590000146000003904640000001400000010400001280630000000000000005700000000000000000000048008193340000170000000006000000000630004900000000004700004600000000000000000000000390000000000000005700038000000000710000001040000000000161007567083000000000900000000000000390008657380000000330000370940102045000360000022021300000000000000001200000000000260000000000000000000000000000000000056000000004600000068000000001000000380620000000000000390000000000140000000000000000380860006900000059000000000015200000000010900000430000000000000021000000000750000000000000047000730000000003300000000000860000000000006001180000001940000000000890017859058970000065000000005700278000140
SPN215Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;sp. HMT248 nov_86.74%00000000000000000000125000007917501000000014700000000000830000020000900170000000054000000380000001851457701700080000490030000004100027001190000000000000000000000000000000000000000026700000000001500000000000015000012100000002270000003800000011900000300000220000000000000000000006500000170004200000018800000003000000000000020500000000000000000000000000000000000010800000000740000010000012200000000000000011001190000016000980000063000000081080000000000000000000000001100000000000000012000000000000000013000000000000090000000132000000086100000016000000016070000000002503500000052000000000000000000000000000130000007800040000006000031065210000001030000160009000019635039000056900000026800300005700000000000920000000000000000000570000022004300000700000003800000090000000000004000000000000
SPN216Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;indistinctus_nov_85.15%00000000000000000000000000000000650000031300000000000000000000000000000035300007000000000003500000000000840000000000000125000000000000000000082000000000000000001800000001030000000450000001310000000000000820000037413700000000000000000141000013400000000000103000000000294000980000640000000000000000000000000000000000000000002400004500000000000000000000010900000119000000015000000000033000000000009200000000077000017941000001200000004900000000000000000000390000000000051000000000000000000000000000000000000000000000000810000000000000500000008900000112000000380000000000000000000000000000000000165000018703201040000000000000480000000000019400095000000202002774000000000000000000000700000000062000000000000000000400000164000000000000049000000000000000000000003800000
SPN217Bacteria;Firmicutes;Bacilli;Bacillales;Alicyclobacillaceae;Alicyclobacillus;acidiphilus_nov_83.26%000000000006706300000000075000000690900000000000037000011600000710110000460000098000101000138000123211070000032000000000000000006601700001060000000000000000000000880710000000000000000000021000000000010000804200060360000290005410100000006000000000046007500274400152004815902300000110000042125000000000610000770350610000000000960000000000000000013000000000860960420000000135000000121000003090000000000000328200000005000000360000000010373000000001210025000000000000000000004500006400000320000900000000000000200000000000000130000006000000028000800018008170000059000000000000520000004500000000000000027000000001300000063000000000000000000000000590007300150000000000530000000000000000000000017400000000000000490000000000003200000000000000082000000079020033000083002800000000000000000960073000009100
SPN218Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Bowdeniella;nasicola_nov_86.78%0000005172385183484303005988706725517025000000337006400004600000000000103047001571530008000022000002060050083000393089009494175007415110975645403023000022701185048714200252000077091317306000046362512000004174000000388000082023200000954730009500019000547900015500000828327705650000083990740007849001530012458580023934106000970000185001071470208099250017201000714955870107009001200092712448827000000117152000365611450104415620116003500409020709502600595807701400000053325201611530001290001800017000359000000096064121000002200000423806293561140000278289001391605010400971000670007900490000032803818996647816109818500020822023818704100710423915391026141080161791420420001231000004036326407801051002790600000000061000240913000191610265120159015301240305900560007600530014307200000005297522322932580086010000276156007600750041172005306736341600000007459833701280010800173000190024000118115009885001946957033131000014801060940630752000001215467215120045390002001138701480093001292932221170047092116411048702200197007171092190012406701400165500020000037900365000115000000003601900049014800000047272418003112008000321503760
SPN219Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Thermotalea;metallivorans_nov_87.32%0990000000907715201800000000890000000000000012200000000000117002440770000000000000000000000000117000000272500119000000000252000158000000000000000000000000000000045000000000000000000000000001240000050000009300000000000000000010900000000000150000105051000000000000000106000000570063000630065000000700000003300032267200000000000000000000000276467804500670000085000000031000000432600001000030000690062000100000000003207600000011300000008900000025000000000001820000000000690006100001130000000000048000000000000000000000000000000044000000000003100000000000055000000051000000000000000000000000000000000000074000000000000000023074000004200000000000000000034000000000000000000000003405700000000011901500370000000009700000000070115000000036002508300230000104007104000000000000000000133000000115027
SPN22Bacteria;Actinobacteria;Actinomycetia;Propionibacteriales;Propionibacteriaceae;Tessaracoccus;lapidicaptus_nov_87.1%000000430002580000000000087000000000480001970087000000000000000033238120000000000008500001402500007700900001010002490120001260000038400050017000010900000018900000000016000000000000116000000960720080283190022000000097000000000000000008600013100107000000000110790000178000001060008720200571650001300000001280000068019400000000000000013000163001000000000005800008100000000370000058000000000000000000000000300080001071105500000000005313717068000000000000610106670000013000000790001730000000500096000000000000000000000000000000000000000000000000006210111000000000077008300480000017206700007400000007600668028000007300000022200000074000000000072000000000000000000083015603800000001100000000000000080000110910079000000700000000010700000000000003888000000001270000000000000000007800167000000060000000001880108000000000000000000000000004900
SPN220Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Sneathia;sanguinegens_nov_85.23%105320199000005903400000000000000000000000000097000660000011300000005200000000000000400000000000000072000250000000000000511000000000000000000180000000000650220000000000000002300220000031002370000019000000000187101000000035464700037000440003100000000900000039000860004100052000000000000000442000000009739000000000000000000000000000001080000008996000000000000000000000000000089000000170000005800009800000000000000000000000009100000000000000001360403902400000000000000000000000000000004300000000760000000000001500000025000000220005981000000000000000000000000630000000093000024000000000000000000212100000000000000001900000900000000000960007900000000000000000000000000000000000000000000281900000003200000000000080011100605400013101600000005800001210006500000000000152023000000000
SPN221Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Promicromonosporaceae;Isoptericola;cucumis_nov_88.91%000000000005600560136000018508700000084139064000067000000000000000000000000000001409400000000020100000000008200001310000000000031000000127000000000000360000000000000000000000705300000008100000560000039000000000000004500000000000129000000000002200005000000000000000000000000420000000000008100000000000771770000000005500068000000000000009700179000000002340000000390178000000000000000000000000000000001200000470000000000001260000130000008200000000000000000000066000000650000000000000000000000044000000000000000000000000004300068000000001971000000115000000000000000000110000040009509000050000000000000000990580000000000000001000000000008800005700035000000000000083000120000000000000000000700001700000000000000000000054000000000000000000000008906100000115000000000002880000
SPN222Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;acetobutylicum_nov_85.54%000000000009000024500000000000000001900002700645000000518300000000122900000003000000000000000000145078000000000000000000000000755000000000069000000000045000000000000000000000000000061108000036350000000013200000000000000000000000000050000003997000000000000000000000000000923500000018700000046500000000000000000000000000000000000380000022900000000000000012600000000153600000008610000000026000000103000000000000000008409945001200000000000040000000032000000000000000000000000000000000000003800000000011800760000002429000000000000000000000227506200000000000000000000005000000000000000016000000000006200000510000097000660000000000097000000000000054000000000000000000000004900000000015400000000000000000000000000226003000005400000000001838900000000000001000000000000
SPN223Bacteria;Actinobacteria;Actinomycetia;Streptosporangiales;Streptosporangiaceae;Nonomuraea;lactucae_nov_85.43%00000000000000000000000000000000200000000000000000000000000360370000000099000000000000000690000000000003860000000000000279000000000000002101120000000000000000000000047003300000000074000000179000000003003900000000000000000000000000008500000000000000000000000000000000000000044000000000000000000760000007000000000000000000000000000000000000015800000000000000000000167000000000000000000000000000068000000000000000000000000000000000000000000000001500000000000000000000000108000000000000000000000157000000740000000000000017000000000008360000010519900000000000000053000000000000000000133000000165000070000000000000720000000007600000000000000000000000000000000000000015700000000000000390000067000000000000000000024500000000052000000018000000081000000
SPN224Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Promicromonosporaceae;Xylanibacterium;ulmi_nov_87.14%005290000000000000000000000000000001660000000000197000000000000000000000000155000000000000000000000000000000001200000000000000000000000000000000000000000000000001740000000156000000000000000000000000000000000000000000000000001230000000000000000000000000000000006500208001900000000000000000000000000120000000000000000590017000000001130000000000001070000000000000000000000000107000000000000000000000000000000000000000000228000266000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000084000000000000000000000000000000000000002040000007801220000000000000000000000199000000000000000000000003400000000000000125000000000000000000000060000000000000001070000007805152240000000000006170000000000000000
SPN226Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_90.82%0432231271216284280419029319101888934025907980161090024273000149002000005200157942753693620923510009200392004800490031305314344278740000755280000154470000005669703720000070093003880009200353615200000128002160002600003890001525700003100193910000017990014003703100601701780065104680497001300220001190283832120240026752300761510000020614016010401391609000159326140510005469003750625444068009300431010014016407150003411900000193695960112129102024314100141024300371090445190000000677050158000000401200230007205517455029080073198682570365153510701012732600048004201122329037610463306511300323370146190390206026624500650272179156000000026007129742011400000041900000002202668119520005300213331300000000696100000001500092702310000224363803600040070000680000730000170014459000894287734701530008400023000708004035320004095340000142001503300320000914300250076139314790001640001280090012965400011670000180005307536050085007401290112111220110002370000191013001230005620504000000001200000630129244000256020202374000000000691062500109404770001870082840000142059002469930031310213813000324234000479056001120440000378420045901160000070
SPN227Bacteria;Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus;sulfureus_nov_88.64%0016700138000000177000083000006500000000000000000083000000001380000000590000000002200000000000196074068000000000250072000024178001570000000000000089000000000007600020001100000002900000000000003700000001780000000000000000000000000000000000026000000000270000000000000000000020000593500000262400000001850000000000000000000009700260000009500000000000430650000010600000000000000660000000880004500000000000000004100000890000000000000000002200000000002000000351100000000730000000000000000600000000150180000000000180120000000000000470000000000000000450000000000000000220016000000000000068000040000040047065000250009600000000000000000000000000064000000000024000000000230000000000000000000000000000050000000000332027000000000000000000000008704500000000560036006812000000000000000000
SPN228Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Weeksellaceae;Chryseobacterium;taeanense_nov_85.32%0000000000810000000021000000176005300000004115036000000000000000001480000000000000000000000001622337059000000000051000000000012088000000000000000000000530003000004000000122000000000311780002600095000004264000280000004900000000507862002700000000024001060700440000480069000100000280000690032003300580000000000450000000000050000001112500005900190000000190000009400000000000000330000000480000000077009000000380003100000000000002006800000313235000032460000900000000000000000000000000000000000000110000018000000000000000000000000000000670000000000000000062089000570000000000057000000490000000000000000000001200000000000000003895070084000450008285000000034000000058004345001000004800017000101000000000000000018006900000003700000000000000002639009700000000250000000000000000000004800000000000000
SPN229Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Arenibacter;algicola_nov_85.44%000000000000041000000000069007401420730000005947000000000000007500000014700000000000000000102027100000066026000000000005300004300000000000047000000000000000000000000006478000000000000000043000001090000000003433133000000055009700000000000350012200000190000000610000000000000000000000000000000000000000000000000000104000059002800001500000068000000450000000713033056000000088530003405441000012000000000510000000000000139600000160000000000000000004900000000000000000000000000050003000000000000000240000000000006800000006701680000000000000580002601040002800047000000000000000780130010100000000000000000000000508400000064000000000076000000000000000044000731200000000008000000000018200000000000000000180000001447900000000146000000000000056000002700000000003100000000000000000000000000
SPN235Bacteria;Bacteroidetes;Bacteroidetes_[C];Bacteroidetes_[O];Bacteroidetes_[F];Bacteroidetes_[G];sp._Oral_Taxon_B68_nov_82.03%66002410265007132701470104005201313301471172585490204000210236440145027602011821590021625527607227617418205181460920126506212994000126282560013723410685331032395828570015366000513593797018823000224001161190001061600049312119127346414114098061850500021309942301020080713903110570308148002810112928425514700096286970750363900191001751710046190014914610513701249901382392398000011757280114119035011315911120935846200017100047011406395783050018917490931590015212200143051002722171138487253000199321546800101001455101261270173025131018502141461682301200164001180016800003941632672422423376246880142170138001918417000500080197020693936435018136217312901281424590878483071570483468278100830063490067106173019001381600251012402054547610169012512058067011607834500044907302124200234011402860220125069105521750100071942570139002381203070012011706110553004500661120134555900225690234597800007985000075006600266177022101066932010756191357168039017223140000000861421780421030027420113001200561320980381570740117023591117083770866490440122048387226053224001252769001170069870073011285478002700002210961593012015700823720700647800111022219048263500082419210516146047298030072001120910051013600000216219022531006438307800131084123161009473005600647200000650026325402181492542251040131415322002220034243680141374010638000548018726253399
SPN242Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;curvus_nov_91.68%73020315800232760910963047791082231201120130343116308014000266073192118001770143116010182110013193542022912430172266500125077079047683293152025824300810191717002327322925550241913457467018401101480670840002771550146068179651081133502232020000840166176120190901670024721210800113157221980122018201619036007202250470452801781463312211713509500086292281770109150263936230746123023390237233821719692111173011473013908328301971762402713193801398421203841200192262150071103188504979791674396207063683007602255018523271612679517729001200184390411065452249630107221231126183113556241062001481251170272237028181731621381558314491158012102531749710121512000830342081770131583321882363152882639635017058246010016313086151200340124875214748292234170220011819846135044005901067179006905366183117195115851701469911613376630165160114108661129296144861269488831304900602496046002911145700710620902214246097983690767476008143550146430707758370518882820779689006171611256137913706218309020006917651718269851600724317958187230008010913402276161440060027001900108139134531232808701094968810375824112410153581780101444011114114880077200014414974000879221615548536420711607275014832700863791164212376083017323002031467700629350105142560850719919210722899411455169580650440002159041155331151000007051067467098991290084078781807162960112190801820017013712916765319612661297232372370831811361037906404250186018701550002494211592621131300138
SPN246Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Coprococcus;eutactus_nov_89.48%08350000000000011800062159005934069260330000000950000008004600000007200001867107000002300001400004601341210001090000640340000000721020420075410070059109110800123003122247000071005710848133000000000071003802656200000000109000004300001305000006600000000000058000109000105000629604300027053731032504705800276700002300092000000162037006801400000000880000028000000000005700572220616000001320000000004100071000000000620985921679001250710000470007700011000600210000140000003352000000860000850000990000000000000000310370381500000000000002422000005700000000000000005033005206600000042000000036000400049000000000000035000003300039000036000000000000692600000000000002200001300570000000000000000000071000390001090023000000670000000000011000000000000000110000900000750000032004304000000000001347500730018000000000000350500000052000000056000000000510058149450001110012459036
SPN249Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_90.65%001220025093760262983010335700038830134000382024058481908127708396104056150000860000153321201050072521300201300010800011043517074668170013010507290116338316739516012004307747201241524046019016776280699242720810010362000834972072008980161126600072000905201070150001180060400064020504704902776913166013800036115281000000890032223168001751233912745615436400346136012416609151112000820116053259000086500201572502100510000527212030015212116138514421334537005203333238017065914805113100002302700131716204224742360081177150021802315008557160310000662100006400001170037762275076097000370300093007966136000079000000004802083501165017620021372405960448024610847540244014601214102514193034301637002669000000004223310016302531924000950410031003322530850000104600565350270016703720002509258276851704203347000001380035254280242501424035062310830012700792601901090103036018193396190197401700190684019077300000000046000229004740500002747605207084250178300170068004103110714200024376150068028270735336109700410965001130000559601155200130001469108301761532080038000700000165307247559061000000642810151181740480626901010122356634031017897138929616213943023900000007236035000
SPN254Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;pyogenes_nov_89.52%02348430000820013800720000003231310053100419003503400000621700000007600013550001789002421665700000154700002350048000016400152029502670127023951446068000252278500003700698008460454140085000000010100000440000005700000001914400210005400012300003100053200000368065000000129006963630003227405414915487010042303017250034137938000015900109398000585330001013000000017001429000732070489000000000002703350300016200002402230000038000002660023000022000003392120012100001730392435500383040863430008301210000000872340005252000076310000136001510301020096001211213060140003710326601440160245085900034086150000004700000000011022632800037546300000220000048056000002969002290002202152000001170190900401430000020001250027800000054808410000000700000106000000821891781070689036400020690000002941000000000605671600014000593000019300233944233001128000019703926300240000107140032152741070006403660000012322400042000036039000003427320001910000000271420003316397000406041004201621070001300183500120018226200002340254461968202400000089269000000052612150127016
SPN261Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;terpenotabidum_nov_92.31%0039086025414154002365809001890000000002526720501771100011200860157003300169408800088202321910440008603321181510000001620512008300804501470114500000121440007305180205134396032001290002000111002101960003105600000000000001070000000000174220210800000000970440000000002115200000677100091114000303000244060000000000413200450025000000002572100357000012235900022600196115000000463210000000000000335309700000144072000001830004005400094000000001535840000000000000813103400792270000000000064000001438485025200000057260030598000001490260013813507400110000000014020805004160001970164000000054005300000420000000000090008983000018000000200000210000000000000484010801540013400000017000649000145740000398000022201600520013706400006127144380000015117300033210290000000130300000000002020000006100160000776557345059015051102800152035000664400114300000807410060108049037011824008000016056010786750000023049415300000000137000000131848242000000016069166410870003800017440000530004530000005100000049000000135
SPN273Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Geosporobacter;subterraneus_nov_88.04%19301000561201300030401630083095908932422001060000299430000009627600011654220048304819000012400165074300117012900010314700571980024747860212013501120515500352253184902200127000286091018763111260116330289000146000000217704200029500000254081003711210509000085237151159002480391000025600065740022521818700278244358111597714713600617600018117700007153471225400091270001230207589115543000674105157213283011439410051697409676123226001120090131780740175270803237027415619401890067012537313151310224013602044011114565015407800030703601762670270045701101360106175090004093733301300003400243365816228608001720109035000491882310056681700155000012215563108422000109002310003910235152191237160035116022032022301600001070331044014901142580786308004110028049620076971780010600430488898001600015903800000824815900917290331444868053416000703243780146193002366662275800116038020023302648100220001711106008200000056000000000444002400379368000059000000035682000490000072011505595000836007857006064006400571215300058030007697007700000830196300840413005100104180000899101380220370013274000143000016016915746340115534021312233200720000630510139165179314578495328710293000171220063006523201521411500193000117
SPN293Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;pyogenes_nov_89.52%03684957615496327501162886509253769459133120114888664001731704318919220308244012535851490703540546002838139410635309223169125310613202257505967506792161910290146956599199152109533022028955628276968454421388108242411615070616129242344740912100305113179192613319909474232401820001780002775114407350679415024949470189826067120020826322549037770004702279230304791274167510410501842546906673422248823404400810119405623949070783151758400396223914810021722984180178167666120846191762360544236820319752721131307651579024912803326214521654369770201251527106168125119127227843889732001062713554961725190030894929314476512231331182023800143135611480583011926978582338224446412164441134334260296065873888027702973856920018051514821270165611214858703967374030704328014076167781520458455584568996033836920025323350240298206026319211134316801343491273303969277021026014180211694551638600761024129175077191894296709271741813030328543717103931471101629219282460002479381022051461351581854209148034908789728514450047021512980862171274100775196358216070151105211740324119052162671513490043732867011019026091252457516581424215226432896124523045111620133173212003771448040394962757172429784424876215581262981145502629926747925812473871791349217670156104040612610138502051024651650008091952128002893101760186965937110312518305830187332433204170656215413370043410730187142281049184738691399180761226760118002930569332186212020016389250064274042216042773410189684292757598863771890547119493259711998925232326660057434453390074776351180152810451000058257108402691942077215938002888621020650079800233093142552653881222135237710100416159298470491016436602003823951790205000188905386814944930851888056274113931036074840158809637829217021489580431773165580151
SPN31Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Bowdeniella;nasicola_nov_81.4%2350012500000172000000000000000320000081000001950000021100000263000000000011200000000012200004900000000046160000000000000000000630000000000000000000000000033300000000000000000000450000000223001040000000001010007000175000000010700000149000000820000105000175000076019100017900000000000005000000000460000811673000000000000003100009100830046000006900517418009900008501010000000010500000000000010523600000000000112041000000000000000002650001610670000000076800051000000000000009500000000000000000000000000000000000000000000000000000000000000004300000000000069000000000000000000000000000000002032000098000000000000000000068000000000000025000000002910000000000000016800000000000007800000000000000000000230000000000000000000000000000000000006700000013503900000008400000000600000000015900000000000000
SPN320Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;diolis_nov_84.18%00413204000200019800177000074026852000000045010469000000072000161182730276005224501040142236001190000541210019518654078056001660253089040704701901050143440182160015900010300183910054580154026707100001242360001065200002370013700018607701070000004601710171504905511400260000009020019100101000129875601567515117401857317002410920212293448000000108103115200057690001160003352300224164004400622520126490381360233105591723400850470600002507110109400002270810129001000258000001941401400042860151215083360870004302194393011201464674100206167012201432090077000281591004000027924091001767600143005795819965000590149830105100081004103300008230204300000150193102230530022000000000044000000075001690764300000000000079005003700006100000110061493662000910009200106176000780450001020001274407400000012900006805203800001510173280040280000913700880770000710000007403400011131230007371340001850299000007000010700014106356890000250025169002280002755911952000000811510048003300021146011700874200000000000680330000033410300541219300440020714302415400381300112129331040530816630400000061043708520700
SPN328Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Kocuria;indica_nov_89.33%0023300017900000002260147122298000019725013100731010321300004600000440004640000184064001690900001180114000000000026802322240229071002700000077051024100022800115129930013700385023919300165000000066000019800180001170490000125009400105422800005610700000000000076000027200005000000000000000000001080000120011500106000006309417685830179000000500004700001060159013418711488000001000043000082045000000000304100012601680000000830019300000003100008004600000000183404000010201040000000105000000000021300000000684000183000000012520000018701620012300590029838068000871330002540165800000940157034000120140025000000000010900044000000710011910959500550001330000000002690004906800000000000000000124059000007200000001104900066500050000000000000000000570000000351130000000000000000011500000000000571000062860465200012401200003574000000770000106000000255000410005200003400031000010060002891449500000084000058052076000002321360027200000000157000000133000000000000231324
SPN349Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_91.68%007702170012821445473431380161327000045388223082125903274005691803612220763810000711630000146091101901800520161012796265282605299196185900019844226326670510137645211937700963782217077535181051529731011342601433056672713933852445950018961650860884707009438320763590093210965260309000315439019818616700138000001320006022954629220719374024101766700307560162667127729105664907772218630014007650431481306003100178847996868932064009074890536001369370387143412021372190289251062116472190010531511002743195610025426011494667901160103612758290083000021212359000248036913505823991496402170420343936019320800150000004000023018817322934195000000008319800018201440001537034093182004172206000345490000138028273689000003334862816792100001310001095397624339744721150001376000136003105843302111802693088130135230011230685661046119195103167445224363016590000084224642311206252240417342732914500001036711527616613200202813637800000049295020357169038524423700046245132442440114415716130200078712202773272218980600254102802361170001030127698208061382205404798178052569136111553098316010467601913490483749569247189001151522542770012803900080000256045449317239218109796671943004939701160023441261360036129641242125000020252000001337831230013456258613283107000021030314641378775270153355032953800010334539238727302390516387800054816533365163762700000097474822027140580837700018433100174009900113248616035663310105077659610501951396935903091731786255424781640003501112001566893100017479
SPN356Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Natronincola;ferrireducens_nov_85.53%7670012801070001430820019316233704714400471450121001450001551380160011400003702649217634900001150009600138091021302270168000002223901391510182000011171970210910000015600028300661651330562151701160213830177000045000130190001682940106000028178094000127101001001780940410042004800000000550005704753116001510307019737880222690110000080126680000102246000000021716700000000267940000060347600010399837410873830004900010607600360573920083000001540000068000086012643006192001530111550041117110128032709200003558001590730134100108008258066260390003277002937006101620109006880165011500001031028700870249806801260105050092000810010500001210920108440000008855038037314000105009200000068035707600000917785000154000025200551020740660086000101460470550001882012101635002706100958800012800013100083000000060190000176000000023000000002368181077015115300000113000001090003062011106800000000153008000636405000500088079000000002000998103574077005407600001680000084000000009405647072170000056029000970057045000002550065001400000321120010201480006100000040002040000000185
SPN362Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_90.59%000122000628100077000033101441396500740000515000011310432900032219400057000000000001490000000890000551240004600014800058109013500000870005600370000127007984000000000000000000000136011400000010009087662000012000130000390742051201354800041000044000014827000930870022187007574000000054000016212000000015500437036000045175902917039839602940295600000295000086800000000830053009900001280000512019600000018000000199000170236600083590370008300000820000065209500023800000001370000205330490018000015800850280690042520000000045010630000201000028025800001800024300000178000362000007702000000007300116000431115012900160180001304000005440000610003201840000000006600188000109072001700002462012302306606500830000001400006630000610155000490000000027000001635200004200000145000000000000000205005820084013000000112601500000152300006100000019000000148008800017001390001200000001363402052310110000000000000000002556300000001254315400000009700000158000000000
SPN37Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_90.67%0127007452627800346006890590137912800000330202002310000000000000222000117000002370070404595000950159101313883100000740000000000180550301026000046940000000001321030009100860078203852780002178000004200025212629401936624890560000000022800000000047867800005900980062007100123142000720960000137000680001459415800079267118200003481079001491150000010900077028098024165670224700001000000169028401000037017624019804288700000003710330000000007700007699680030105098000056313862026600000489260006413300695628000016929000006800660206322045000053001610162000012400000006800000000223050800000412420000014201590951420156000000980000122009801360854200012015999900082010200000645600510000000003100000551150000551037240003900056000003650000000001020008205500210000008300030101204281003045001678500800698900260000371150400000000008900000131000015242600005800001280008900000205234700007600004800108106000000001080105015270099404322580000015900960000834840000002200009500000000005409881083280017100639683024444327901680065036190000010040000
SPN38Bacteria;Actinobacteria;Actinomycetia;Streptosporangiales;Thermomonosporaceae;Thermomonospora;curvata_nov_84.68%1450000000000000000000138000003890000000000000011200141000000000088032900265000000000015598000023800000002390000018100000000000000003210000000000001930000000000000000000002310000000000014200000000000000000000000000000000028000010702100000000001010004710000000000000000000000000000000000000000003070000000000204000000000000225000000002470016200000000000005500000000000000117000002060117009945300000256000282000000000000000790000000000000000000001200000000000000000001380520000000000000000059000000000000000000000000070000000000000000000000000000690000000000046000280000630000000800000000000000000000000000000000000960000000000000950000000000097000091000000640006300024000000000000000000015900000000000010700870000000000000000000000000000027900000000000000000000000000028000000
SPN389Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Promicromonosporaceae;Isoptericola;jiangsuensis_nov_88.29%0603780003081142000001545000000000043031405170000760131000020052000000000780000162575000000000581770188590012200001823012901430015605300024400000003000014507220001010049100000000000001443770013029508600000001030000000090000001840000004106102530002020420254903900000005300000023400000360040154000000000006100160052000000009500236710000000000281190000968700360132192000003100002100209000001840000000101259028660000000013000800002290640050048000000877126000080053495100000019186000051000000000002416000730000000000387047000007806077000860748430593019031700000003879000000000028744114000049000142000303005201480339094521004900000001280000000000420000000000001070012100337000000162033000001390002100000700000000000068028050004300080280000141132000000490096001899000000000200000101000000000000000020300002049246002859151680000695474000007500040000960480444302640062006700151900168000000006421700020020300017000370000516000064002200
SPN397Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Arenibacter;algicola_nov_84.87%0012200000143000010600006306400012102141260209001260002140328300000011100000640019703000456957716000009814000000000069356522459398019101060400014900095000008200002401580811760000049042000000000011600770006900000080893230155000012900126000000019490018100741091780000740046111160008407001863807114100671040000196471614100817500004200010367000222000460010500000000000152003419000000014400000001220000014000045016214405100223000000009706300410006100001030000040096113442975000001897200005600143092047870000000016100079007810900001490024701213500200050002040017425900000031000000000661000000033000000000440000730440000007000000740330000029015424000000000010561010300000001414400002901300587822609300000000066000600000006300128000000000000000003500092024015127801020000017002750001490950135078013720900000048420000000126260148129007600071101990960640692000790000087013200000546052047000000445700120900001985100001480001010043073000004883000770013600000000000043001250000003700010200
SPN4Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Cellulosilyticum;lentocellum_nov_84.21%00000000000000000000000400220000000211045029300000102520000000000000006300079107000000690067002800000012700640000021400000000000640207770142099001820000000000000004700000000001140000000000000000063005802140000000000000000000008714800170000000000007103003200000010700001330000000000000000074000000000060730007700000038004500000000470000000071205000000000000006828000265972160119000010200006400008200092830056009300000000150000000068042000213006704700000002220940000000640005300000000000000000000000000000720000000043000005701270000000000000000000000000000001100000015300000000000000000000000000000000160042008778000000000001950000000000000000000000004800000004700000000850072003600020056000000000000000000340000000000000000000137000000000000035000260007301601220000000009222001260001600000740000355000001740000030820
SPN405Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Geosporobacter;subterraneus_nov_84.49%00391307016567000000035000701080116370088002050261180000030500139006906227201470033715000000150000000000490000000296000000170005500008909500014265000192122197000006100000000217176000191007100342000000008601085500001690016500001040142012196087009500000777701301860890114060001586500000000017000781410000002400105000187000980214102005215996700001620000155026148109000001020015500000624026000910000938400690002500000178001390000011802120010194148000000001272767017308914110600122000064147300017000080107000009800000008800875559130000958901850200000122054401820000000580680003180370000000000500128500000000000780057045011000000746002040139001545212701540000570860019001070327530000560023600003601600012420012000001130027000073001320010400000004303800012300544000249000010100000170290009900000000094000900000320690000000173078000049001124660062001500000111001350000770000009200010500000000509423387008600001120585504900098008293000000113000000139610161000000001320670000881046000370
SPN42Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Dermatophilaceae;Tonsilliphilus;suis_nov_84.02%000000000001540000000000000272000000000000000005270000000003040000000000000038300000000000000000000008800000000000000000000000000000000180000000000002650000000112000000000000000000000000000000941870162000000094000000000000026200000000027843000000000000000000000064000540000000000000000048000000000000009500000770000000001780010600000000000000000720000000000015000000000041000000000000000006100000000130000003190000000000000000000059000000000000000000000083000000000000000000000000000000000000000000000000000017103500000000001297000000014600000000000000015700000000000000000000001120000000000000000000000000000940000000000155000000028773000000001410000008708800000000000000000000000000000000000000175000077000000000000000004290000585000000000000002480000000005460345
SPN420Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;rifensis_nov_90.43%00160000000000000000130001300000000000000000000000016800025900013300000008200407003600823000002690489100000066011940680002210000000000010100000000000000000180000000000000000000000087000000000000220008300030000000516000000000000000000000840011400000128000000000120000000000000000004400000000000000000620000430631660000540000000000000000000000290000000000010900000000000690000011200000000000321000000000000070873000000002220000280000000000042010811400010700260000000030000000049350000000347600000000000000000000000670000000000000290025000062027000760002400175000002630000000860000620012300000000007210000005200146005410000000000000000035000005200002600000000000016320960000034000011601290000000004700010700000000005170000000162000013400000000000000000649000001470000000020000012800000046000000005200012600051000059000000
SPN443Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;pyogenes_nov_85.12%03540000081024000000001377815500013419000021422200015602150850732800027200900000050000104000062083000003284201970004300000024100000000001610011239401477500000000004103107994127000040000203246400012500012400108000000000114067000130000950770000000000001630000001200000014700008116900884500001560009213700119000090000079019500174002041082601121431460009077000001851180000006152170014500012012403260000291660000012061000000001840081000000060860001770000000007994117000003100000008210600000089000044123000000002580000070430000018200000043000000365760139121643901091000000000001000000000068185890000002600071129004779032000000035602370000000000000000000004890000272709220079000000000000000311001500540710220002700001750001540800283230027000784600280000500590000720000000400000543800000620960000176411511101100000001560010084000330700078240270000000028001400077008600780600000000012008400000001960180013300000013016390001770178400190002360004220000
SPN449Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Dermabacteraceae;Devriesea;agamarum_nov_86.9%0000000000022700000000000000000002190027700000000000000015220042000000000126700000000000000620134000000020100000000000000000027024000002270010600388000000332000000000000000033000020844300000000000109013500000056000000360000000000002260460000000470000000000000000001120000000000002900000000000000000000000002500003170007200000000000069000000000000006600000000730000000013500162000000000000017762500000000000000000000001900023099000000001350210000000000000000000000000000000050000000000000000000000440000005000000000000000000000000001574006107600000000078000000024462000418000000000000548000000029001884001511000000000000000439029589460000000059593200000000042011300000000239000000310000000000177000000000870000000000940022500027000000000000310016600000000009900000000000719000002600000810025330000003100000000
SPN454Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;acetobutylicum_nov_85.27%0000000000033061000000000010826307402200000037001370007000043000000320000021000000169000292901830000020300480000271000000760008400096000025590000000074000000001391640000109000000000013505927410007407800360001821400000375100000680000070528500050060000000000004700000430023006100098121480000006800000000000000000057002726000000400000000000000000221650068006400004800000034004600000000000000650000000000500000000007000000001620000000628000240000000000000001800420241000000371090000045000000000042000001540000000003700000000004385000940006600000000000000370017300000002214670000000020000000004400011500230000500670000000000000380002070500002900000087133460000000000000047000180108000000000000000023000000620000000056606900034000000000000002200100950000000000000005700225400000000580000001660000000000006900000190000120000005560000
SPN458Bacteria;Firmicutes;Bacilli;Bacillales;Bacillaceae;Oceanobacillus;senegalensis_nov_85.28%006900008211200001900580621130000820192210150810940000662292800000014600000000870146202000001210000106222054000000018009707515100089000000006918901000000001662961970015400000000000210000000000000000000001012200029181087093630000010300270179120016780011108071000731320140100013696183119170115000000000047171620001240000180026000001370100000000000189056936203330058194500000011039006200010615800085747600009895188011500159420990438300000035201704017571023710011600093110121123000430490148011600069003471481600092036000000114005100710001091304714615213719303000001350080000018900043032013300000000580000000750029000400000000000000730360000000004100000510021300003413140000014289440000011300360001540124022024042037062000148001700000002010000950000000000000048000000000630000521578068560580930000047043041000000000050004811233001200002008002900004201820000000880700000024740190000000002900290080000085440008904332000000010305304114902732200002714400001870001200013200000296001770148
SPN471Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Anaerovibrio;lipolyticus_nov_84.95%433006800016305006700610000031020649800000000401001800014312400017301807604700044001340000002080900009104887131001640531940032007000013800000000352008736400086001060000127090000000026000000036400017900000211296590000000000000000157009400000006401850000028100006600851360005902730000000530003200178631000010303000141730005700000000052066074000001970007500012342200000890001430166000500105560122210000065165161265300156012453103830650159004700688400290108175000000236190000627600177001297300000092720075000000027002410007061012308800059126000000000000000003330000000000000000075750000000001040000000634500000000000000000000009900000061000270076000000000007500441160014000000000116000017900012766004640048000241900037043607001030150013200005900001090001130175004800480000043000000007500026170000250000500000000000730000003200000024168400000000100900000512800000076027003490299324000001300037001290003132700001450000000000104059000000068150
SPN483Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Sneathia;sanguinegens_nov_85.05%572437000641358101891383020181736011115153601533315752903230007580888924000000449681493883197011800001701030001512770014729984248000371112721230242942611921323752775646515400018402210088318661120518707340000000854820780919000001710203251079258000780066544000018530210003521578482760007426105401140000017120560999450200260394011686163360007381247010200929204037490137206007201000361352243232210045499013871002124790004954405293269728922800158402173683540300184000463024231821100731826765501093311810686014932302144225232607041231112833614900431048627706702731602157427703900001716211864590294147010813626816296398174721351974350084500115154000348640166126221495500130421891466615013192031144218412203218430214326880330030893901636220111021501668501680116019841921153612834215814019930331012147300189002740854065601535726203922101201291161000261439500338180870710061000191820006578012500002690540276110713360016900741579027290560597233000180642310366069957634012801649124111690002330014717607341300208139058000000190002082508212902940054500175001171630010050034423409000300750000661030013000056298187014814717880020600730000888769051000001750000350289720146029001740177171395004078228400000041259050233131636046919052002329922444406800000000546830177235005633784880242057013924202880833158100415489230492202168000000652350158006135130919529003720380749
SPN484Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lacticaseibacillus;porcinae_nov_86.26%009900000720000000000022600018102410300000000370005100000000031000000002170000000000000000000003081240022306900000007500000000000000000000001150000000000000000000000000000119000000550090000094000000000000009400750980000040037600000590000001160000029291000550000840000041003500012500000000040000158000000930000000000000002804000055430000000000000000000000000025300000000000016400005732055000000000000000000003500000071000000000000000000000041141000290009400000000000000013100000000000000000000000000000525400000000000567000000000000000000000000000350000000000000000990000029000129000000000000000000000000000004600000041001600490380000000260000000000000000000000203320000000153000000490000000000000000041001400000000000097000000000122000000001310000000000000052000000180000805900002001551400000
SPN504Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum_nov_86.73%0000000013209600000000021000002180200040000179220200000000000000081009500180000000001300000000000004060614000000000000110001673800000066223000000000000000000000250000000012500001095600000000021400000000110000012511700000004502800000000005800050000000390000221030000550000661002470000760039180020000088001580023831800000082000000046000000191000006000000257006315000025000000000000002100000140011500000000160990000144002060000000000000170000400026000039900008900048200002900432000000001380000000090000000001430000000000000080000001060000000000000004600000000240480001450195000000132000000140002800008100000000006200000022100900000000000000610000000000000000000003890364059300352380002130000000031300084000000143568001200000164400000011110000000024000000000005500000000000000000000000002520000235053014600830000014000000122000000002360200000000013400
SPN510Bacteria;Actinobacteria;Actinomycetia;Streptosporangiales;Streptosporangiaceae;Streptosporangium;subfuscum_nov_84.24%0000000001810001440000256000000000001770000000000000000449109033000000970000000000000013900000000000000000012201510000000000000003760000476000000000000000004200000000000000000000000000000010915500000000000000001940690000001000000000073150007970000017402600000000860000000000000153138183000023500000000105910091018300000000018100000000000003500910028000000002840000000014600000000133002520000000000000000002801590000026208270000000000136000000000185000000000500020000011100000008800630011100000000000000000000000499720000260000000000000000000002100000000000000000000000000000000000001420000030000000001680010400105000000001910166000000000000000016000000008300000000000000000356000000607000000263000000003540000390130013800079400000000012961000002660000000000000014900000000000000000114000000168002470412000000000000159000001320
SPN515Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Bowdeniella;nasicola_nov_87.61%000000000000000400000000187000023000029208150930000251000001370000000000000410000000000000084690000010200000000016913500000020963015601030008370000000000000135134200011432470000000000000000000450114000000000500000000000000000053000200970000000000004800000051000001870007100000000005300000004800024026518400000064990113009200009900001770000002600015443012000190008400000210000015700000000001050000066300790000000131000000000000000019700000000028000000001354702232670004800950001607273000000000930137072000000000000000124000012800310000000000008000000450000299000043100000000347078000135000000000000000000000000000000000063000000000000000150001900000040000000012061000000003700000000004602200001600000505500000044300000075059000000790810005700000000032000000000030000000000550000000800000000004301280000000016400000000002330112000234000000
SPN52Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT498 nov_84.5%00000000000007000428000000002610000000000000000237000000600000000000009900000000000003210058100000000004830000000000000000000000000000000004790000000000000000000000000000000000000008900000028200000000000000001601049516700000000490000000003000000000560178000000000000000380000015412200000028100000000000009373004101810000000000000000000098018301230001020000014600113000000000000000060000000000000192000098000000000004112200000000000000000021500000000000000158000000134000000006300000000000170000000000000000000000000029000760000001170500000000150000004300000210001113700000000009100000000000000000002800000000000000000000000001056800770004509500000000022000000000000000000000000000000012200000000000000098630000000000000000000000000148001150000000000410000000000000000000000000000000
SPN530Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Anaerovibrio;lipolyticus_nov_85.06%00650010500069061001650001670003100000100003000001450000000097000018502840370015045000002448490000510000000000007902140000153028800000025700119000011900013715605200300550006500000000590380144000000002700000990012000005002800104000008107913500000000000242047000465700630000000005901180139283000000122084082000166602900000360189122010507700540004800000164000360770000210710000000620810410000165194063000000010816974004000060026833044840019305905900065000000000001167200300000850000021000000026087000520000000026000070000069450000000006500000360004100000000000000001300000000000006200009446038014000038000442686060000005600000000000410000000106000000071000003200000005900400016000000000002270000250000000001310000040076001411300155010800000000000043059093000038000000007400080020000000014000000083000000064046000000006700000000030960039450100012900010659000004863111715200000148020801881000218000005600
SPN531Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;suis_nov_88.37%0000205000000000000000000000000000000000000000000000000180000000000000000000000000000000307000001740000000000000000000000000000000000000350003746000000000000000000000000000000000000000055800000000000000000000000000019300000247000000000000000000003600000000123300000000000000000000000000133000000009300000001000000625000000000000000000000000000000000000000000000000012400000000000000000000000000000000000000000000005800000000001130820000000580000000003290000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000045000012000000000000000000000000000000000000000000000000000000000000000000000002930000000000214000000314000000000000000000000000000000000000000000000000016800000000000000002030000001690
SPN536Bacteria;Bacteroidetes;Cytophagia;Cytophagales;Reichenbachiellaceae;Marinoscillum;pacificum_nov_80.04%27900000001280000460000031002505800000001041380000003320001891110520019800000010400018608906000000106016100820000283024000118097008860000540045500000009900350383300000000014000003414700000114023000022000750007500000211000080001330000680000001030720110740011113100170115005100000810056370000000000000001311105300250003008400007261041000000040000160159007984101000110630072708000000000001372000000107000132017200000092000000620626400581220000100174184009956000430542200821330000005200000000000680147013900001310041050000271010000000000000019100113119000000003705800000011300000310034320047100000000530023002300000000300030000841170011000032000180000042000104320000000000490074036000000087004200000000001900690381500000000000008100009410160750009200000000007600000002284017133000000000000000000082003300000000450000010000027004600000000140650486707900005500003600068163000123003907916000000104690011900000000109420
SPN541Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Kocuria;indica_nov_89.81%001000000000058801630048039300002483220058037006016200000000000000517492630000004758000000000230046700003504000002657000468770478533000001700094258000000000036700000000282352810000038041130014700000000000000156000000004700007620000149000002200000060012612637229000026708410000591494000373219500461890002090001743600311980050148000017770000003300071090264400495813013931200930049100001280002620000092553301447014501600058176187800066251180000001817390013000000163061808046383402084199079033210800002240003760000052700191910000078963460163000000185000021700022046380007062500018484020800000500016122801404550000003000000000009000000132159000000000000002720170700000256002800017706740000027000010480000000000209000002277000516000023305000013101500070000436152885380000135000000183290000001770000000000000000000012511900032560000000000174000187000116421174004490003400250012501890006022220980089103000364027000000000140266480000000000001000860000950010940000520044030000027743290269154570000677045400000816025790000000935041200035
SPN544Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Peptostreptococcus;anaerobius_nov_95.34%0001260000000006100000264710001110000000000001640153000014600079206007500810000329047005400259004100300000171000006304366000000007400126000000066000006200000000000000165006700670000000700663600000097013691009200012417900140000000014100150921700001260076000000135340000011600142016822085167680000000000000112000000007578534901650000135126651702100014120800000000006017300083000016590001010874201383170034000074000147000024000000009900180006001652772000500055710822303900001051490000000086011800011100004002300000102011200000000001013100000162000000240000000000003200217800000006806600000015100002200000000000013312600000605400001310590610000000000004200000000000000055339400000794000008000000000047000000000000000003351152000019008400000300510000000001000032072000000000097014010003853000000037014500008900000001100800000000034740916069064090340036001540014000008005608600000085600000000000002840359
SPN551Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Natronincola;ferrireducens_nov_83.89%2510011500001620000000000690001500140037001990000011414714200017700330012800000082025015900008500104044127652300000116151113187580048061000000001780015764000000000000129000000000000004800142009600128000048016502500540364201478670000107190005001250474700007200071003800004306612458597872000000119003500010217271000000109570000000000022005700565100000008928000003000000000050000157931000006400540000135040019854058005607900007540180033250107010900100111001750936935018448870000003518109000050008253000000000000892702806277000006810900000000753000000029003500000160635700000340000260000005606000023081000830055000049000910000150046054010100870000000043036341630030022566260426855000000008067770000000000000000000000000000042059006075000000714400018000000091620000000000000480004500000000000029000305416000000000000000390117940000000085480697400000001940001780089112249200000104025480000000480168000000000571500047090000790000111
SPN565Bacteria;Actinobacteria;Actinomycetia;Streptosporangiales;Thermomonosporaceae;Thermomonospora;curvata_nov_84.47%274000000000000016000000000000000023502440000030700001920228000000066100776000000035500000000000001260018400000131219000000000000201185000000000000000000000014400000000000000001090012800018400000000000000016400000014000026000000117000001222304600000000000680000035700000610000000310000000000087000000011300015500000000000001290000043000000233020400134000000035600000000000000000000111123550001420000940093180000780017800001440320005200000000000031038520200000000225000080000000355000000000000000000240010000000800132000000000000003800000000000000045000000000126000070053000000480001260000001410000290000000000000000000000000000000000000001910000131000011800000117000000000127151520000000002270170644508700000000000000000000000500000000000000010300730000000000000000000000000015401050310022013204200000108000174000139000000000022200000000017700
SPN571Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;slackii_nov_90.12%0000000000000000000000011300000040500000179011500750106028700021900000033900029600000000000000000046000029401760000155000000000249000000000690000000000031800000000000000338000226281000000000000074000000000000001610051860000000007100000000000000001090000033800000221007515300000000000000000016931000018500000000000000000298441218000880000001640159059000026000000370000006801210087000114011400000000001000012100000000000112053510000000110000000000000590000000100013800000000000000000000000000000249000000009900000001300000000007800002280000000013600000000017700017500000350000000000000000001690000000000000025000000000000000000000000073000021100000000000076690185000070501170000000000000000003900630000000000000000018200017600000179000000000000000950000000000000000001075300000041000169003450000040500019400000000001310419000012700000
SPN578Bacteria;Firmicutes;Clostridia;Clostridiales;Peptococcaceae;Thermincola;potens_nov_80.71%506810000018576030137007303508600057002801400001530215000036016200026211300000001071190045050000001350000018619200000025000000000088127000000000000019100410000000000000001850000000000118412000000000690000001200230000000000106000122490000000000000006407302534000000000001260000007015217900790077066000805700028000000000000000397900000007800000306400047078124000000062000000020600000013602360770139000690000000000000000025043000018600008800810095000053000000000010200018900000000076131000170191000053000000000000000000000071000073081000000005400000000000010100000110033000000000004907400005300001830000215000083050360000001010006200810000064000108000000000000300000001070000000081000012800010907242000000140000000000130038000000000004600011160000000000327215200000000000000192210000007000000000000826027106290161128000310107820000003800041900000000000000000000000001570207
SPN585Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Alkaliphilus;peptidifermentans_nov_82.53%113142000000730790018000000000195001100000007000000127000013411900001350012517246920323300040001180002106610200000000000000010700133000000004014000017900000001060000000000289000000000012711306200069135000000000936315600000000930000000000000007864005640710910012300001330000000000000936900000083000201000000000000073013000000000000900001239810700000132000401181560073010600100142000000083101000000001079200290000018200000001970000461560115110000012200126105057136002021464300880000000034092000510000000480000001260000000000066194012087013400000002040008000006700000064000433000000072000011500000023019000000029005100021000000081078005000000000004500007800034000000006300004000000000000000000000000000001530002118005307894006500515900000000000963400000012000072000105000000230000001460000000004700000000000035070000000000860032226000000000000502900931430094751042600000000000000101016600000000144
SPN586Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;israelii_nov_96.89%000000000001840000000000000000000000000921370000008700000000194000001080000460000028312300000000000000023200000000000000000000000010400000000000190000000000000000000002100000000000000000056400013100000520000660005800000000000000000012161000039400000410000000000181120001670000172000000000015311800270000000000000000000000000000000000000008900002721920000000000000111001080001090000000007000135244000000000016000820113000008600601110000000008900001390000001731200000000000000000000007800000000000000087000133000000000000000051000000000000000004814602400000018114000000000007000063000000000000106000000124000000001640000000007700000000000001180003100000000720000000082000007300000000000000000000000000000000000000000000000001190910000000000000372000010700000125000000990000000000000000035901420000890000000
SPN600Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Promicromonosporaceae;Isoptericola;cucumis_nov_86.73%0000000000000001460014200891691888000000000001632600033000000000137000000000000000971800000000000000000003070065000188202000000000132000000017006110400000105000013900025808300000000242082000000000082000000000000000000510000000000007401116000000001240000000000000000000000000000000000000092126057023142000000004002880000011106800000000000000000000152000100000840000000000004647300000010600001730000864300000063000000026000000000000000000000000000000000000026000000000000000000000000000000098000442531400057000000000000000004990006400000280596000000000000000000077000000000004400004220000000000000000000530000048070000104000000449900000000072000340000023000000025500000220013800000000000001470000000000000026000003400960000000001240000000018800000000093470000000240000000000550000000500440000000000000010000006500
SPN613Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;acetobutylicum_nov_85.65%477000022603123148389106013298012911221501725777322501351290000419162117431039065426614518102532662312281020300010913287415940882040810325282301260000168230811020536101141212561613000321620347171502644648386400018003959161060003302250170001881480415390001120264016100013300175037503562818123007028800234300258600112154185018102531722420203195638780861196120119026489849602922868444027037388017304536697010841282145462431650069026002988651199521269107851513711888620810028763719109602002600148000742761110432272261020173101393516036611419415961238154145217392061161438611221603829011048011600140594550181960118179289112158421580063336103612175331912172832213145102280499434060952262170035641852331142310269423163534860073011698178467443178964202930029537000140123473153064089412127321244033301622861821284714300321202217410698241990352329002517564002265129113952003001040153775250710979000290461496018107130000100109404075155149472480155001883875173131163003912759040822090818465877201187303425598288042834243839546137305227819143162901401150291913800234400049021003503368430006658154321235115440000001240113001444766762371510092105750407132138002313162990802766606458219290163000020367181261144015298111241441824811300175062591730200919100010500017525012017402122861103019525922061658001247911273552023871401091627600152701246325911006811833231120216529521400210013710700253228015122575468232455515112433600908014320168001410184012711008736031358775
SPN614Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Promicromonosporaceae;Cellulosimicrobium;arenosum_nov_91.54%00111000016800008700000001560000032189000000006700017287000258001350098000000213265000000000180000000000019000480188000000000001430023700000000000000000000000151002300061000000135005500001680000012800450941770641320000001481907500950000001350000054000710000000079010100000001524900000001084400000096000000660000000000000163151165450009800000055100121000790000000430027001030000000000000000000000000000000006300000000000619500000001660000126009315300017600810109000103000011900000000000015200071870061790000000000026000640000005101600640930000007812200000000700060046000000001060000006600124001270000000000105000006800000000000000000580000000000007400000026000000000710000000000730590000141012700000056000154127000000000000000000000000620000001890000000162000000788200046846300012700000035540109000003700860005500000000103166660000000000002010000001670000002390000000
SPN62Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Sneathia;sanguinegens_nov_85.47%23011000020000000025070000000001700000004200003093200010440000420000000000007100000017811400000180001100021167072000000000000019800000000145000000000000451801930000000000000000007700000000000000000046032000067009600024637012401070650042010200000000390005809000000000019002900287000330000146026011605800000025002200008250000000000000310015403502010001600008300031231550076000048053045150000000380230010800000270015000500240052005800230002700040000000000000136000570000023075057001700125620000000210001000000000000410000650000000294100000413500000000003200000000001700056012008100048001901400100000055079063620970004343000005800380000360000000000000200000000400640000000000000000000025000000000000000000180000000000000001000000530000000000000000210000000000006405428000000014500049000000000000000001090000000340000000000906701040001250003000
SPN630Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;rectus_nov_94.88%510000000770000590000008600015400380002324000001121050000000020000020000007014818400000016088016000103000310198140147127540000000000083000017000001251340032040000000000035000000005400000000063156740840010801015074630012000000099130850002720200000310000011907014711795700076000004049000014200000118000083000470590000027000200072001862032107000000430600000001220490000000016698015800155000081500520007900008400001240052000005904231000000047000113005201000000000190000006300946200000082114005100811138600000000000000230000000000000000104900004500000012480067000000000000000400510006000003300090007402030002200005800007407301030155020806947032000000003405000004605590000008900000000000000000013300810000085173800084000155000873600056008210500124200001190655500340000128100000021601940000000000000096520780500000000000000000497900050000148000220840520000200212800000000003500341060000000034000310101
SPN635Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Alkaliphilus;peptidifermentans_nov_87.82%00661800003400000000670132000000420760013467480009092000092180075001000000000089000105013013500000171000958703800095141000000530000155350107020979000001330000830153137001585100039280053000000000000001804901340890000063000000760000002000000137104617400007510700000000127001860004294003000000000006578110000096000036000000000124751441000670007000000004200630000910000000000069008094130054104000046078890000750000000006013011100129009100068000000000000000000610122097000406097013701000000026730127000006200430000000009300650006047000038000000103000000003682000000041650000000053085004100000000000000550004449000082187716100000015100000027000000000033000000015300005200035000420008000000000000000000068055000569200002900000340022360787906400137538133851800000000000000109010800000000091520301004855000000000000072000061232900000001811801210600079001860092130220000001464200890000101000000009300690144
SPN64Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Anaerovibrio;lipolyticus_nov_85.17%001637501320000000000001310000000000000450048016700003900000000056000031100680000071000450000770144620232000252000000000136000000000000001430000000000096000000000053018501900000015600000000000012700000000000000029000000000000009100000003000145000106102000000000000000000000000000000001110030260018800000000066000000000000000000000000690000000360008400000000000000000001220000000171000118066005700880000000330000000000000000000000460011301020000058000054061006100000000005000000000000000000390059000810000000000000000000082000000000035043000071000000000000351580000006700000000000009200000000000000000001200017700000000000000000000000001330000000000179000000000001450850450000000370091014500550151000000000000000000000007500741010000000001400041002648440003100327900480000000000000000000005702750000003000012200
SPN645Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Weeksellaceae;Chryseobacterium;taeanense_nov_85.77%0138700000113011600000000004400115012213201231780000057000000001090079093470000000144068890071000001680078000411349547013000007000055820599089000000001331580002140000000000000012100086000000000000037086014705048010400266500280001510300001250460042073000434800116584800216612680005366000000826769065000005720200000027000012009885000123000040550000840070120121001840009510000000610011014865001500000001504600320240920000803700083001191800800011540003900014400000056099009004201070550000000001100001140631310120004500038640000001440180000570045000002000000001754000904900470000300009000002601900926000039140000001300000000043002700000000000000000460760012500005701104615000000110013100916000000022000041000000000006300000035015000000400100000000009900430000000147343900350660056190080000790567205818000000031000700000000000000000000681204000000460092005400000005901700028000021000000000159000008800360000
SPN66Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;terpenotabidum_nov_92.36%006100000000411030199000000700000000099510176000000000000000000000002621660018692000000015301280003000000001020000002000025800000000001790061008700000000000000012500081000000000000000000013500000041000460093000003300000670000000071600070000000000020000000000670000000000030000000000001910000380037000010000060013500000000000000000000000002442000000000008800170000000000000032000105940000000000000980000021700000156129004300000000000500000000000012100003500056000750000000000000000000000045000000052000000000000000106100823500000002010000009700001320030000007704300260000000000000000002360000000089000000000000000000630104000000000001400216000380330000007800450000000001090001230000000000001780000000008600000000000000000000000590000000000000000000002500000620157000480000152000000000000000000000020600000001240
SPN662Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Flavobacterium;subsaxonicum_nov_81.99%31200000008400008800900000075000000052076000014305200000000000008700000000185000001490000000000052000000000000000000011538301960000460640000000000001140013300000110000000000000000000005701130000000000000752280000000000000340000011200006900000000000000000000000000005200000000000001410000039013164000232000052000000137008700000000008000000381333291130003000000570001420840018600014800033000060076530000047009600159000012700086000000001608800041000091000290000169900003300000006020016025400036000000012400047006800009700004600000000000000000000000000009300006000000000022003000000000380000370000000005406503700000000000000000094000001040000000003156000030000000017000101172000000000000055000005900000000000000000000470011900000009017000000000000000000000000280000000000000001420000077001260000000077000000005700000000097
SPN667Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Arenibacter;algicola_nov_87.21%00000014100001708400004504600001200060378400000000000000000005800000571600067000000540810000000010101290330000000250015501420000106771136700155001240010800007314710900000670000007117700006800000000256195000000000017900015300000004900004500043470029609700121621146009818212000000000000800000088890013170012300086000000006647045560000013042000000000220010111500024000114086750000147000000013010300000440082008201120000000013963597300000057000000451700608511300001220000000000510004800006300113001680730000140042001265000062000000052000004609900000024740000002830000000090000000042488000055000000700000500000520000000021000041043000032005869000000630005400069030000000000090000000003300000000290926800620008009500125000011300000095000000006211800830580000435829000353200000000000000001605988052800000027143001052400000043620000002000001180000000000008000830000010707800000000059000000
SPN676Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;rectus_nov_94.49%0017083044860161000000005510717200000121000016737707600833600180051005081000000000920560000993701471000053000000000000000570804710138167719633119000000003201510000000000000000000101710000015000000003810608300000360000013100134007000000000000000137000720470062507705607810600005908869058105000012000710003110600022000000760660100095670011001100054006940080102420130005100000090035000620740000000005700011611105503600006300102000836547400000000001000780074008800005232002300038000520200000000610000700002292038808600000260000000960000000017017000015550001807200000000950000077038090062000000440000340006200117000006100480000610900000008200000000050073479600004847000000002500510000000320008500001082400018018740000681570009536062360000000010800470000560526300884654000349100001142105000000002000000111760004001220194010047210089540100379600000374501510015001400066000000000780004800000000014070031000950
SPN682Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;terpenotabidum_nov_93.1%002050000000000000000078000000094000000016900000000000000000000001980000000000000000000000004280371010500000000050200005500013700000000000000000000000000000000009900008005900000000000000110000056000000000000240000000000001260000000064400000001645400000000000000000000000000051234800670000255000000000000154000000000000000000029000472000000000000005800000000001830000433000000000075005104400000003500000000000000000000000000000000490000000000497000000000000000000001490000000242300000000000000003800000000000000021000000000000000000000000000091026800000000004000970003300020000000000000000000000000550005600000000000000000000000000250000000000000000000120000000000411000000000000000000355000024500044000008000000167000000003302310000000234383000000000000000000000000000000
SPN689Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;terpenotabidum_nov_92.32%02020002351228158345052852200529700002491503272290213248001831419766488603120522420700982340032728508600000050016229069082538082017201714102700249021900015003970000010381050017063014201875430036275125000810202160160165023530009556783040006002590008000328674002634000653000030201144631660188150102730448573902740557230850001520103300123078151002635025600027975474191450100039737315500730724002410025601551010809150000859224061384200216000000244105720005041400100882070000000195001960272127168217107280125600320199010601136327001190000901271010038861020100811329011852800245200340012603300007716339355042507190019200050570875522553600212136360205013400151103034131024532046076022504371961300031494002280000701194232961927201830100043135356900590000001620016160088121980000170203000000107158246002805801553300000006953007301080078320230010330330016348000700032004800650255360000007200113042800592200545885880494470764880000639047133344001076202390087001130162016180921370001010291410002690353980214001101753759520603041421144410000012622303500414266023212000037894867006006703485485524000000207394007361160443005505025318901360103150560601410260903323714226407776323000244015155800365580006471001550003861315198733282315062701364044301640007464581490015500
SPN690Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Bowdeniella;nasicola_nov_87.76%02397000006200024010315000000194000002341400243300628100001472860000000037001380029800000123000001660190000000000590000000035000000007302101700000000000014880000000000000326082000000000000000002800001095000000000000005200121460000860000031000000560007200000014134000000000000000000000000970038000006040000000000000002200000260000001250000000000000000000000000000000000003800080009500000000000068593000036000000064027000710000650000000000000002100000000000000000000000000000000000004600000000550124152000000000000005910350001300000420072000000061187000000005000000000002600000000300000000000026000000000161600003800260000000002202300016003700570000001900003586023101001199700000000620000000000000002500290000000000000000800000644129000000000000007623240008000000000324500212004400000920000000136000000009500026000000216476
SPN700Bacteria;Firmicutes;Bacilli;Bacillales;Planococcaceae;Bhargavaea;cecembensis_nov_82.42%700760000031920000003900139176073000000001380000018501700001544400000000051014129000073000000003503209600000034013706569390071000000000025000010810677995000000000000002900059001890800000340521430046008772000004200490940000001260005206010147011400000000044070023000440000100490009201180104000000050123028000000000001570220734200138013606512206207606312959260270797000001400000068000089860000000217000000667408301167500074000480000382700000000732400001301800000030000307004700864106100071000000009107748001110000102000000007200000220027000013600000000018000032028003800202606200000000270002000000000000061220017002803609000136000007000002105700000000000900000420001251003500000800030720011500000000000000007501624000210000010032000083006000007300000000019000000000000000000064004200033011800190000071650100000000000730004131570622700280000098000953600000030121000000010213609000000084001034934
SPN710Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Dermacoccaceae;Dermacoccus;sp._str._Ellin185_nov_89.57%00000000000000252770360000000197065000000000128000000006400000000000000000000011300130000000000013019200008400019300000000089000360192000195000000000002160000000000000000000038000009200082000000410000054541600084086015200079000000756300000000069670154000000000000480450001570237000106009900007118700000000000005400149000000000000001090170000390162000000000000000520000001900003711500000000000000000001089501650990026200000680000000005311020600007817800003400216012500002700570770000450005600062095190000000000000000000000000000000000072000082000000000000000990628400153000000002580050000162000000000000000000000000003500000000960000000000065000720001350000000000000099002253191000000000000000013803709800360000340000000880000000890600000000000000243000000002700007400000000500000000082000000000000000000004800058016403042890000000000
SPN721Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;indistinctus_nov_86.39%0010400000007500860000001070000000008700000000000000000000000600078039000000000000006400000000015305901250003907500990000065000850000000000000690000000001260000000067000000000000017700000000017144096000112124000000510091533000030000129045600108000000001120000000020900012700011400000000000000001476609400000000000000000000000000000102049000006000000000005600016700135000085000000000000000904100000133001180592924720114001090004900000056104000022750517006100139000078000016600000000214000000000000000004900000000030520099000001190000000000000000390870000001100001120000000000000560000000001820000024000000008900063000000400000000000000000000001470031000063039000000001520000670850000888200000007072000660000000790000000050200000000000000106127000000000145002130000011338000224001790000076015400016055000006800005000000000011100000000000000
SPN729Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Anaerovibrio;lipolyticus_nov_86.86%001030000000000000000000000980000003019800012400001500036340000880000033001550440193181000600000005807111100000000000000010500930000000000016500000000000272000000000079000000000118233003500001480000110013020000003200000327000000270010900000032000000000000010000013407974130000000025004700000000000000420200000000000000109000000000001930248000000000611381330010846325538135000000000000000005000002260000009075000003000890000000088175000131830021600006000570001680000000012500019707800000090000000001510000000000000004300000000007900000000000000000000000256000000000200000000340010900000000007400000000122000000000000640000430000007600000009100011900120000000000000360000000870000000066001710000011800920000000240000000000000000000000000000000000000000000000000000000000001070016122002900125001063400113000000002100930000000339031600030000005874222
SPN736Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;pyogenes_nov_90.1%000000080000000000011000000000038029000000001650000482000000000000200138000072004100044000000914000000000000137000000013700000000000000000000003000000000000311000430000000000015800000007790370152000000000124000000000004500000000300001601900000000000120000000000000640000000017100470000000470058022700000000110000000000000720000000000003200000000027450121000000000000000010803200000000014900000004100000000000000000000000000682000000000000000000360840250000000000000000000005318530000000130000000000000960000000001070000065000000000840000000000460000873900000000002220000034000000300000000000000780000003000000000000296900000070900140000000000017900000000000550000002100002900000000037800000300000000000000000000000000000000000000000000000000037600000000430800116000000002500000000000
SPN750Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Alkaliphilus;peptidifermentans_nov_86.76%284000000000871690000400190001524200000015207000000140000448000005400016304760000000149800390006400000001090000000000177000000000000052290000000000000000003800000000097530440000600000045000450997400000007800002312500091510002438400000001958000000770557005106000100035471221030000057001221200000000118000012000000000010413300084241001406872000000001380019800500001900000000003800458705101270100000000000000000000000097572350420000000070076000730028990000055002307400096128060000000350000001300000360000051098009500000001320008500000330000000006388000000000000000005500000050000000000000028000015800008600000890673700000000002300000000750004378000000000001100000203720000000001240004200000000000097890024000007000000000039000099000060000000029005784001300000000000510000005476070000000000078001960073730002508400280000830009121000000000600000590620130000000
SPN76Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;indistinctus_nov_85.71%00000000800000000000000080009717201340750160009901280000000000000006603800144000000009000810282000000006900000820000141000000000002800144000830000006200000007900000001070000000000041099751041050563936000036000121000007000005714300007300000001770002900000000035110440000000032000057000000006600000001000005400001210071000000000000550000590000000119008707200000000890000000000000000670007500010779640000001210000000000720000000000000860000000023000049020000034000000000000000000000000000000541040000065056620000000000000000000000099850000000137041004100082190910000000000000470001120000000000000002626730000000008600000000029000000000320000771911000028003700000001133000460000000000000087000000054049000000520000021000000003500000000000104000000138000065000720006200000000111000000000000390134000007500000000000000000220600000
SPN770Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;sp. HMT248 nov_86.16%005640000000240000000000000000000007600000000000014500000027100007300940000000000000000135000000185000104000000001770001260000000002201300000000184000000000000000000000000000000000000003000000000027049900480000000000000000001430000000000006700149000000000000870000000000000000900000013600000000000005204700000023200000000000000907700000000000000000000000000000000000000000070344000000000037815500215000000000000000730000000057000106000000000000000000013000000000000000000060000000000000000000000014700000000024000410007506200000000000000210000002780000000000050010900002540000000000000000022000000000000000000000047000000000000036300190016800000000000000105000000000070016302700000000000000000470000530000000000000001150000000013300971490103218001200000000008100000000228035601210000004218500
SPN779Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;dianae_nov_87.22%000000035070013602300000053001130000000000070013903700003400920001842512800000055000000000001220067000000000000000000000000000000001010000000000000000000000000001213000004800000003200009200001270000000280000000000790088000008700000940005100000009700003133000017000017800000001270000000000000000000700000900000000007304600000000000420000570072016190054109138900710109000000600012694000505605307710678000000001540000073177240021000000008800000017710303301270000963501780003390000113000000000500001400094000000000023000000000000242000000000000000012000000000008488000000000005900000000000000065000050000000001150004770008463000000000061001400001160034000000260000290000016000000000001400000495600056079000800000002000000380000880000000000000530000000000497572006300000000940100010001200000009200000099040001390003461000000000000000000028051
SPN90Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Geosporobacter;subterraneus_nov_86.78%590000000000990000000000000000000011400000036000000150000048350023000025064000007100000000200000480000000000000000000000269000000010700000000001010000000000186000000350000000000110017000000000820000000000000000000000000000000206000000000000086980000001090001340007200000000619901450124000001756300116130000014000000000000690000000000000008313100005400010000260000000000000000000119400911700003800238790251450010417869000000000016000001202100052000012600003300000000000022900007400000000000000000000000000000000000000005300000054000001640000007200000000000131000000000000087000000000000000000017034000125000000000001900000086000000000000039000126322300710001170000000000004400000000000000003600000000000009323000000000002100900000078000000000000003916700823321007308400067000225160001220000000000000000000000004500
SPN93Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Gramella;marina_nov_84.87%0006900540001434200000166236049000580000129000000380047002000000053670560001180139000009800011400000000001900001120163000000000000000013800000004700000000218001300000007400284003113000482700000000024000001900000000000000165000000000820016600680000000016000043000298998000000000076029000000131000000000000112054730000000001090000000000193000000083079001770088000000098016001588479391300003800000000000000000000000000000000164440550000000070000000211200000000259000000000820000000000000000000000000000360000000000000254000000000000000000000270000000000000000110540000000000000007200000006400000000000000000000000000000032000007100000630000300000560000500000000000000000000000000054138420000000783508500000000055000000000000000000207000087000041000000000006600000000430000000170000127000000000000000000000007400000
SPN96Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Cellulomonadaceae;Cellulomonas;gilvus_nov_87.87%710009100022600000284234115021020601720000850000024500000000000000104098072700224012611134304374134521932480002110351005323008236000009339360000062023810290260000003670049313465200739008713900124001420482000000000000000000009100011900003830025500000031050128251000440002280001091194000009606100000181049003510700156672773930005601700004000036051022100022900000563203450010800000203251092270024281005483800012203200011420019505200340103023150007708300090018700099000011815900126391670000013900000002116400004800000000130122006065014426900120314053401205887000870002800004111200005501000008627603970000304001205870300192000001220046000000000601245112400135021249003702600000000004200000000009910001675301020000039258001150043600141290078185000000010311563019220000018902710530003849000000163218578060227220000008700101271600036165022077900003300000000000015400167000000310000084790005000000400140400069100008196810021700803100530014100770213944516071233114800003330352001590690184057000000000830000019518100038135700297000001551247000000521002464245056008601140
SPP14Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp14_200000156161000860014918800012800000000012317330000000000040000000000000005801610147250000000016000000000070000002933015800100000000000510055000030000000020500000104000000000000175009500000000000000230000112000000000017600090026800120000000016700173000000180890000000000477800670000000001440226000670000000242740000000420020800000010500078000000001800009400000012900005300068118812840000012435000008137000450000000000000000000000000000065002130000000000000700000005200000130000000107000000000290220000000003400012000180000000000890096690000000000000010059000570000000000320000000000000000000000400000000340000000000005000003030000000131000000005600000000000036000000000000000000000000000030000065500003100000000000000000045017100004600054114009700000009900000410000000230000060000000000002310000001620002940241050000001130133000000
SPPN1Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_sppn1_2_nov_97.18%113000000000000288007700051000263018700113000000000370000000001020000750000074000000040400000073000660000000044017100000019004400011000560830000540000000000000007700004400000003702241040000000000000000000000550000000000007200000147099001190000000000012000009900015310600000000000000000000000000000003530002002300000000000004660000060028252000025300000000000000000000001500000000000000012100000000000028390000080000440000005000036058020800000002090000000400000000000000000000000000027260000927800000000000000000000000000000330000000460000063000000000064074000450523500078330000000000072000000006700000000070000500750000000006300000000000000001530000000000003054060000030011000001400000000070002700001080000000000004710506600000000000000024000010100000250144006900000000000030000000000000134000000000000000143
SPPN9Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Mycobacteriaceae;Mycobacterium;multispecies_sppn9_2_nov_83.57%092263210818461008109003370558436010107902590442049126421980000157012882600003156000025830323502270114132735889294005761240000120900006560298256025900057611194032700000217000004660269843980165200534341029000000005659734560003612022174136127000534007998002103006311416012773352263428384910389076000080853318000007400024600001085319280149815021920010190000000313133000628656324045038056206014310340000007462754002370387083500013364557000716399961600990337303634872581145670227028002155014440920970039192764100252269094004557525302093289100036001183000036690151000478405100013000519008792025471652632039844322000913700192272600071600372212008820241002419550458861365470540001010989140279150641502295247011300086502514012200115004460684200023930018100003834030904950019104825615051000319170919215218598523006312049108587056800097196009600025549550009024003201147592137279600183012522100074800001025006990420814000000060079221720909009285042055901475623150017910347054500000000000032737200457871221330000380745141783000000504094001870050760050022875430127156211299000186010381648001601030490001080007691155000133194900000013540834807130000080200174300006300000197041031284002000632111248100137701737238108101260001135427814800000508005412346031470093407840024127000166027110379028441000001082000000000715821445094520160005676384014425781191510800066010004501710007942154401324240400510
 
 
Download OTU Tables at Different Taxonomy Levels
PhylumCount*: Relative**: CLR***:
ClassCount*: Relative**: CLR***:
OrderCount*: Relative**: CLR***:
FamilyCount*: Relative**: CLR***:
GenusCount*: Relative**: CLR***:
SpeciesCount*: Relative**: CLR***:
* Read count
** Relative abundance (count/total sample count)
*** Centered log ratio transformed abundance
;
 
The species listed in the table has full taxonomy and a dynamically assigned species ID specific to this report. When some reads match with the reference sequences of more than one species equally (i.e., same percent identiy and alignmnet coverage), they can't be assigned to a particular species. Instead, they are assigned to multiple species with the species notaton "s__multispecies_spp2_2". In this notation, spp2 is the dynamic ID assigned to these reads that hit multiple sequences and the "_2" at the end of the notation means there are two species in the spp2.

You can look up which species are included in the multi-species assignment, in this table below:
 
 
 
 
Another type of notation is "s__multispecies_sppn2_2", in which the "n" in the sppn2 means it's a potential novel species because all the reads in this species have < 98% idenity to any of the reference sequences. They were grouped together based on de novo OTU clustering at 98% identity cutoff. And then a representative sequence was chosed to BLASTN search against the reference database to find the closest match (but will still be < 98%). This representative sequence also matched equally to more than one species, hence the "spp" was given in the label.
 
 

Taxonomy Bar Plots for All Samples

 
 

Taxonomy Bar Plots for Individual Comparison Groups

 
 
Comparison No.Comparison NameFamiliesGeneraSpecies
Comparison 112 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 224 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 3Baseline.A.Plaque 2 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 412 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 524 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 6Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 7Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 8Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 912 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 10Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 11Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 12Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 1312 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 14Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 15Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 16Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 1712 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 18Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 19Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 20Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2112 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 22Baseline.A.Plaque 1 vs Baseline.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2312 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2424 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 25Baseline.B.Plaque 1 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2612 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2724 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 28PDFSVGPDFSVGPDFSVG
 
 

VIII. Analysis - Alpha Diversity

 

In ecology, alpha diversity (α-diversity) is the mean species diversity in sites or habitats at a local scale. The term was introduced by R. H. Whittaker[1][2] together with the terms beta diversity (β-diversity) and gamma diversity (γ-diversity). Whittaker's idea was that the total species diversity in a landscape (gamma diversity) is determined by two different things, the mean species diversity in sites or habitats at a more local scale (alpha diversity) and the differentiation among those habitats (beta diversity).


References:
Whittaker, R. H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 279–338. doi:10.2307/1943563
Whittaker, R. H. (1972). Evolution and Measurement of Species Diversity. Taxon, 21, 213-251. doi:10.2307/1218190

 

Alpha Diversity Analysis by Rarefaction

Diversity measures are affected by the sampling depth. Rarefaction is a technique to assess species richness from the results of sampling. Rarefaction allows the calculation of species richness for a given number of individual samples, based on the construction of so-called rarefaction curves. This curve is a plot of the number of species as a function of the number of samples. Rarefaction curves generally grow rapidly at first, as the most common species are found, but the curves plateau as only the rarest species remain to be sampled.


References:
Willis AD. Rarefaction, Alpha Diversity, and Statistics. Front Microbiol. 2019 Oct 23;10:2407. doi: 10.3389/fmicb.2019.02407. PMID: 31708888; PMCID: PMC6819366.

 
 
 

Boxplot of Alpha-diversity Indices

The two main factors taken into account when measuring diversity are richness and evenness. Richness is a measure of the number of different kinds of organisms present in a particular area. Evenness compares the similarity of the population size of each of the species present. There are many different ways to measure the richness and evenness. These measurements are called "estimators" or "indices". Below is a diversity of 3 commonly used indices showing the values for all the samples (dots) and in groups (boxes).

 
Alpha Diversity Box Plots for All Groups
 
 
 
 
 
 
 
Alpha Diversity Box Plots for Individual Comparisons
 
Comparison 0Baseline.A.Plaque 1 vs Baseline.B.Plaque 1View in PDFView in SVG
Comparison 112 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1View in PDFView in SVG
Comparison 224 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1View in PDFView in SVG
Comparison 3Baseline.A.Plaque 2 vs Baseline.B.Plaque 2View in PDFView in SVG
Comparison 412 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 524 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 6Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1View in PDFView in SVG
Comparison 7Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1View in PDFView in SVG
Comparison 8Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1View in PDFView in SVG
Comparison 912 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1View in PDFView in SVG
Comparison 10Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2View in PDFView in SVG
Comparison 11Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2View in PDFView in SVG
Comparison 12Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2View in PDFView in SVG
Comparison 1312 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2View in PDFView in SVG
Comparison 14Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1View in PDFView in SVG
Comparison 15Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1View in PDFView in SVG
Comparison 16Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1View in PDFView in SVG
Comparison 1712 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1View in PDFView in SVG
Comparison 18Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 19Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 20Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 2112 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 22Baseline.A.Plaque 1 vs Baseline.A.Plaque 2View in PDFView in SVG
Comparison 2312 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2View in PDFView in SVG
Comparison 2424 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2View in PDFView in SVG
Comparison 25Baseline.B.Plaque 1 vs Baseline.B.Plaque 2View in PDFView in SVG
Comparison 2612 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2View in PDFView in SVG
Comparison 2724 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2View in PDFView in SVG
 
 
 

Group Significance of Alpha-diversity Indices

To test whether the alpha diversity among different comparison groups are different statisticall, we use the Kruskal Wallis H test provided the "alpha-group-significance" fucntion in the QIIME 2 diversity package. Kruskal Wallis H test is the non parametric alternative to the One Way ANOVA. Non parametric means that the test doesn’t assume your data comes from a particular distribution. The H test is used when the assumptions for ANOVA aren’t met (like the assumption of normality). It is sometimes called the one-way ANOVA on ranks, as the ranks of the data values are used in the test rather than the actual data points. The test determines whether the medians of two or more groups are different.

Below are the Kruskal Wallis H test results for each comparison based on three different alpha diversity measures: 1) Observed species (features), 2) Shannon index, and 3) Simpson index.

 
 
Comparison 0.Baseline.A.Plaque 1 vs Baseline.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 1.12 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 2.24 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 3.Baseline.A.Plaque 2 vs Baseline.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 4.12 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 5.24 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 6.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 7.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 8.Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 9.12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 10.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 11.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 12.Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 13.12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 14.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 15.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 16.Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 17.12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1Observed FeaturesShannon IndexSimpson Index
Comparison 18.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 19.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 20.Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 21.12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 22.Baseline.A.Plaque 1 vs Baseline.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 23.12 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 24.24 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 25.Baseline.B.Plaque 1 vs Baseline.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 26.12 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
Comparison 27.24 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2Observed FeaturesShannon IndexSimpson Index
 
 

IX. Analysis - Beta Diversity

 

NMDS and PCoA Plots

Beta diversity compares the similarity (or dissimilarity) of microbial profiles between different groups of samples. There are many different similarity/dissimilarity metrics. In general, they can be quantitative (using sequence abundance, e.g., Bray-Curtis or weighted UniFrac) or binary (considering only presence-absence of sequences, e.g., binary Jaccard or unweighted UniFrac). They can be even based on phylogeny (e.g., UniFrac metrics) or not (non-UniFrac metrics, such as Bray-Curtis, etc.).

For microbiome studies, species profiles of samples can be compared with the Bray-Curtis dissimilarity, which is based on the count data type. The pair-wise Bray-Curtis dissimilarity matrix of all samples can then be subject to either multi-dimensional scaling (MDS, also known as PCoA) or non-metric MDS (NMDS).

MDS/PCoA is a scaling or ordination method that starts with a matrix of similarities or dissimilarities between a set of samples and aims to produce a low-dimensional graphical plot of the data in such a way that distances between points in the plot are close to original dissimilarities.

NMDS is similar to MDS, however it does not use the dissimilarities data, instead it converts them into the ranks and use these ranks in the calculation.

In our beta diversity analysis, Bray-Curtis dissimilarity matrix was first calculated and then plotted by the PCoA and NMDS separately. Below are beta diveristy results for all groups together:

 
 
NMDS and PCoA Plots for All Groups
 
 
 
 
 

The above PCoA and NMDS plots are based on count data. The count data can also be transformed into centered log ratio (CLR) for each species. The CLR data is no longer count data and cannot be used in Bray-Curtis dissimilarity calculation. Instead CLR can be compared with Euclidean distances. When CLR data are compared by Euclidean distance, the distance is also called Aitchison distance.

Below are the NMDS and PCoA plots of the Aitchison distances of the samples:

 
 
 
 
 
 
 
NMDS and PCoA Plots for Individual Comparisons
 
 
Comparison No.Comparison NameNMDAPCoA
Bray-CurtisCLR EuclideanBray-CurtisCLR Euclidean
Comparison 112 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 224 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 3Baseline.A.Plaque 2 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 412 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 524 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 6Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 7Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 8Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 912 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 10Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 11Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 12Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 1312 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 14Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 15Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 16Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 1712 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 18Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 19Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 20Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2112 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 22Baseline.A.Plaque 1 vs Baseline.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2312 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2424 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 25Baseline.B.Plaque 1 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2612 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2724 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVGPDFSVG
Comparison 28PDFSVGPDFSVGPDFSVGPDFSVG
 
 
 
 
 

Interactive 3D PCoA Plots - Bray-Curtis Dissimilarity

 
 
 

Interactive 3D PCoA Plots - Euclidean Distance

 
 
 

Interactive 3D PCoA Plots - Correlation Coefficients

 
 
 

Group Significance of Beta-diversity Indices

To test whether the between-group dissimilarities are significantly greater than the within-group dissimilarities, the "beta-group-significance" function provided in the QIIME 2 "diversity" package was used with PERMANOVA (permutational multivariate analysis of variance) chosen s the group significan testing method.

Three beta diversity matrics were used: 1) Bray–Curtis dissimilarity 2) Correlation coefficient matrix , and 3) Aitchison distance (Euclidean distance between clr-transformed compositions).

 
 
Comparison 0.Baseline.A.Plaque 1 vs Baseline.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 1.12 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 2.24 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 3.Baseline.A.Plaque 2 vs Baseline.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 4.12 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 5.24 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 6.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 7.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 8.Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 9.12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 10.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 11.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 12.Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 13.12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 14.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 15.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 16.Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 17.12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1Bray–CurtisCorrelationAitchison
Comparison 18.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 19.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 20.Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 21.12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 22.Baseline.A.Plaque 1 vs Baseline.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 23.12 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 24.24 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 25.Baseline.B.Plaque 1 vs Baseline.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 26.12 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
Comparison 27.24 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2Bray–CurtisCorrelationAitchison
 
 
 

X. Analysis - Differential Abundance

16S rRNA next generation sequencing (NGS) generates a fixed number of reads that reflect the proportion of different species in a sample, i.e., the relative abundance of species, instead of the absolute abundance. In Mathematics, measurements involving probabilities, proportions, percentages, and ppm can all be thought of as compositional data. This makes the microbiome read count data “compositional” (Gloor et al, 2017). In general, compositional data represent parts of a whole which only carry relative information (http://www.compositionaldata.com/).

The problem of microbiome data being compositional arises when comparing two groups of samples for identifying “differentially abundant” species. A species with the same absolute abundance between two conditions, its relative abundances in the two conditions (e.g., percent abundance) can become different if the relative abundance of other species change greatly. This problem can lead to incorrect conclusion in terms of differential abundance for microbial species in the samples.

When studying differential abundance (DA), the current better approach is to transform the read count data into log ratio data. The ratios are calculated between read counts of all species in a sample to a “reference” count (e.g., mean read count of the sample). The log ratio data allow the detection of DA species without being affected by percentage bias mentioned above

In this report, a compositional DA analysis tool “ANCOM” (analysis of composition of microbiomes) was used. ANCOM transforms the count data into log-ratios and thus is more suitable for comparing the composition of microbiomes in two or more populations. "ANCOM" generates a table of features with W-statistics and whether the null hypothesis is rejected. The “W” is the W-statistic, or number of features that a single feature is tested to be significantly different against. Hence the higher the "W" the more statistical sifgnificane that a feature/species is differentially abundant.


References:

Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome Datasets Are Compositional: And This Is Not Optional. Front Microbiol. 2017 Nov 15;8:2224. doi: 10.3389/fmicb.2017.02224. PMID: 29187837; PMCID: PMC5695134.

Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015 May 29;26:27663. doi: 10.3402/mehd.v26.27663. PMID: 26028277; PMCID: PMC4450248.

Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020 Jul 14;11(1):3514. doi: 10.1038/s41467-020-17041-7. PMID: 32665548; PMCID: PMC7360769.

 
 

ANCOM Differential Abundance Analysis

 
ANCOM Results for Individual Comparisons
Comparison No.Comparison Name
Comparison 0.Baseline.A.Plaque 1 vs Baseline.B.Plaque 1
Comparison 1.12 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1
Comparison 2.24 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 3.Baseline.A.Plaque 2 vs Baseline.B.Plaque 2
Comparison 4.12 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2
Comparison 5.24 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 6.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 7.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1
Comparison 8.Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 9.12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 10.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 11.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2
Comparison 12.Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 13.12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 14.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 15.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1
Comparison 16.Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 17.12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 18.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 19.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2
Comparison 20.Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 21.12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 22.Baseline.A.Plaque 1 vs Baseline.A.Plaque 2
Comparison 23.12 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2
Comparison 24.24 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2
Comparison 25.Baseline.B.Plaque 1 vs Baseline.B.Plaque 2
Comparison 26.12 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2
Comparison 27.24 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2
 
 

ANCOM-BC Differential Abundance Analysis

 

Starting with version V1.2, we also include the results of ANCOM-BC (Analysis of Compositions of Microbiomes with Bias Correction) (Lin and Peddada 2020). ANCOM-BC is an updated version of "ANCOM" that: (a) provides statistically valid test with appropriate p-values, (b) provides confidence intervals for differential abundance of each taxon, (c) controls the False Discovery Rate (FDR), (d) maintains adequate power, and (e) is computationally simple to implement. The bias correction (BC) addresses a challenging problem of the bias introduced by differences in the sampling fractions across samples. This bias has been a major hurdle in performing DA analysis of microbiome data. ANCOM-BC estimates the unknown sampling fractions and corrects the bias induced by their differences among samples. The absolute abundance data are modeled using a linear regression framework.

References:

Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020 Jul 14;11(1):3514. doi: 10.1038/s41467-020-17041-7. PMID: 32665548; PMCID: PMC7360769.

 
 
ANCOM-BC Results for Individual Comparisons
 
Comparison No.Comparison Name
Comparison 1.12 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1
Comparison 2.24 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 3.Baseline.A.Plaque 2 vs Baseline.B.Plaque 2
Comparison 4.12 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2
Comparison 5.24 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 6.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 7.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1
Comparison 8.Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 9.12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 10.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 11.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2
Comparison 12.Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 13.12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 14.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 15.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1
Comparison 16.Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 17.12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 18.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 19.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2
Comparison 20.Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 21.12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 22.Baseline.A.Plaque 1 vs Baseline.A.Plaque 2
Comparison 23.12 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2
Comparison 24.24 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2
Comparison 25.Baseline.B.Plaque 1 vs Baseline.B.Plaque 2
Comparison 26.12 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2
Comparison 27.24 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2
Comparison 28.
 
 
 

LEfSe - Linear Discriminant Analysis Effect Size

LEfSe (Linear Discriminant Analysis Effect Size) is an alternative method to find "organisms, genes, or pathways that consistently explain the differences between two or more microbial communities" (Segata et al., 2011). Specifically, LEfSe uses rank-based Kruskal-Wallis (KW) sum-rank test to detect features with significant differential (relative) abundance with respect to the class of interest. Since it is rank-based, instead of proportional based, the differential species identified among the comparison groups is less biased (than percent abundance based).

Reference:

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011 Jun 24;12(6):R60. doi: 10.1186/gb-2011-12-6-r60. PMID: 21702898; PMCID: PMC3218848.

 
Baseline.A.Plaque 1 vs Baseline.B.Plaque 1
 
 
 
 
 
 
 
LEfSe Results for All Comparisons
 
Comparison No.Comparison Name
Comparison 1.Baseline.A.Plaque 1 vs Baseline.B.Plaque 1
Comparison 2.12 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1
Comparison 3.24 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 4.Baseline.A.Plaque 2 vs Baseline.B.Plaque 2
Comparison 5.12 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2
Comparison 6.24 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 7.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 8.Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1
Comparison 9.Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 10.12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1
Comparison 11.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 12.Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2
Comparison 13.Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 14.12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2
Comparison 15.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 16.Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1
Comparison 17.Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 18.12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1
Comparison 19.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 20.Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2
Comparison 21.Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 22.12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2
Comparison 23.Baseline.A.Plaque 1 vs Baseline.A.Plaque 2
Comparison 24.12 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2
Comparison 25.24 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2
Comparison 26.Baseline.B.Plaque 1 vs Baseline.B.Plaque 2
Comparison 27.12 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2
Comparison 28.24 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2
 
 

XI. Analysis - Heatmap Profile

 

Species vs Sample Abundance Heatmap for All Samples

 
 
 

Heatmaps for Individual Comparisons

 
A) Two-way clustering - clustered on both columns (Samples) and rows (organism)
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 112 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 224 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 3Baseline.A.Plaque 2 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 412 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 524 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 6Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 7Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 8Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 912 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 10Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 11Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 12Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 1312 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 14Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 15Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 16Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 1712 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 18Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 19Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 20Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2112 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 22Baseline.A.Plaque 1 vs Baseline.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2312 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2424 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 25Baseline.B.Plaque 1 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2612 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2724 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 28PDFSVGPDFSVGPDFSVG
 
 
B) One-way clustering - clustered on rows (organism) only
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 112 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 224 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 3Baseline.A.Plaque 2 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 412 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 524 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 6Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 7Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 8Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 912 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 10Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 11Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 12Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 1312 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 14Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 15Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 16Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 1712 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 18Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 19Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 20Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2112 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 22Baseline.A.Plaque 1 vs Baseline.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2312 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2424 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 25Baseline.B.Plaque 1 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2612 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2724 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 28PDFSVGPDFSVGPDFSVG
 
 
C) No clustering
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 112 Weeks.A.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 224 Weeks.A.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 3Baseline.A.Plaque 2 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 412 Weeks.A.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 524 Weeks.A.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 6Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 7Baseline.A.Plaque 1 vs 12 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 8Baseline.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 912 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 10Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 11Baseline.A.Plaque 2 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 12Baseline.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 1312 Weeks.A.Plaque 2 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 14Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 15Baseline.B.Plaque 1 vs 12 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 16Baseline.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 1712 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 1PDFSVGPDFSVGPDFSVG
Comparison 18Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 19Baseline.B.Plaque 2 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 20Baseline.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2112 Weeks.B.Plaque 2 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 22Baseline.A.Plaque 1 vs Baseline.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2312 Weeks.A.Plaque 1 vs 12 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2424 Weeks.A.Plaque 1 vs 24 Weeks.A.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 25Baseline.B.Plaque 1 vs Baseline.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2612 Weeks.B.Plaque 1 vs 12 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 2724 Weeks.B.Plaque 1 vs 24 Weeks.B.Plaque 2PDFSVGPDFSVGPDFSVG
Comparison 28PDFSVGPDFSVGPDFSVG
 
 

XII. Analysis - Network Association

To analyze the co-occurrence or co-exclusion between microbial species among different samples, network correlation analysis tools are usually used for this purpose. However, microbiome count data are compositional. If count data are normalized to the total number of counts in the sample, the data become not independent and traditional statistical metrics (e.g., correlation) for the detection of specie-species relationships can lead to spurious results. In addition, sequencing-based studies typically measure hundreds of OTUs (species) on few samples; thus, inference of OTU-OTU association networks is severely under-powered. Here we use SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues (Kurtz et al., 2015). SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. SPIEC-EASI provides two algorithms for network inferencing – 1) Meinshausen-Bühlmann's neighborhood selection (MB method) and inverse covariance selection (GLASSO method, i.e., graphical least absolute shrinkage and selection operator). This is fundamentally distinct from SparCC, which essentially estimate pairwise correlations. In addition to these two methods, we provide the results of a third method - SparCC (Sparse Correlations for Compositional Data)(Friedman & Alm 2012), which is also a method for inferring correlations from compositional data. SparCC estimates the linear Pearson correlations between the log-transformed components.


References:

Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015 May 7;11(5):e1004226. doi: 10.1371/journal.pcbi.1004226. PMID: 25950956; PMCID: PMC4423992.

Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8(9):e1002687. doi: 10.1371/journal.pcbi.1002687. Epub 2012 Sep 20. PMID: 23028285; PMCID: PMC3447976.

 

SPIEC-EASI Network Inference by Neighborhood Selection (MB Method)

 
 

 

Association Network Inference by SparCC

 
 

 
 
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