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 17, 2022

Project ID: FOMC6488

I. Project Summary

Project FOMC6488 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


F6488.S1013 TUKzr6488_10V3V4_R1.fastq.gzzr6488_10V3V4_R2.fastq.gz


F6488.S1114 TUKzr6488_11V3V4_R1.fastq.gzzr6488_11V3V4_R2.fastq.gz


F6488.S1215 TUKzr6488_12V3V4_R1.fastq.gzzr6488_12V3V4_R2.fastq.gz


F6488.S1316 TUKzr6488_13V3V4_R1.fastq.gzzr6488_13V3V4_R2.fastq.gz


F6488.S1417 TUKzr6488_14V3V4_R1.fastq.gzzr6488_14V3V4_R2.fastq.gz


F6488.S1518 TUKzr6488_15V3V4_R1.fastq.gzzr6488_15V3V4_R2.fastq.gz


F6488.S1619 TUKzr6488_16V3V4_R1.fastq.gzzr6488_16V3V4_R2.fastq.gz


F6488.S1720 TUKzr6488_17V3V4_R1.fastq.gzzr6488_17V3V4_R2.fastq.gz


F6488.S1822 TUKzr6488_18V3V4_R1.fastq.gzzr6488_18V3V4_R2.fastq.gz


F6488.S1923 TUKzr6488_19V3V4_R1.fastq.gzzr6488_19V3V4_R2.fastq.gz


F6488.S013 TUKzr6488_1V3V4_R1.fastq.gzzr6488_1V3V4_R2.fastq.gz


F6488.S2024 TUKzr6488_20V3V4_R1.fastq.gzzr6488_20V3V4_R2.fastq.gz


F6488.S2125 TUKzr6488_21V3V4_R1.fastq.gzzr6488_21V3V4_R2.fastq.gz


F6488.S2226 TUKzr6488_22V3V4_R1.fastq.gzzr6488_22V3V4_R2.fastq.gz


F6488.S2327 TUKzr6488_23V3V4_R1.fastq.gzzr6488_23V3V4_R2.fastq.gz


F6488.S2428 TUKzr6488_24V3V4_R1.fastq.gzzr6488_24V3V4_R2.fastq.gz


F6488.S2529 TUKzr6488_25V3V4_R1.fastq.gzzr6488_25V3V4_R2.fastq.gz


F6488.S2630 TUKzr6488_26V3V4_R1.fastq.gzzr6488_26V3V4_R2.fastq.gz


F6488.S2732 TUKzr6488_27V3V4_R1.fastq.gzzr6488_27V3V4_R2.fastq.gz


F6488.S2833 TUKzr6488_28V3V4_R1.fastq.gzzr6488_28V3V4_R2.fastq.gz


F6488.S2934 TUKzr6488_29V3V4_R1.fastq.gzzr6488_29V3V4_R2.fastq.gz


F6488.S024 TUKzr6488_2V3V4_R1.fastq.gzzr6488_2V3V4_R2.fastq.gz


F6488.S3035 TUKzr6488_30V3V4_R1.fastq.gzzr6488_30V3V4_R2.fastq.gz


F6488.S3136 TUKzr6488_31V3V4_R1.fastq.gzzr6488_31V3V4_R2.fastq.gz


F6488.S3237 TUKzr6488_32V3V4_R1.fastq.gzzr6488_32V3V4_R2.fastq.gz


F6488.S3338 TUKzr6488_33V3V4_R1.fastq.gzzr6488_33V3V4_R2.fastq.gz


F6488.S3439 TUKzr6488_34V3V4_R1.fastq.gzzr6488_34V3V4_R2.fastq.gz


F6488.S3540 TUKzr6488_35V3V4_R1.fastq.gzzr6488_35V3V4_R2.fastq.gz


F6488.S3641 TUKzr6488_36V3V4_R1.fastq.gzzr6488_36V3V4_R2.fastq.gz


F6488.S3742 TUKzr6488_37V3V4_R1.fastq.gzzr6488_37V3V4_R2.fastq.gz


F6488.S3844 TUKzr6488_38V3V4_R1.fastq.gzzr6488_38V3V4_R2.fastq.gz


F6488.S3945 TUKzr6488_39V3V4_R1.fastq.gzzr6488_39V3V4_R2.fastq.gz


F6488.S035 TUKzr6488_3V3V4_R1.fastq.gzzr6488_3V3V4_R2.fastq.gz


F6488.S4046 TUKzr6488_40V3V4_R1.fastq.gzzr6488_40V3V4_R2.fastq.gz


F6488.S4148 TUKzr6488_41V3V4_R1.fastq.gzzr6488_41V3V4_R2.fastq.gz


F6488.S4249 TUKzr6488_42V3V4_R1.fastq.gzzr6488_42V3V4_R2.fastq.gz


F6488.S4352 TUKzr6488_43V3V4_R1.fastq.gzzr6488_43V3V4_R2.fastq.gz


F6488.S4453 TUKzr6488_44V3V4_R1.fastq.gzzr6488_44V3V4_R2.fastq.gz


F6488.S4554 TUKzr6488_45V3V4_R1.fastq.gzzr6488_45V3V4_R2.fastq.gz


F6488.S4655 TUKzr6488_46V3V4_R1.fastq.gzzr6488_46V3V4_R2.fastq.gz


F6488.S4756 TUKzr6488_47V3V4_R1.fastq.gzzr6488_47V3V4_R2.fastq.gz


F6488.S4857 TUKzr6488_48V3V4_R1.fastq.gzzr6488_48V3V4_R2.fastq.gz


F6488.S4958 TUKzr6488_49V3V4_R1.fastq.gzzr6488_49V3V4_R2.fastq.gz


F6488.S046 TUKzr6488_4V3V4_R1.fastq.gzzr6488_4V3V4_R2.fastq.gz


F6488.S5059 TUKzr6488_50V3V4_R1.fastq.gzzr6488_50V3V4_R2.fastq.gz


F6488.S5160 TUKzr6488_51V3V4_R1.fastq.gzzr6488_51V3V4_R2.fastq.gz


F6488.S523Dzr6488_52V3V4_R1.fastq.gzzr6488_52V3V4_R2.fastq.gz


F6488.S535Dzr6488_53V3V4_R1.fastq.gzzr6488_53V3V4_R2.fastq.gz


F6488.S546Dzr6488_54V3V4_R1.fastq.gzzr6488_54V3V4_R2.fastq.gz


F6488.S559Dzr6488_55V3V4_R1.fastq.gzzr6488_55V3V4_R2.fastq.gz


F6488.S5610Dzr6488_56V3V4_R1.fastq.gzzr6488_56V3V4_R2.fastq.gz


F6488.S5712Dzr6488_57V3V4_R1.fastq.gzzr6488_57V3V4_R2.fastq.gz


F6488.S5813Dzr6488_58V3V4_R1.fastq.gzzr6488_58V3V4_R2.fastq.gz


F6488.S5915Dzr6488_59V3V4_R1.fastq.gzzr6488_59V3V4_R2.fastq.gz


F6488.S057 TUKzr6488_5V3V4_R1.fastq.gzzr6488_5V3V4_R2.fastq.gz


F6488.S6016Dzr6488_60V3V4_R1.fastq.gzzr6488_60V3V4_R2.fastq.gz


F6488.S6119Dzr6488_61V3V4_R1.fastq.gzzr6488_61V3V4_R2.fastq.gz


F6488.S6224Dzr6488_62V3V4_R1.fastq.gzzr6488_62V3V4_R2.fastq.gz


F6488.S6329Dzr6488_63V3V4_R1.fastq.gzzr6488_63V3V4_R2.fastq.gz


F6488.S6430Dzr6488_64V3V4_R1.fastq.gzzr6488_64V3V4_R2.fastq.gz


F6488.S6532Dzr6488_65V3V4_R1.fastq.gzzr6488_65V3V4_R2.fastq.gz


F6488.S6633Dzr6488_66V3V4_R1.fastq.gzzr6488_66V3V4_R2.fastq.gz


F6488.S6734Dzr6488_67V3V4_R1.fastq.gzzr6488_67V3V4_R2.fastq.gz


F6488.S6837Dzr6488_68V3V4_R1.fastq.gzzr6488_68V3V4_R2.fastq.gz


F6488.S6938Dzr6488_69V3V4_R1.fastq.gzzr6488_69V3V4_R2.fastq.gz


F6488.S069 TUKzr6488_6V3V4_R1.fastq.gzzr6488_6V3V4_R2.fastq.gz


F6488.S7039Dzr6488_70V3V4_R1.fastq.gzzr6488_70V3V4_R2.fastq.gz


F6488.S7140Dzr6488_71V3V4_R1.fastq.gzzr6488_71V3V4_R2.fastq.gz


F6488.S7241Dzr6488_72V3V4_R1.fastq.gzzr6488_72V3V4_R2.fastq.gz


F6488.S7346Dzr6488_73V3V4_R1.fastq.gzzr6488_73V3V4_R2.fastq.gz


F6488.S7448Dzr6488_74V3V4_R1.fastq.gzzr6488_74V3V4_R2.fastq.gz


F6488.S7553Dzr6488_75V3V4_R1.fastq.gzzr6488_75V3V4_R2.fastq.gz


F6488.S7654Dzr6488_76V3V4_R1.fastq.gzzr6488_76V3V4_R2.fastq.gz


F6488.S7755Dzr6488_77V3V4_R1.fastq.gzzr6488_77V3V4_R2.fastq.gz


F6488.S7856Dzr6488_78V3V4_R1.fastq.gzzr6488_78V3V4_R2.fastq.gz


F6488.S7959Dzr6488_79V3V4_R1.fastq.gzzr6488_79V3V4_R2.fastq.gz


F6488.S0710 TUKzr6488_7V3V4_R1.fastq.gzzr6488_7V3V4_R2.fastq.gz


F6488.S0811 TUKzr6488_8V3V4_R1.fastq.gzzr6488_8V3V4_R2.fastq.gz


F6488.S0912 TUKzr6488_9V3V4_R1.fastq.gzzr6488_9V3V4_R2.fastq.gz

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

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):

R1/R2281271261251241231
32133.91%42.59%42.45%42.44%42.61%42.86%
31137.80%47.60%47.67%47.86%48.48%48.70%
30137.76%47.50%47.80%47.85%48.58%48.58%
29137.64%47.34%47.31%48.28%48.49%48.68%
28138.06%47.66%47.89%48.70%48.89%49.03%
27138.00%47.41%47.54%48.52%49.04%49.11%

Based on the above result, the trim length combination of R1 = 271 bases and R2 = 231 bases (highlighted red above), was chosen for generating final ASVs for all sequences. This combination generated highest number of merged non-chimeric ASVs and was used for downstream analyses, if requested.

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:

 

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 IDF6488.S01F6488.S02F6488.S03F6488.S04F6488.S05F6488.S06F6488.S07F6488.S08F6488.S09F6488.S10F6488.S11F6488.S12F6488.S13F6488.S14F6488.S15F6488.S16F6488.S17F6488.S18F6488.S19F6488.S20F6488.S21F6488.S22F6488.S23F6488.S24F6488.S25F6488.S26F6488.S27F6488.S28F6488.S29F6488.S30F6488.S31F6488.S32F6488.S33F6488.S34F6488.S35F6488.S36F6488.S37F6488.S38F6488.S39F6488.S40F6488.S41F6488.S42F6488.S43F6488.S44F6488.S45F6488.S46F6488.S47F6488.S48F6488.S49F6488.S50F6488.S51F6488.S52F6488.S53F6488.S54F6488.S55F6488.S56F6488.S57F6488.S58F6488.S59F6488.S60F6488.S61F6488.S62F6488.S63F6488.S64F6488.S65F6488.S66F6488.S67F6488.S68F6488.S69F6488.S70F6488.S71F6488.S72F6488.S73F6488.S74F6488.S75F6488.S76F6488.S77F6488.S78F6488.S79Row SumPercentage
input40,75245,86037,22937,32034,79241,59347,53645,71135,42145,55736,48949,21934,67343,81844,17844,26740,29647,56840,40646,88432,72850,37648,45243,54140,46449,98839,01246,83932,34446,80449,00351,40436,39043,03238,86546,16940,59946,27254,56146,18948,80559,78148,08155,40547,25765,10556,46761,23736,27845,07033,34845,06035,47242,47546,17140,54054,55259,37947,72160,89357,67455,27657,89847,55741,48945,71145,56644,91238,43752,55653,81149,57443,93046,56935,50345,0769762,88350,5853,586,802100.00%
filtered40,41345,44436,91937,03734,50941,24247,15545,32435,12945,18136,16848,80134,38843,45943,79843,89039,96847,16440,08446,52032,48249,96148,05443,17340,11949,58338,67346,41732,07046,42648,57950,96436,08242,67538,53645,72740,25345,88554,06045,78148,40359,29447,67154,96046,83664,61655,99360,69635,98144,69133,02344,69235,15542,06645,80940,19054,12158,86247,32760,35957,24554,81157,38147,18841,12645,34145,16844,54738,15152,10153,31749,17143,51546,12135,18444,7369662,33550,1473,556,51999.16%
denoisedF39,00243,99535,81535,72833,35138,84045,35744,45533,83643,67434,60247,19632,94342,25342,50342,94839,10845,63638,79045,21231,43848,80647,57641,70538,24447,14837,68445,17630,68345,29447,35449,49034,95340,71036,03244,41338,40445,19751,18344,48746,74956,42846,49852,88745,19861,58753,93958,91934,80343,72232,19941,36832,77240,27641,78338,13251,36256,41644,67157,14154,27151,51053,38542,87738,47643,21643,35840,90034,91648,59349,11846,01737,86443,26231,35742,002257,38047,9213,394,49694.64%
denoisedR39,31044,30636,16835,88633,69539,19845,72344,30133,97943,84335,17347,32633,43842,32342,60142,82439,15846,04539,01045,35831,82548,77447,39441,88638,76647,30037,94545,07631,17445,17747,31749,38435,02840,98136,91744,58938,91844,98051,53544,66846,66356,62746,78753,47845,66461,91254,12459,03234,94443,51232,15642,28333,24140,26942,87938,42251,73556,46745,09957,52255,19852,10954,04444,09338,92143,04743,52441,97235,90649,70450,28246,75640,74544,05233,01942,136159,45048,5113,425,58595.51%
merged37,30142,12734,67433,61231,97333,18241,88642,71331,54839,96131,91044,44431,36939,43339,68440,84637,37043,46937,30243,47530,59346,84946,94439,82334,92242,10236,86843,20028,63843,55145,41246,34033,64236,10232,46342,58535,73944,07745,46142,75142,75450,57745,13548,60542,57354,84247,94755,82632,43841,86931,17135,61428,62735,78630,69633,35745,08451,18439,67050,23949,35645,74145,94137,47934,50239,44539,20335,80529,90642,45841,41739,92529,97338,26926,51536,672050,58843,6873,107,21786.63%
nonchim6,70411,0407,2818,2395,09811,17310,5629,0896,52810,43810,41210,6496,1557,8948,8537,0465,4487,2537,1547,6684,4329,8218,1529,83910,27712,5016,5439,9256,67910,59511,43110,5866,03511,81210,55910,2618,4487,80315,9999,6028,52114,1959,63612,7338,87315,46712,1879,6286,3027,7604,90417,08913,37313,08512,49210,52315,99312,28713,09914,21315,23916,24822,71914,13412,1989,36210,13116,81911,32613,93717,53016,54516,49714,45212,64713,394026,81712,655860,99424.00%

This table can be downloaded as an Excel table below:

 

5. DADA2 Amplicon Sequence Variants (ASVs). A total of 16197 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

#SampleIDSamplesStatusSourceGroup
F6488.S013 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S024 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S035 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S046 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S057 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S069 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S0710 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S0811 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S0912 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1013 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1114 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1215 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1316 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1417 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1518 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1619 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1720 TUKHealthy ControlSalivaSaliva Healthy Control
F6488.S1822 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S1923 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2024 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2125 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2226 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2327 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2428 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2529 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2630 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2732 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2833 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S2934 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3035 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3136 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3237 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3338 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3439 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3540 TUKPeriodontitisSalivaSaliva Periodontitis
F6488.S3641 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S3742 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S3844 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S3945 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4046 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4148 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4249 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4352 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4453 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4554 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4655 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4756 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4857 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S4958 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S5059 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S5160 TUKParkinson + PeriodontitisSalivaSaliva Parkinson + Periodontitis
F6488.S523DHealthy ControlFecesFeces Healthy Control
F6488.S535DHealthy ControlFecesFeces Healthy Control
F6488.S546DHealthy ControlFecesFeces Healthy Control
F6488.S559DHealthy ControlFecesFeces Healthy Control
F6488.S5610DHealthy ControlFecesFeces Healthy Control
F6488.S5712DHealthy ControlFecesFeces Healthy Control
F6488.S5813DHealthy ControlFecesFeces Healthy Control
F6488.S5915DHealthy ControlFecesFeces Healthy Control
F6488.S6016DHealthy ControlFecesFeces Healthy Control
F6488.S6119DHealthy ControlFecesFeces Healthy Control
F6488.S6224DPeriodontitisFecesFeces Periodontitis
F6488.S6329DPeriodontitisFecesFeces Periodontitis
F6488.S6430DPeriodontitisFecesFeces Periodontitis
F6488.S6532DPeriodontitisFecesFeces Periodontitis
F6488.S6633DPeriodontitisFecesFeces Periodontitis
F6488.S6734DPeriodontitisFecesFeces Periodontitis
F6488.S6837DPeriodontitisFecesFeces Periodontitis
F6488.S6938DPeriodontitisFecesFeces Periodontitis
F6488.S7039DPeriodontitisFecesFeces Periodontitis
F6488.S7140DPeriodontitisFecesFeces Periodontitis
F6488.S7241DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7346DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7448DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7553DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7654DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7755DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7856DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
F6488.S7959DParkinson + PeriodontitisFecesFeces Parkinson + Periodontitis
 
 

ASV Read Counts by Samples

#Sample IDRead Count
F6488.S214,432
F6488.S514,904
F6488.S055,098
F6488.S175,448
F6488.S336,035
F6488.S136,155
F6488.S496,302
F6488.S096,528
F6488.S276,543
F6488.S296,679
F6488.S016,704
F6488.S167,046
F6488.S197,154
F6488.S187,253
F6488.S037,281
F6488.S207,668
F6488.S507,760
F6488.S387,803
F6488.S147,894
F6488.S238,152
F6488.S048,239
F6488.S378,448
F6488.S418,521
F6488.S158,853
F6488.S458,873
F6488.S089,089
F6488.S669,362
F6488.S409,602
F6488.S489,628
F6488.S439,636
F6488.S229,821
F6488.S249,839
F6488.S289,925
F6488.S6710,131
F6488.S3610,261
F6488.S2510,277
F6488.S1110,412
F6488.S1010,438
F6488.S5610,523
F6488.S3510,559
F6488.S0710,562
F6488.S3210,586
F6488.S3010,595
F6488.S1210,649
F6488.S0211,040
F6488.S0611,173
F6488.S6911,326
F6488.S3111,431
F6488.S3411,812
F6488.S4712,187
F6488.S6512,198
F6488.S5812,287
F6488.S5512,492
F6488.S2612,501
F6488.S7512,647
F6488.S7912,655
F6488.S4412,733
F6488.S5413,085
F6488.S5913,099
F6488.S5313,373
F6488.S7613,394
F6488.S7013,937
F6488.S6414,134
F6488.S4214,195
F6488.S6014,213
F6488.S7414,452
F6488.S6115,239
F6488.S4615,467
F6488.S5715,993
F6488.S3915,999
F6488.S6216,248
F6488.S7316,497
F6488.S7216,545
F6488.S6816,819
F6488.S5217,089
F6488.S7117,530
F6488.S6322,719
F6488.S7826,817
 
 
 

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=0.01%(>=84 reads)
ATotal reads860,994860,994
BTotal assigned reads842,077842,077
CAssigned reads in species with read count < MPC014,964
DAssigned reads in samples with read count < 50000
ETotal samples7878
FSamples with reads >= 5007878
GSamples with reads < 50000
HTotal assigned reads used for analysis (B-C-D)842,077827,113
IReads assigned to single species381,405377,541
JReads assigned to multiple species273,533271,969
KReads assigned to novel species187,139177,603
LTotal number of species1,329676
MNumber of single species429305
NNumber of multi-species13888
ONumber of novel species762283
PTotal unassigned reads18,91718,917
QChimeric reads2,1772,177
RReads without BLASTN hits114114
SOthers: short, low quality, singletons, etc.16,62616,626
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.
SPIDTaxonomyF6488.S01F6488.S02F6488.S03F6488.S04F6488.S05F6488.S06F6488.S07F6488.S08F6488.S09F6488.S10F6488.S11F6488.S12F6488.S13F6488.S14F6488.S15F6488.S16F6488.S17F6488.S18F6488.S19F6488.S20F6488.S21F6488.S22F6488.S23F6488.S24F6488.S25F6488.S26F6488.S27F6488.S28F6488.S29F6488.S30F6488.S31F6488.S32F6488.S33F6488.S34F6488.S35F6488.S36F6488.S37F6488.S38F6488.S39F6488.S40F6488.S41F6488.S42F6488.S43F6488.S44F6488.S45F6488.S46F6488.S47F6488.S48F6488.S49F6488.S50F6488.S51F6488.S52F6488.S53F6488.S54F6488.S55F6488.S56F6488.S57F6488.S58F6488.S59F6488.S60F6488.S61F6488.S62F6488.S63F6488.S64F6488.S65F6488.S66F6488.S67F6488.S68F6488.S69F6488.S70F6488.S71F6488.S72F6488.S73F6488.S74F6488.S75F6488.S76F6488.S78F6488.S79
SP1Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter;cloacae00000000000000000000677000000000000000000000000000000000000000000000000000000000
SP103Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Roseburia;intestinalis00000000000000000000000000000000000000000000000000002621230037102451420331000014900013420200000137
SP104Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT346000000000000004603600890125058507322146027273166157017916503080150227031200222291205200340219000000000000000000000000000
SP105Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;eggerthii0000000000000000000000000000000000000000000000000000000041600030600000000000000000
SP106Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;sp. HMT180000575000000620002150000000059084000000025300177000000000061000000000000000000000000000000
SP107Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Holdemania;filiformis000000000000000000000000000000000000000000000000000005000541600000000000000000360
SP108Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;parainfluenzae5388000568135333723162330701200001271500004270000000099123000960000102268253371060210000021146000020900000526000000000
SP109Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidales_[F-2];Bacteroidales_[G-2];sp._Oral_Taxon_2740279600000100010001400748000013600043055371607315801261570000600340187000000000000000000000000000000
SP113Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Micrococcaceae;Rothia;aeria000000000279147001480000000000000000000006602500000000000000000000000000000000000000000
SP116Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Rothia;dentocariosa7938601700018618513524344448842437907441563034100000267000010000000000002706130701261720000000000000000000000000000000
SP117Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-1];[Eubacterium]_infirmum0000000000000000000000000114000760000000014500221000000000000000000000500000000000000
SP118Bacteria;Firmicutes;Bacilli;Lactobacillales;Aerococcaceae;Abiotrophia;defectiva0233013300027102245210900000000000127851000000634220087727003341180032102007300500000000000000000000000000000
SP119Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;fragilis00000000000000000000000000000000000000000000000000000000131000159014900028119000000115000
SP120Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Citrobacter;braakii00000000000000000000000000000000000000000000000000000000000001140000700000015600000
SP121Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;massiliensis0000000000000000000000000000000000000000000000000000000000032200108002610000003200000
SP124Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;periodonticum1700001751690688727145003800000029089000000000030410051000000000000000000000000000000000000000
SP125Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-6];[Eubacterium]_minutum0000000000000000001300000068000038000000013800002360000000000000000000000000000000000
SP126Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Butyrivibrio;crossotus0000000000000000000000000000000000000000000000000000000000000202258044001660011833213502271931850
SP127Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Senegalimassilia;anaerobia00000000000000000000000000000000000000000000000000000000000000015600000014380000970
SP130Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;oris0000000000000000000000000000000318000160000000000000000000000000000000000000000000
SP131Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Blautia;faecicola00000000000000000000000000000000000000000000000000012200880000000000000008532400001320
SP132Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT34900360000055000000001617200000310010411822616812800023274265622995403541241520016016357065000000000000000000000000000
SP133Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;sp. HMT17200000030800034500000000001330038042100000001820000261000000000000000000000000000000000000000
SP134Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT952000000000000000000000000000000058007619300000860000038000000000000000000000000000000
SP135Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Sutterellaceae;Sutterella;massiliensis00000000000000000000000000000000000000000000000000002267800000006800000029230003090000
SP136Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;elongata00000065000000000000002160860000007000274000000000000010510144000000000000000000000000000
SP137Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-2];Saccharibacteria_(TM7)_[G-5];bacterium HMT356000360000000340033150091160310691380443952304148390126195179547344491701901045441672911100000000000000000000000000000
SP138Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;onderdonkii0000000000000000000000000000000000000000000000000000000039129304028200000000000000000
SP139Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Bulleidia;extructa0000000000013000000000000000000000110090000006402600000000000000002000000000000000
SP140Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;thetaiotaomicron0000000000000000000000000000000000000000000000000000000001211170590000023400000000000
SP155Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcus;stomatis762722455014641520229114600191114187253140084343111018302630390473742964159251551523051871490501220732835579550127990130000000000000000000000000000
SP158Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Tannerellaceae;Tannerella;forsythia000000000000000000106130001115917506600460017300283236200161023907751210010000000000000000000000000000
SP159Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Lautropia;mirabilis0000002430011600000000000001030000000000000040000000000000000000000000000000000000000
SP160Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Holdemanella;biformis0000000000000000000000000000000000000000000000000000131000274000085255001300004600950000
SP163Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;salivae06400028700002260000000000000000000000000640000025003400177000000000000000000000000000000
SP164Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;caccae0000000000000000000000000000000000000000000000000001667801840153246000025718003700005202797400094
SP165Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;pittmaniae0000018600010200000000000000000000000000000000000000000000000000000000000000000000
SP168Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Gemella;morbillorum00000000037000000000000001238200000000000095320016900273000028000000000000000000000000000
SP169Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Alcaligenaceae;Sutterella;wadsworthensis000000000000000000000000000000000000000000000000000042001231820000000035100000001500480
SP170Bacteria;Fusobacteria;Fusobacteria;Fusobacteria_[O];Fusobacteria_[F];Fusobacteria_[G-1];sp._Oral_Taxon_A7100000000000000000000000000016800260090001700000000000000000000000000000000000000000
SP171Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-3];bacterium HMT35100163020917979280062144501030041130002297126800539565105284112785412712420823635422113334217448705005450482119154142352000000000000000000000000000
SP174Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Tannerella;sp. HMT286061037062000250003079000000000000001500001625000000000000000000000000000000000000000000
SP175Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Blautia;obeum0000000000000000000000000000000000000000000000000003100017416510200243000010700000120258000000
SP177Bacteria;Actinobacteria;Actinomycetia;Bifidobacteriales;Bifidobacteriaceae;Scardovia;inopinata00000000000000000000000000000000000000020000770000000000000000000000000000000000
SP178Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Spirochaetaceae;Treponema;denticola000000000000000000000008107003200000158210612147600013100780007000000000000000000000000000
SP179Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT32217401729600157111642202221131672000000214098034000200139500000060056600275001090000000000000000000000000000
SP180Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Phascolarctobacterium;sp._str._YIT120670000000000000000000000000000000000000000000000000000000000000000000000046900000277
SP181Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Atopobium;sp. HMT41600000000000000000000000000000000000000013300000000000000000000000000000000000000
SP182Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonellaceae_[G-1];bacterium HMT155000000000000000000000000205490073000038007702400508257032599649000000000000000000000000000000
SP183Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;histicola000000000014000012000000000000000000000000000043127045900000000000000000000000000000000
SP184Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;lactarius0001700000020000300062800500021540097000000000171520300000000000000000000000000000000
SP185Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Fusicatenibacter;saccharivorans00000000000000000000000000000000000000000000000000016818386321631323681851231930102080260170670011524766000194162
SP186Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-1];[Eubacterium]_sulci04528213710051037032525001081026160710000551001009401512930031592854405700561561583213982070260000000000000000000000000000
SP187Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;communis0000000000000000000000000000000000000000000000000008368000004605529000000000061550000
SP188Bacteria;Firmicutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;faucium00000000000000000036400550241014408306415251092650740113692916966036127051199335000000000000000000000000000
SP193Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Agathobaculum;butyriciproducens00000000000000000000000000000000000000000000000000086000991352447517027000069800000124060034000
SP201Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerotignum;faecicola0000000000000000000000000000000000000000000000000000800005400000000008400098000000
SP203Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Phocaeicola;massiliensis0000000000000000000000000000000000000000000000000000000000016100000251000000000000
SP204Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sp._Oral_Taxon_A480000005421000000000000000000000000000000000000000365902000000000000000000000000000
SP205Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F];Clostridiales_[G];sp._Oral_Taxon_G74000000000000000000014010016000000380005100440000191024008800000000000000000000000000000000
SP206Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;sinus00048028912903113092451060099000000077000030000009600008000010200850000000000000000000000000000000
SP207Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Barnesiellaceae;Barnesiella;intestinihominis0000000000000000000000000000000000000000000000000002451150355001270241029000000000016200690
SP208Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Megasphaera;elsdenii0000000000000000000000000000000000000000000000000000000000371000233000000000007135000
SP209Bacteria;Firmicutes;Clostridia;Clostridiales;Peptoniphilaceae;Peptoniphilaceae_[G-1];bacterium HMT113000000000000000000060000000000000000009800003340000000000000000000000000000000000
SP218Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-6];bacterium HMT87002100000000000000001700000014000000000000072347086000000000000000000000000000000000000
SP219Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroidaceae_[G-1];bacterium HMT27200000000000000000000000442500802189002800055002290710332525000000000000000000000000000000
SP221Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Klebsiella;pneumoniae000000000000000000000000000000000000000000000251000000000016100000000000002160000000
SP222Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;melaninogenica262921130019721513790209201194054350000380000000530000018420500000065251260312265206831350000000000000000000000000000
SP223Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT0850040000100006768000162270250001600192500034694501001027123342135020146500108766416015048000000000000000000000000000
SP224Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Odoribacteraceae;Odoribacter;splanchnicus00000000000000000000000000000000000000000000000000086886400001113174050002012027606800560013515
SP225Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae;Methanobrevibacter;smithii00000000000000000000000000000000000000000000000000000001030000013727033800030978139003160250000
SP226Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Sutterellaceae;Sutterella;faecalis00000000000000000000000000000000000000000000000000000000000000000001600064120000333
SP227Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Erysipelotrichaceae_[G-1];bacterium HMT905000000000000000170023270005400008773345200320520370000270026123230038000000000000000000000000000
SP229Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;denticola000003100000000000000000000000000000000000200000239089000000000000000000000000000000
SP23Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Gemella;sanguinis000010528113964358102219195238278171164193250000001250132017108700114020276000000199900000000000000000000000000000000000
SP230Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;pneumosintes00000020000000000000000005100000000000088003208901200000000000000000000000000000000
SP233Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;sp._str._SS2/100000000000000000000000000000000000000000000000000058000003820198000000000000000000
SP234Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT34501850424702297720440000163239000000083168015019450000041670167018336640400158008114000000000000000000000000000
SP236Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;concisus2900002241480031000000977000000000000300006101003360040040004035271900000000000000000000000000000
SP238Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Parabacteroides;distasonis0000000000000000000000000000000000000000000000000001364822250763601682964420000000011780016100056
SP239Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT443094000000000000000000000000017000000000000000000077000000000000000000000000000000
SP24Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;callidus00000000000000000000000000000000000000000000000000064035103400000013700000129185175323025801780233
SP240Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Parabacteroides;merdae00000000000000000000000000000000000000000000000000021810611100000212000003320361719006925502790
SP241Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;graevenitzii0460210489027006020470310000000000059000000013010305100000031301200000000000000000000000000000000
SP242Bacteria;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;orale0000001600000000000000000000067040000000038100000001070000000000000000000000000000000
SP243Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;putredinis000000000000000000000000000000000000000000000000000122389571390003482820000040000000113001240
SP248Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;endodontalis0094062000540095002000087140280021100017402971474301204439040409365000001942800000000000000000000000000000000
SP249Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonellaceae_[G-1];bacterium HMT135000000000000000022000000000000101000000000000000000000000000000000000000000000000
SP25Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Micrococcaceae;Rothia;mucilaginosa1810542222851498367214286269654246273492343576463547316391398445484191268247007385115738041537549017103109904654052663654852208717416919672000000000000000000040000000
SP250Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;sputigena000000111000000000003500000000110000000740012800276000000040000000000000000000000000000
SP251Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;dentium00000000000000000000000000110000000350000005806706600000000000000000000000000000000
SP252Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp. HMT285036100000000000000000009100039201760000000000273200000068284000000000000000000000000000000
SP254Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Mediterraneibacter;faecis000000000000000000000000000000000000000000000000000138000580000001038607900000920000384340
SP255Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Slackia;exigua000000000000001020000000000144000025002027035000525610961451280000000000000000000000000000000
SP256Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnoanaerobaculum;orale00000159780001630000000000000000000000000000000000000000000000000000000000000000000
SP258Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;sp. HMT13600000000000020600460000000000000000000000000000100000000000000000000000000000000000
SP259Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;rogosae0000000000000000000000000000000000000000000000000000160182032982270209333150161870175027002492732512262904901220190
SP26Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae_[XV];Eubacterium;rectale00000000000000000000000000000000000000000000000000000306015722824637450924707101421910012325159221972810780141
SP260Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT3650000000000000000000140000000400000000013780000005000000000000000000000000000000000
SP261Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-4];bacterium HMT355000000000000000000000001701202201613254440590210000000000021000000000000000000000000000000
SP262Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT28000000000000000000019000050000170220007000128553000540452508300000000000000000000000000000
SP263Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Romboutsia;timonensis0000000000000000000000000000000000000000000000000000131900221054901119687773090342237820000002546
SP266Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Coprococcus;eutactus000000000000000000000000000000000000000000000000000021700252960000360198631950025261368343760026401510
SP267Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Treponema;sp. HMT2370000000023000000000000000000000000122000072000000000900000000000000000000000000000
SP268Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;gingivalis149300490792242550720384010000000540870300000004957000000000380127000140000000000000000000000000000
SP269Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;champanellensis00000000000000000000000000000000000000000000000000000000000000110000000000000000
SP27Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri000000000000000000000000000000000000000000000000000001197014290000012846810651107106226648169399134398071358754761972
SP270Bacteria;Proteobacteria;Deltaproteobacteria;Desulfovibrionales;Desulfovibrionaceae;Bilophila;wadsworthia0000000000000000000000000000000000000000000000000004038101600219577310018590801574700007543001490
SP272Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3130310007000000000000000000460000000000000000000000004246000000000000000000000000000
SP273Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Dorea;formicigenerans0000000000000000000000000000000000000000000000000001687413100140070073370166536600005369494100630
SP274Bacteria;Firmicutes;Mollicutes;Mollicutes_[O-2];Mollicutes_[F-2];Mollicutes_[G-2];bacterium HMT90600000000000000000000300000027022380018000000000000180000000000000000000000000000000
SP275Bacteria;Firmicutes;Bacilli;Bacillales;Gemellaceae;Gemella;haemolysans19217520800972062910280012155000039035219605077020400005337924429101381144020493113366164023812704269920000000000000000000000000200
SP279Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Treponema;socranskii0000000000000002400000003904500003500756717001960010208900021000000000000000000000000000000
SP28Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Blautia;luti0000000000000000000000000000000000000000000000000001200003171351472034982700014088001760025106215700274110
SP280Bacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium;durum000008053612827136000001500018000274000003100002600000014800300000000000000000000000000000000
SP283Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Stomatobaculum;sp. HMT09729000010296290370790486519000002805402650002808001000000000000000000000000000000000000000000000
SP284Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonellaceae_[G-1];bacterium HMT12900000000000000000000000000000000000000105016003700290000000000000000000000000000000
SP288Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;shahii00000000000000000000000000000000000000000000000000012000000000007566000115000131960003930
SP29Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospira;eligens00000000000000000000000000000000000000000000000000003351425850341458265001630000281049550715912618316412714100
SP295Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;sp._SS3/40000000000000000000000000000000000000000000000000001570012075189276394008198012407800530145593901180112121
SP296Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Stomatobaculum;longum000007200001150000000000000000000000000000000000900000000000000000000000000000000
SP297Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Coprococcus;comes00000000000000000000000000000000000000000000000000014321519007118300285184101174199363111143291241274287154272075134400158
SP30Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;pallens0302001229311000020150004000000000000006000000000003813051701254100000000000000000000000000000
SP301Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;bromii0000000000000000000000000000000000000000000000000002551360179100002621520043853700000201000128001150
SP303Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Mitsuokella;jalaludinii000000000000000000000000000000000000000000000000000000000000001180195000000000015200
SP304Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT30400000000000000000000000000000250007000000000001521500670000000000000000000000000000
SP305Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Slackia;isoflavoniconvertens0000000000000000000000000000000000000000000000000000036000000003055000000021541800062
SP306Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides00000000000000000000000000000000000000000000000000000000000000000002010000000000
SP307Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Roseburia;inulinivorans000000000000000000000000000000000000000000000000000008416801970000029900016900040805300096496
SP308Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gingivalis00000000000000000000000350000026000016050000006211000000000000000000000000000000000
SP309Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Catenibacterium;mitsuokai0000000000000000000000000000000200000000000000000000026704490000002970779002192113852396210018012400
SP310Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT30500000000000000120000000000000000001000000049190002800000000000000000000000000000000
SP312Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;cardiffensis000000000000000000000000000000031000180910000000000000000000000000000000000000000
SP313Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;tannerae030000877009000000000000000000000000000050000000148483590160000000000000000000000000000
SP318Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Catonella;morbi058260023330000049000000100000019000000003501900800000382050000000000000000000000000000000
SP321Bacteria;Firmicutes;Firmicutes_[C];Firmicutes_[O];Firmicutes_[F];Firmicutes_[G];sp._Oral_Taxon_A55000000120000000490000000000009000000075809313028000013514074000000000000000000000000000
SP322Bacteria;Bacteroidetes;Bacteroides;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp._Oral_Taxon_B430000000000000000000000000000000000000000000000013500118000000000000000000000000000
SP323Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;leadbetteri0500000299000025200000027002608100000980232434000500000164010500154815000000000000000000000000000
SP325Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-4];bacterium HMT369002800000000000180009516022076252830125033133001264232422201526025003010110015000000000000000000000000000
SP326Bacteria;Firmicutes;Mollicutes;Mollicutes_[O-1];Mollicutes_[F-1];Mollicutes_[G-1];bacterium HMT5040000000000000000000701100017000000000040000000000000000000000000000000000000000000
SP327Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-5];[Eubacterium]_saphenum00000000000000650000220004900025001670087000005600000000000000000000000000000000000000
SP328Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Alloscardovia;omnicolens0000000000000021000000000000000000180000800107161001489800000000000000000000000000000000
SP329Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT874000000000000000000770030026000000002406700004100000316876000000000000000000000000000000
SP330Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Adlercreutzia;equolifaciens0000000000000000000000000000000000000000000000000003624001455000000000000000000000
SP332Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Treponema;sp. HMT257000000001000000000000000000000023000006000000005900000000000000000000000000000000
SP333Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3060000016500000000000000000000000000092000058000000000000000000000000000000000000000
SP334Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonella;parvula01590000000000000000000000000000000000000000000106720000000000000000000000000000000
SP338Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Eggerthella;sp._str._1356FAA00000000000000000000000000000000000000000000000000063000005100000000000000000000
SP339Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Eikenella;corrodens000201000000000000000001560000000000002710000000000000000000000000000000000000000000
SP340Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;stercoris000000000000000000000000000000000000000000000000000031800000215000000000000002350000
SP341Bacteria;Firmicutes;Negativicutes;Acidaminococcales;Acidaminococcaceae;Phascolarctobacterium;faecium0000000000000000000000000000000000000000000000000003150013601480000000000150010002880000
SP343Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;shahii0350001455000000000000000022000000000000000000000000000000000000000000000000000000
SP344Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3090000034000078000000000000000000000018000015300000030900000000000000000000000000000000
SP345Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Atopobiaceae;Olsenella;uli0000000000000000002100007000000000000004200001090000000000000000000000000000000000
SP349Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;clarus00000000000000000000000000000000000000000000000000000000000207000000000000000000
SP350Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Coprococcus;catus00000000000000000000000000000000000000000000000000015139360611590048144059297220000263004042122001840
SP351Bacteria;Lentisphaerae;Lentisphaeria;Victivallales;Victivallaceae;Victivallis;vadensis0000000000000000000000000000000000000000000000000000000000000042000000000003202660
SP352Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Ottowia;sp. HMT8940000000000000000000005500680000000026260000000000000000000000000000000000000000000
SP355Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Granulicatella;elegans157011400000033800000000000000000000019142800000087000074069002450000000000000000000000000000
SP356Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;hominis6000000000200280002503021033183400015010150910000110000160000000000000000000000000000000000
SP360Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT2060000000200321000000000000000000000000014000000000000000000000000000000000000000000
SP363Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae_[XV];Eubacterium;ramulus000000000000000000000000000000000000000000000000000042053008101703650000581170000000003460
SP366Bacteria;Proteobacteria;Deltaproteobacteria;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;piger000000000000000000000000000000000000000000000000000009200000000229000000005000240000
SP368Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;bifidum00000000000000000000000000000000000000000000000000000000024800000003191440000002270000
SP372Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Filifactor;alocis0000000000070000002400943000019440000270250000000000240000000000000000000000000000000
SP373Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;sp. HMT4780000059000000332239000000000016800000000000077000000000000000000000000000000000000000
SP375Bacteria;Firmicutes;Bacilli;Turicibacterales;Turicibacteraceae;Turicibacter;sanguinis0000000000000000000000000000000000000000000000000000000043000025011700000000000000
SP376Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;finegoldii00000000000000000000000000000000000000000000000000001060000000000000000000000000
SP378Bacteria;Actinobacteria;Actinobacteria;Propionibacteriales;Propionibacteriaceae;Propionibacterium;acidifaciens00000000000000000000000000000000054000055000000000000000000000000000000000000000
SP38Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;stercorea0000000000000000000000000000000000000000000000000000058300000000002480006725520000018200
SP380Bacteria;Firmicutes;Tissierellia;Tissierellales;Peptoniphilaceae;Peptoniphilus;koenoeneniae00000000000000000000000000000000000000000000000000000000000000012700000000000000
SP381Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Dialister;invisus000501300000000000000000000000007000000000000000930000005709528100000000000000030000
SP382Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Paraprevotella;xylaniphila000000000000000000000000000000000000000000000000000016134000000000000000000000000
SP383Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;succinatiphilus00000000000000000000000000000000000000000000000000000000002570000140037800000000000
SP384Bacteria;Saccharibacteria(TM7);TM7_[C];TM7_[O];TM7_[F];TM7_[G];sp._Oral_Taxon_A56450039047850014100000000000000960000022800000000000005011100000000000000000000000000000000
SP386Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae_[XV];Eubacterium;ventriosum000000000000000000000000000000000000000000000000000346129028000018719504200011200001720000700
SP387Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Megasphaera;massiliensis00000000000000000000000000000000000000000000000000000000000000000000000013200000
SP388Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;sp._str._L2_500000000000000000000000000000000000000000000000000001790263287111000000000000017926364870012500
SP39Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnospiraceae_[G-8];bacterium HMT50000000000000000000081002603657860560330003901900302000000000000000000000000000000000000000
SP390Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;viscosus00000000000000000000000000000000000000000349000000000000000000000000000000000000
SP392Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;argentoratense00000000000000000002352100000000000001320000143810010800000280000000000000000000000000000
SP393Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;faecis00000000000000000000000000000000000000000000000000000000015718500000000000010101260000
SP395Bacteria;Firmicutes;Tissierellia;Tissierellales;Peptoniphilaceae;Peptoniphilus;grossensis00000000000000000000000000000000000000000000000000000000000000037600000000000000
SP397Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Schaalia;turicensis00000000000000000000000000000000000000000000000000000000000000038300000000000000
SP40Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Massiliprevotella;massiliensis000000000000000000000000000000000000000000000000000000884000000980000042385101407407940436
SP400Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;finegoldii00000000000000000000000000000000000000000000000000018300000198002210000032800000000012312
SP401Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Parabacteroides;sp._str._D1300000000000000000000000000000000000000000000000000000000750122000164000012400070000000
SP403Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;muciniphila00000000000000000000000000000000000000000000000000016001560000141730041304004082910000345000225258
SP405Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Flavonifractor;plautii0000000000000000000000000000000000000000000000000000000002460271180000013000000000000
SP407Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Eubacterium;siraeum00000000000000000000000000000000000000000000000000002600000920002330710025500003623341141590
SP408Bacteria;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;salivarium022000000000000000000000001000000000000064000047037240000000000000000000000000000000
SP409Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sputigena102000000690924701420000000000000000000470000000000420239049000000000000000000000000000000
SP41Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Phocaeicola;vulgatus000000000000000000000000000000000000000000000000000399170200158019105612317280292002490022238101032173443700127
SP411Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT8750037006100000000000000000000000000021000016900000001310000000000000000000000000000000
SP412Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;gerencseriae000000000000000000000000180000004300000018200490200000000000000000000000000000000000
SP414Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT2150000015700004001503600000011700000001500001350000000000001380950000000000000000000000000000
SP419Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Sutterellaceae;Duodenibacillus;massiliensis0000000000000000000000000000000000000000000000000000014600000001844900007270131001130023700
SP42Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;xylanisolvens0000000000000000000000000000000000000000000000000000015000146040000000000000000000
SP422Bacteria;Firmicutes;Tissierellia;Tissierellales;Peptoniphilaceae;Anaerococcus;vaginalis00000000000000000000000000000000000000000000000000000000000000015300000000000000
SP423Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotellamassilia;timonensis0000000000000000000000000000000000000000000000000000000000000000243000000000014100
SP426Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Veillonella;atypica00000140000015400000000000001239500000000000000023402640208002200000000000000000000000000000
SP429Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-6];[Eubacterium]_nodatum00000000000140000000000015000200000000240000300009000000000000000000000000000000000
SP43Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;pasteri488240044303227143172714301332601691480370020300160142370195205890190000225000350011612549121651011601000000000000000000000000000000
SP434Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Atopobiaceae;Parolsenella;catena0000000000000000000000000000000000000000000000000000038000000000000000000390601800
SP435Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;noxia0005000001100000030000000660002800000630290167005070000000034000000000000000000000000000
SP436Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Caecibacter;massiliensis00000000000000000000000000000000000000000000000000000000000000000000000000010700
SP438Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT3470980000000000000000000000000000000000000000000000000000000000000000000000000000
SP439Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae_[XV];Eubacterium;hallii000000000000000000000000000000000000000000000000000000200515913845183201007498113004678531890890000
SP44Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Enterobacter;mori00000000000000000000804000000000000000000000000000000000000000000000000000000000
SP440Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT907000000000000000000000000000000000023000360005000001960000000000000000000000000000000
SP441Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Kingella;denitrificans00000000000000000097000000000000005000000000000000000000000000000000000000000000
SP458Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Veillonellaceae_[G-1];sp._Oral_Taxon_G40001000000000000000000022000000000000000002302480000520000000000000000000000000000000
SP459Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnospiraceae_[G-2];bacterium HMT096000000340009500000000000000490000000000000000000000000000000000000000000000000000
SP461Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;angulatum00000000000000000000000000000000000000000000000000000000000000000000000004080000
SP471Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;sp. HMT05600000000000000000000000000000000012000000000009000000000000000000000000000000000
SP472Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;chartatabidum0000000000000000000000000000000000000000000000000000000000000000000000910000000
SP473Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerotignum;lactatifermentans00000000000000000000000000000000000000000000000000000000000019700000000000000000
SP475Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;sp._Oral_Taxon_17100000000013700000000000000000000000000000000000000000000000000000000000000000000
SP476Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Limosilactobacillus;mucosae000000000000000000000000000000000000000000000000000000000000000000000000009614000
SP482Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oulorum0000000000000000000000000000000000000000000009600000000000000000000000000000000
SP485Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;mutans000000000000000000000000001700000010700009900860420000000000000000000000000000000000
SP486Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;salyersiae000000000000000000000000000000000000000000000000000000000000004000000000000002330
SP487Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Spirochaetaceae;Treponema;lecithinolyticum0000000005010000000000000000000000000130000000037870000000000000000000000000000000
SP488Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT4170000057420002210050000000000002000000000000000000000000000000000000000000000000000
SP494Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Treponema;amylovorum0000000000000000000000000400000000220000430000000003200000000000000000000000000000
SP495Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Treponema;sp. HMT258000000000000000000000000034011000005500000000000000000000000000000000000000000000
SP501Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oris00000000021000000000000000000000000000440000080013500000000000000000000000000000000
SP504Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-2];bacterium HMT350000000000000000006600000014300000000000000420000005957000000000000000000000000000000
SP505Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnospiraceae_[G-3];bacterium HMT100000000550000230000000003300000000000000003000000000000000000000000000000000000000
SP510Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Cryptobacterium;curtum000000000000000000000000000000180000000001969862800116000000000000000000000000000000
SP511Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;timonensis00000000000000000000000000000000000000000000000000024000000000077300000000000000
SP513Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;sp. HMT13700000000000000000000000000000000000000000110000000000000000000000000000000000000
SP519Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT29200000000000000000000000000000000000000000000071027000000000000000000000000000000
SP524Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Odoribacteraceae;Butyricimonas;faecihominis00000000000000000000000000000000000000000000000000000028000005800000000000000000
SP525Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT48800000000000000000000000023300000000000000000000000000000000000000000000000000000
SP528Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Veillonellaceae_[G-1];sp._Oral_Taxon_155000000000000000000000000960000000000000480000000260000000000000000000000000000000
SP529Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT3080000014303016940000000000000000000000000000000000000000000000000000000000000000000
SP53Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;prausnitzii00000000000000000000000000000000000000000000000000064910849321248744836401550997841626882579355285645007565541108865595616949522520775
SP530Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Megamonas;funiformis000000000000000000000000000000000000000000000000000017218000000000000000000000000
SP536Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Erysipelatoclostridium;[Clostridium] spiroforme000000000000000000000000000000000000000000000000000000000610043000006600000000000
SP537Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Tyzzerella;nexilis00000000000000000000000000000000000000000000000000000000000000307000000000000000
SP538Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;sp. HMT949000000000000000001600000000000000000000111000000000000000000000000000000000000000
SP539Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;lingnae_[Not_Validly_Published]0000000000009800000000000000000000000000000000000000000000000000000000000000000
SP544Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Coprococcus;pectinophilus00000000000000000000000000000000000000000000000000000000000000218000000000000000
SP545Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Eikenella;halliae00000000000000000000074000000000000000000000006900000000000000000000000000000000
SP549Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;sp. HMT4480000000000000000000000000120000019000000000135000000000000000000000000000000000000
SP55Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;sanguinis01220000130155945501032400000000012016000032001601819102701400790000000000000000000000000000000000
SP552Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;intermedia00000000000000000000004000000000000000000000037300030000000000000000000000000000
SP553Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Faecalimonas;umbilicata000000000000000000000000000000000000000000000000000000000112000000000000009200000
SP557Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Erysipelotrichaceae_[G-1];bacterium HMT90400000000000000000000000000000000000000146000000000000000000000000000000000000000
SP558Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Acidaminococcus;fermentans00000000000000000000000000000000000000000000000000000000000054500000008412300000000
SP56Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;subflava022901120000051001100000003100670001120000000004260004890002817422610427200000000000000000000000000000
SP560Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-8];bacterium HMT955053000000000000000000000000000031000000034000000000000000000000000000000000000000
SP562Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Murimonas;intestini00000000000000000000000000000000000000000000000000000000000000125000000000000000
SP565Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Parabacteroides;johnsonii000000000000000000000000000000000000000000000000000000210037400000000000000000000
SP572Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;timonensis00000000000000000000000000000000000326000000000000000000000000000000000000000000
SP573Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Blautia;stercoris00000000000000000000000000000000000000000000000000000000000000000000000000002770
SP580Bacteria;Proteobacteria;Deltaproteobacteria;Desulfobacterales;Desulfobulbaceae;Desulfobulbus;sp. HMT04100000000000000000000000000006000061000050000000000000000000000000000000000000000
SP582Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;medium00000000000000000000000000000000012800000000000000000000000000000000000000000000
SP584Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;nanceiensis000005211000290000000000000000000000000000000000000000000000000000000000000000000
SP589Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Mitsuokella;multacida0000000000000000000000000000000000000000000000000000000000000019600000000000023000
SP59Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;anginosus0000078410000000157011700010800000001610000142000007017021602500290316000188000000000000000000000000000
SP591Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Erysipelatoclostridium;ramosum0000000000000000000000000000000000000000000000000000000000000000000000008600000
SP592Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonellaceae_[G-1];bacterium HMT14500000000000000000000000005400041000000000000000000000000000000000000000000000000
SP593Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Atopobiaceae;Parafannyhessea;umbonata0000000000000000000000000000000000000000000000000000000000000015600000000000019800
SP596Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-5];bacterium HMT4930000000000000000000000000000000000000092000000000000000000000000000000000000000
SP597Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;disiens00000000000000000000000000000000000000000000000000000000000000112000000000000000
SP599Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sp. HMT33200000000011800000000000000000000000000000000000000000000000000000000000000000000
SP60Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-1];bacterium HMT075006310323933542730118512606227200112411122711805119725711717401692512483222041813418001011978924700288164284174356249128000000000000000000000000000
SP600Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;intestinalis00000000000000000000000000000000000000000000000000000000000000000000000000002290
SP603Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidales_[F-2];Bacteroidales_[G-2];bacterium HMT2740000000000000000000200000022000000000000000340000700000000000000000000000000000000
SP604Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Coprobacillaceae;Coprobacillus;cateniformis000000000000000000000000000000000000000000000000000000000000000910000013039000000
SP63Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;sinensis00041000000000006400065300142000040020000000000232100109000014000000000000000000000000000
SP630Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;unclassified_Ruminococcaceae;sp._str._D160000000000000000000000000000000000000000000000000000000000880000000000000000000
SP631Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XIII. Incertae Sedis;Casaltella;massiliensis000000000000000000000000000000000000000000000000000000000000002927200000000000000
SP634Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Odoribacteraceae;Butyricimonas;virosa00000000000000000000000000000000000000000000000000000000000000000000000000001450
SP639Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;nigrescens0000000000000000000000087000000000000000000000212370000000000000000000000000000000
SP642Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Eggerthella;lenta00000000000000000000000000000000000000000000000000000000000017800000000000000000
SP655Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Leptotrichiaceae;Leptotrichia;buccalis0000000008900000000000000000000000000000000000000000000000000000000000000000000
SP657Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Intestinibacillus;massiliensis00000000000000000000000000000000000000000000000000000155000000000000000000000000
SP658Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Anaerotruncus;colihominis00000000000000000000000000000000000000000000000000000000010000000000000000000000
SP66Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-9];[Eubacterium]_brachy000000000005900340000000020901623128140360021339617254375481964615703270270110000000000000000000000000000
SP663Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;flavefaciens000000000000000000000000000000000000000000000000000000000000000000000920000001360
SP664Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;sp. HMT458000008700024000000000000000000000000000000000000000000000000000000000000000000000
SP666Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes00000000000000000000000000000000000000000000000000000000000000108000000000000000
SP67Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;ovatus000000000000000000000000000000000000000000000000000002500000000580000051420000000156
SP677Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcus;anaerobius0000000000000000000000000000000000000000000000000000000000000008900000000000000
SP68Bacteria;Firmicutes;Tissierellia;Tissierellales;Peptoniphilaceae;Parvimonas;micra000001000000000000000000116011342000250001980002410001282330191028901170038000000000000000000000000000
SP70Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT352384304217257191399321338207023027822822424501253280292044300476351219364476288643216083143403221276283581113981642803273954112750235240000000000000000000000000000
SP75Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Schaalia;odontolytica000009400005000000000000000001830660000001360000028800000000000000000000000000000000000
SP76Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;odontolyticus000002920000000000790000000000000000000000072800002970001870000000000000000000000000000
SP77Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Dorea;longicatena00000000000000000000000000000000000000000000000000012618765811470961163102810215314135103053336289181194325158900261159
SP78Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Subdoligranulum;variabile0000000000000000000000000000000000000000000000000001762463941932013502243502092522442482452143540004841752500450120184174272
SP79Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Collinsella;aerofaciens00000000000000000000000000000000000000000000000000001401440873540142000129408127248940421692729310314912117638138
SP80Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Barnesiellaceae;Coprobacter;fastidiosus000000000000000000000000000000000000000000000000000000000003800000000000370490000
SP81Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Solobacterium;moorei0283113258962202231350275216956175358055054177028010953545245023735128245803214731133894440524339758624956510031327034131135129000000000003519300000000000000
SP82Bacteria;Gracilibacteria_(GN02);Gracilibacteria_(GN02)_[C-1];Gracilibacteria_(GN02)_[O-1];Gracilibacteria_(GN02)_[F-1];Gracilibacteria_(GN02)_[G-1];bacterium HMT8720000000000000000052600320002200000700430003800000001312000000000000000000000000000000
SP83Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp. HMT2780000000000000000000000000000000003200000001230813510002004180000000000000000000000000000
SP85Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT348000000000000000000000000000000000028000011304400490013164029000000000000000000000000000
SP86Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Blautia;faecis00000000000000000000000000000000000000000000000000026320904951600307162693660434011902026600356012123162052295
SP89Bacteria;Gracilibacteria_(GN02);Gracilibacteria_(GN02)_[C-2];Gracilibacteria_(GN02)_[O-2];Gracilibacteria_(GN02)_[F-2];Gracilibacteria_(GN02)_[G-2];bacterium HMT873000000001915000000035000000754500004389156526533000289000049879777000000000000000000000000000000
SP92Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Paraprevotella;clara0000000000000000000000000000000000000000000000000000000000124000000790371932136580000730
SP93Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;longum00000000000000000000000000000000000000002490000000300000299000553102940013702471100091000740000
SP97Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Roseburia;hominis00000000000000000000000000000000000000000000000000000000000000104000001071150000001770
SP98Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;thermophilus00000000000000000000000000000000000000000000000000019301330031179670611790000530008200570047114
SPN1Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Kiloniellaceae;Kiloniella;Kiliella laminaria_nov_87.416%00000000000000000000000000000000000000000000000000000000000000000000000000001910
SPN10Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_88.367%000000000000000000000000000000000000000000000000000000000000007200006400004200000
SPN100Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Breznakia;pachnodae_nov_87.821%0000000000000000000000000000000000000000000000000000000000000089000000000000000
SPN101Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;xylanophilum_nov_97.727%0000000000000000000000000000000000000000000000000000000000000088000000000000000
SPN102Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;champanellensis_nov_95.928%0000000000000000000000000000000000000000000000000000000000000000000000000084000
SPN106Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Alkalibaculum;bacchi_nov_83.108%0000000000000000000000000000000000000000000000000000015800000000000000002180000000
SPN109Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Acetanaerobacterium;elongatum_nov_92.081%00000000000000000000000000000000000000000000000000014000000000002860000288001140490019201240
SPN11Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_94.369%000000000000000000000000000000000000000000000000000000000000006000000000003440000
SPN116Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerocolumna;cellulosilytica_nov_96.833%00000000000000000000000000000000000000000000000000000000000003740000000000000000
SPN119Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_94.144%000000000000000000000000000000000000000000000000000271179203141000016202581952075200533000152328235737155324147
SPN12Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Agathobaculum;desmolans_nov_97.279%000000000000000000000000000000000000000000000000000054000000000000000006656000000
SPN120Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Oscillibacter;valericigenes_nov_94.344%000000000000000000000000000000000000000000000000000140136640620000002200000104403988193580585728078
SPN126Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Erysipelotrichaceae_[G-1];bacterium HMT905 nov_92.625%000000000000000000000000000000000000000000000000000000018500000530000000000530030051
SPN129Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_93.946%00000000000000000000000000000000000000000000000000000122002670000012647500000027921249007600
SPN13Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-2];bacterium HMT402 nov_92.777%00000000000000000000000000000000000000000000000000000000000000000009300008200000
SPN134Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_91.011%00000000000000000000000000000000000000000000000000000000000000015000002200000001950
SPN14Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;unclassified_Ruminococcaceae;sp._str._D16_nov_89.414%00000000000000000000000000000000000000000000000000000000000001736000016000120000920
SPN140Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;stercorea_nov_97.403%000000000000000000000000000000000000000000000000000000023900000548002880054000000046600
SPN144Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;callidus_nov_94.369%000000000000000000000000000000000000000000000000000018304941300001740600015000023423603203310006764
SPN149Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_97.059%000000000000000000000000000000000000000000000000000000990143000016003550015600000127025102950
SPN15Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Spirochaetaceae;Treponema;denticola_nov_90.000%0000000000030000000000000270000432000000770000000300000000000000000000000000000000
SPN152Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnobacterium;bovis_nov_95.711%000000000000000000000000000000000000000000000000000041000000000850000000051170001640
SPN16Bacteria;Proteobacteria;Gammaproteobacteria;Aeromonadales;Succinivibrionaceae;Succinivibrio;dextrinosolvens_nov_96.372%00000000000000000000000000000000000000000000000000000000000000000000000000017300
SPN161Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Mediterranea;massiliensis_nov_92.641%0000000000000000000000000000000000000000000000000000064000000011000000000000002810
SPN17Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_97.732%00000000000000000000000000000000000000000000000000000000000000017300000000000000
SPN170Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides_nov_96.825%000000000000000000000000000000000000000000000000000043065590120024400000002520001360082003388
SPN172Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Tyzzerella;[Clostridium] colinum_nov_95.955%000000000000000000000000000000000000000000000000000000001800180115000004200000000000
SPN18Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Anaeromassilibacillus;senegalensis_nov_88.435%000000000000000000000000000000000000000000000000000000000000000000000000390001310
SPN182Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;prausnitzii_nov_97.964%000000000000000000000000000000000000000000000000000031331632914702640001380775406812681039053001820
SPN183Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;sp._str._SS2/1_nov_96.364%000000000000000000000000000000000000000000000000000400000730047600000000004000000940
SPN19Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides_nov_95.918%0000000000000000000000000000000000000000000000000000000000000000000580002680000760
SPN192Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_93.034%000000000000000000000000000000000000000000000000000069000000000000000000000002830
SPN193Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-2];bacterium HMT402 nov_89.038%000000000000000000000000000000000000000000000000000312625139185600001295244052007139592619713130111803180
SPN194Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_93.919%0000000000000000000000000000000000000000000000000002717415501520000000000001290161065199002000
SPN2Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;rava_nov_92.857%00000000000000000000000000000000000000000000000000000439000000018500000232109158030429700401850
SPN20Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Saccharofermentans;acetigenes_nov_89.462%00000000000000000000000000000000000000000000000000000000000000169000000000000000
SPN203Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminoclostridium;leptum_nov_95.011%00000000000000000000000000000000000000000000000000015413000490006900002027000000000200
SPN205Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospira;pectinoschiza_nov_96.372%0000000000000000000000000000000000000000000000000002987601920195281000022400000000001370000
SPN21Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Parasporobacterium;paucivorans_nov_95.455%00000000000000000000000000000000000000000000000000000000016700000000000000000000
SPN213Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Flavonifractor;plautii_nov_95.711%0000000000000000000000000000000000000000000000000000019000000001500002628000051000770
SPN216Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri_nov_97.397%0000000000000000000000000000000000000000000000000000017402000000407402420000029800002840213
SPN22Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_93.243%00000000000000000000000000000000000000000000000000000000000000000000009800000690
SPN222Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Anaerobacterium;chartisolvens_nov_89.462%00000000000000000000000000000000000000000000000000000000000000000003500000000000
SPN226Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospira;eligens_nov_94.785%0000000000000000000000000000000000000000000000000000165027704922051152954001621350156025438130022702361220028377
SPN23Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;unclassified_Ruminococcaceae;sp._str._D16_nov_93.243%00000000000000000000000000000000000000000000000000011610818701410006807539107600002950601510140881390
SPN236Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;ruminantium_nov_97.279%0000000000000000000000000000000000000000000000000001270152000000001410750014000101270002320311
SPN24Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_95.270%000000000000000000000000000000000000000000000000000054000000000000000000000011100
SPN241Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;hongkongensis_nov_87.220%0000000000000000000000000000000000000000000000000000000000000004100021600000090000
SPN246Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Butyrivibrio;sp. HMT090 nov_92.795%00000000000000000000000000000000000000000000000000000001250000026325000003532840000016700
SPN249Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_90.562%000000000000000000000000000000000000000000000000000406015900000000128000017400305485001710420103
SPN25Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_93.905%00000000000000000000000000000000000000000000000000000000164000000000000000000000
SPN255Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Paraprevotella;clara_nov_97.609%000000000000000000000000000000000000000000000000000730000202032400000000000300000003010
SPN257Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Adlercreutzia;muris_nov_94.796%00000000000000000000000000000000000000000000000000000000000000252580000003702500000
SPN26Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_94.369%00000000000000000000000000000000000000000000000000000000669600000000000000000000
SPN264Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;colorans_nov_93.492%000000000000000000000000000000000000000000000000000000044600000412000000000000031500
SPN266Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-2];bacterium HMT402 nov_91.216%000000000000000000000000000000000000000000000000000000000000000000000000307033000
SPN27Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;succinatiphilus_nov_95.931%0000000000000000000000000000000000000000000000000000038000000002000000000000082210
SPN275Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_93.243%00000000000000000000000000000000000000000000000000049100000002080000000000001091900010251
SPN276Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri_nov_97.831%0000000000000000000000000000000000000000000000000000000380000077402210200250360006046
SPN28Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Anaerovibrio;lipolyticus_nov_93.548%00000000000000000000000000000000000000000000000000000000000000161000000000000000
SPN287Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_92.793%000000000000000000000000000000000000000000000000000000000000048000004300000143001010
SPN288Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri_nov_97.835%00000000000000000000001400000000000000000000000000000023014000003039054104072155063025012055
SPN289Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;massiliensis_nov_90.766%0000000000000000000000000000000000000000000000000000000000000322190000430000024300161850
SPN29Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT396 nov_97.614%0135000000000000000000000000018000000004901000000000098000000000000000000000000000000
SPN299Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Acetivibrio;ethanolgignens_nov_95.909%0000000000000000000000000000000000000000000000000000000000000000000015318100000000
SPN3Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_88.814%000000000000000000000000000000000000000000000000000000180000000000008000000000920
SPN30Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Fusicatenibacter;saccharivorans_nov_96.599%00000000000000000000000000000000000000000000000000000000000000830000000077000000
SPN301Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Acutalibacter;muris_nov_96.599%00000000000000000000000000000000000000000000000000089000000000212119700038007517456601602590
SPN31Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;bromii_nov_95.475%00000000000000000000000000000000000000000000000000000000000000000000000159000000
SPN310Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnospiraceae_[G-7];bacterium HMT086 nov_96.364%000000000000000000000000000000000000000000000000000000452300000038843600000212931018000
SPN319Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotellamassilia;timonensis_nov_95.217%00000000000000000000000000000000000000000000000000000000000003200000000000000000
SPN32Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_89.438%00000000000000000000000000000000000000000000000000000000000000000006000000000990
SPN322Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotellamassilia;timonensis_nov_97.397%0000000000000000000000000000000000000000000000000000000000000000000070734200000000
SPN329Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XIII. Incertae Sedis;Ihubacter;massiliensis_nov_93.002%00000000000000000000000000000000000000000000000000000000000000030700000700000000
SPN33Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_89.414%00000000000000000000000000000000000000000000000000067000000000000000000000000900
SPN334Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_92.777%00000000000000000000000000000000000000000000000000000644218500037802013911030002011081413090382240139230319226
SPN335Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides_nov_96.614%000000000000000000000000000000000000000000000000000000000000008500001361071230117039106700
SPN339Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides_nov_96.818%00000000000000000000000000000000000000000000000000010500001190890000000000000000000
SPN34Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerotignum;faecicola_nov_95.291%00000000000000000000000000000000000000000000000000000000000015700000000000000000
SPN346Bacteria;Tenericutes;Mollicutes;Anaeroplasmatales;Anaeroplasmataceae;Asteroleplasma;anaerobium_nov_80.300%000000000000000000000000000000000000000000000000000000019200000012000019720805100083152000
SPN348Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_91.667%00000000000000000000000000000000000000000000000000000000000000000003130000000000
SPN35Bacteria;Proteobacteria;Gammaproteobacteria;Aeromonadales;Succinivibrionaceae;Succinivibrio;dextrinosolvens_nov_97.079%0000000000000000000000000000000000000000000000000000000000000380000002131782480111005647000
SPN358Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_95.711%000000000000000000000000000000000000000000000000000165017831013300002232120000065138229237100010739136073
SPN36Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminoclostridium;methylpentosum_nov_93.483%00000000000000000000000000000000000000000000000000041000151900045000035000000000000
SPN366Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oralis_nov_92.641%000000000000000000000000000000000000000000000000000000072000002021210406000000090016700
SPN368Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;albus_nov_93.651%00000000000000000000000000000000000000000000000000000000000000000003040000000000
SPN37Bacteria;Proteobacteria;Gammaproteobacteria;Aeromonadales;Succinivibrionaceae;Succinivibrio;dextrinosolvens_nov_96.622%000000000000000000000000000000000000000000000000000000000000070000011100000037000
SPN377Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;succinatiphilus_nov_96.567%00000000000000000000000000000000000000000000000000000001470207031730400000000000000000
SPN378Bacteria;Firmicutes;Negativicutes;Acidaminococcales;Acidaminococcaceae;Phascolarctobacterium;faecium_nov_93.133%00000000000000000000000000000000000000000000000000003030000000000000000000000000
SPN38Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Roseburia;inulinivorans_nov_97.517%00000000000000000000000000000000000000000000000000000000000000000000000155000000
SPN388Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_90.807%00000000000000000000000000000000000000000000000000000630118240098000000000000000000
SPN389Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT349 nov_97.964%0000000000000000000000005200000011000000000019700000014400000000000000000000000000000
SPN39Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Muribaculaceae;Duncaniella;freteri_nov_87.069%00000000000000000000000000000000000000000000000000000266000041500590096003395599038548802900289
SPN390Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri_nov_96.537%00000000000000000000000000000000000000000000000000000003190000016413300000000000035400
SPN398Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT488 nov_97.743%074000000000000000000000000000000000000000000022800000000000000000000000000000000
SPN399Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_93.049%000000000000000000000000000000000000000000000000000101000000000762030000110000006819702080
SPN4Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;chartatabidum_nov_97.959%00000000000000000000000000000000000000000000000000000000000000000000001890000000
SPN40Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;massiliensis_nov_87.810%00000000000000000000000000000000000000000000000000000000000000000001550000000000
SPN408Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Novispirillum;itersonii_nov_87.865%000000000000000000000000000000000000000000000000000000226000000000000000000000660
SPN409Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_91.422%000000000000000000000000000000000000000000000000000000017800000134731820002120014300000035
SPN41Bacteria;Firmicutes;Firmicutes_[C];Firmicutes_[O];Firmicutes_[F];Firmicutes_[G];sp._Oral_Taxon_A55_nov_87.607%000000000000000000000000000000000000000000000000000000000000000000000000013500190
SPN415Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;massiliensis_nov_88.143%00000000000000000000000000000000000000000000000000000007300000430000049000000240990
SPN418Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcus;bromii_nov_97.528%00000000000000000000000000000000000000000000000000000000000000008000000165713310253000
SPN42Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Sutterellaceae;Duodenibacillus;massiliensis_nov_95.085%0000000000000000000000000000000000000000000000000000000220000000019008300000027000
SPN424Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Geosporobacter;ferrireducens_nov_88.764%000000000000000000000000000000000000000000000000000920000000000000000000000001900
SPN427Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT907 nov_97.397%0000000000000000000007800000000500359000000000000003810027000000000000000000000000000
SPN43Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XIII. Incertae Sedis;Ihubacter;massiliensis_nov_95.011%0000000000000000000000000000000000000000000000000000000000000020560002300000000510
SPN432Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_91.480%000000000000000000000000000000000000000000000000000000000000040000002360000000000
SPN436Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Dialister;succinatiphilus_nov_96.360%00000000000000000000000000000000000000000000000000000129000000031925402423290203332198331033905502251620
SPN44Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminoclostridium;leptum_nov_92.135%00000000000000000000000000000000000000000000000000000000000000000000000000001500
SPN441Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;champanellensis_nov_94.104%00000000000000000000000000000000000000000000000000000000000000000000000000002750
SPN444Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_95.701%000000000000000000000000000000000000000000000000000620000716490221286000000000000000041
SPN45Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT346 nov_97.968%00560000003700000000043000460006900022011232302850460107116800012101920214000000000000000000000000000
SPN455Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri_nov_96.963%0000000000000000000000000000000000000000000000000000000800000025900256000000000027200
SPN46Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oris_nov_90.043%00000000000000000000000000000000000000000000000000000000000008700000000000006200
SPN462Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Fusicatenibacter;saccharivorans_nov_97.279%000000000000000000000000000000000000000000000000000206376009679054502840239000006155151168000000
SPN467Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-3];bacterium HMT351 nov_97.072%00980000000000720000000000099000000000000650000002602640000000000000000000000000000000
SPN47Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_92.325%000000000000000000000000000000000000000000000000000000000000000000000000119027000
SPN472Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_89.485%00000000000000000000000000000000000000000000000000000000000000000000000000002690
SPN477Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT899 nov_93.290%0000000000000000000000000000000000000000000000000000000000000623230000397003100019000
SPN48Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;stercorea_nov_97.831%000000000000000000000000000000000000000000000000000000000000000000005328000006200
SPN486Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Parabacteroides;sp._str._D13_nov_91.323%000000000000000000000000000000000000000000000000000000000000024000000059108000020618700
SPN489Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_92.809%00000000000000000000000000000000000000000000000000000000000000000000000026800000
SPN49Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;unclassified_Ruminococcaceae;sp._str._D16_nov_95.495%00000000000000000000000000000000000000000000000000000000970000063005900181403000007442
SPN498Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;champanellensis_nov_95.692%000000000000000000000000000000000000000000000000000000000000000000000020300000630
SPN5Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Faecalibacterium;prausnitzii_nov_96.825%000000000000000000000000000000000000000000000000000000165190004000000000000000000
SPN50Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-1];bacterium HMT093 nov_90.991%000000000000000000000000000000000000000000000000000000000000000000013000000129000
SPN506Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_92.308%00000000000000000000000000000000000000000000000000000000000001813800000000030102241400
SPN508Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_90.337%00000000000000000000000000000000000000000000000000000000000002720000043011021001901240
SPN51Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT281 nov_89.009%00000000000000000000000000000000000000000000000000000007500000000000000000006200
SPN516Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_90.766%00000000000000000000000000000000000000000000000000000000000002588483000073880016700000
SPN517Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_92.135%0000000000000000000000000000000000000000000000000001810000000000047000034000000000
SPN52Bacteria;Lentisphaerae;Oligosphaeria;Oligosphaerales;Oligosphaeraceae;Oligosphaera;ethanolica_nov_91.196%00000000000000000000000000000000000000000000000000000000000000000000000000013600
SPN525Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_93.243%0000000000000000000000000000000000000000000000000001197100780000000000000013100142002000
SPN526Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_94.157%00000000000000000000000000000000000000000000000000000000000000000000000001054901070
SPN53Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Butyricicoccus;pullicaecorum_nov_85.078%00000000000000000000000000000000000000000000000000000000000004500000000000050850
SPN536Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lacrimispora;xylanolytica_nov_97.285%00000000000000000000000000000000000000000000000000043175548081113102016903091100345005216518744301425203442080
SPN537Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT304 nov_92.174%00000000000000000000000000000000000000000000000000000000000000000000000000025700
SPN538Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oris_nov_92.657%000000000000000000000000000000000000000000000000000000016500000398000000000000017700
SPN54Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_91.011%00000000000000000000000000000000000000000000000000000000000000000000000000131000
SPN545Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Butyrivibrio;crossotus_nov_96.591%0000000000000000000000000000000000000000000000000000000000000166137000000001271780128000
SPN546Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruthenibacterium;lactatiformans_nov_90.562%000000000000000000000000000000000000000000000000000000000000059370300001631820000000
SPN55Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-2];bacterium HMT402 nov_91.011%00000000000000000000000000000000000000000000000000021211000000000053000029300244002967004610
SPN556Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;shahii_nov_91.991%00000000000000000000000000000000000000000000000000000002400000025300000317100420481510107
SPN557Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Parabacteroides;merdae_nov_97.397%000000000000000000000000000000000000000000000000000000000000000000000049201000000
SPN56Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_87.416%0000000000000000000000000000000000000000000000000000000000000020000000011030000640
SPN567Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Monoglobus;pectinilyticus_nov_90.112%000000000000000000000000000000000000000000000000000899748227027102371971120000183270791400002953405516
SPN568Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;unclassified_Ruminococcaceae;sp._str._D16_nov_93.018%0000000000000000000000000000000000000000000000000009300000000008500000000088278001820
SPN57Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_94.157%0000000000000000000000000000000000000000000000000000000000000002000009600000000990
SPN575Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Mitsuokella;jalaludinii_nov_96.368%0000000000000000000000000000000000000000000000000000000000000981160000000000003300
SPN576Bacteria;Firmicutes;Clostridia;Clostridiales;Veillonellaceae;Acidaminococcus;fermentans_nov_97.425%00000000000000000000000000000000000000000000000000000000000000000000000000043900
SPN58Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Enterocloster;asparagiformis_nov_96.372%00000000000000000000000000000000000000000000000000006500000000000000005900000000
SPN584Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Breznakia;pachnodae_nov_85.684%000000000000000000000000000000000000000000000000000000000000030000054000000001900
SPN586Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_91.236%0000000000000000000000000000000000000000000000000000000000000010784000212000000002820
SPN59Bacteria;Actinobacteria;Actinomycetia;Kineosporiales;Kineosporiaceae;Angustibacter;luteus_nov_84.633%00000000000000000000000000000000000000000000000000070011100000000000000000000000
SPN593Bacteria;Lentisphaerae;Lentisphaeria;Victivallales;Victivallaceae;Victivallis;vadensis_nov_84.719%00000000000000000000000000000000000000000000000000000000000000000000000000000243
SPN6Bacteria;Tenericutes;Mollicutes;Anaeroplasmatales;Anaeroplasmataceae;Anaeroplasma;bactoclasticum_nov_88.326%000000000000000000000000000000000000000000000000000000000000000000052000000001350
SPN60Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminiclostridium;cellulolyticum_nov_93.243%000000000000000000000000000000000000000000000000000001500000000101000000000000000
SPN600Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_91.704%0000000000000000000000000000000000000000000000000000103000000000000000000000139000
SPN603Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;massiliensis_nov_89.189%00000000000000000000000000000000000000000000000000000000000000800000110000010803100630
SPN608Bacteria;Lentisphaerae;Lentisphaeria;Victivallales;Victivallaceae;Victivallis;vadensis_nov_85.393%00000000000000000000000000000000000000000000000000000000000000000002410000000000
SPN609Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;xylanophilum_nov_97.045%000000000000000000000000000000000000000000000000000387680122000000000008900000000000
SPN61Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Blautia;schinkii_nov_97.506%00000000000000000000000000000000000000000000000000000000000000071000000000000450
SPN610Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Erysipelatoclostridium;[Clostridium] spiroforme_nov_93.333%000000000000000000000000000000000000000000000000000262130131230257501059029400588236700002521601120024775
SPN611Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_90.090%000000000000000000000000000000000000000000000000000000000000000000024500000070233150
SPN612Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Acetanaerobacterium;elongatum_nov_92.081%00000000000000000000000000000000000000000000000000013407605100000000000053550410013210500
SPN613Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Blautia;obeum_nov_97.727%0000000000000000000000000000000000000000000000000000000000000790113000000000243002050
SPN614Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-7];bacterium HMT911 nov_90.652%0000000000000000000000000000000000000000000000000000000000000220000000160210000004600
SPN615Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-3];bacterium HMT351 nov_97.748%00000000000000000000000620000000000000033400000002260000000000000000000000000000000
SPN616Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospira;pectinoschiza_nov_97.727%00000000000000000000000000000000000000000000000000000000149000188000690123000092000000
SPN617Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Subdoligranulum;variabile_nov_97.964%00000000000000000000000000000000000000000000000000023028820068092696000710006800026001020
SPN618Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnoclostridium;pacaense_nov_97.279%000000000000000000000000000000000000000000000000000000000000000000168000000000071
SPN619Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Geosporobacter;ferrireducens_nov_88.170%000000000000000000000000000000000000000000000000000000000000006000001760000730002870
SPN62Bacteria;Firmicutes;Firmicutes_[C];Firmicutes_[O];Firmicutes_[F];Firmicutes_[G];sp._Oral_Taxon_A55_nov_85.439%00000000000000000000000000000000000000000000000000000190000000000000013260470010000
SPN620Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oris_nov_90.043%000000000000000000000000000000000000000000000000000000000000002272000017317800000000
SPN621Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnoclostridium;pacaense_nov_96.145%00000000000000000000000000000000000000000000000000013607916603152601171883060001481082017700100006200108416
SPN622Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Treponema;sp. HMT927 nov_95.484%000000000000000000130000900010300640013300009400000015700000000000000000000000000000000
SPN623Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;tannerae_nov_87.366%0000000000000000000000000000000000000000000000000000000000000951210000042380066906337011
SPN624Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella;boevrei_nov_94.647%0000000000000000000000000000000000000000000000002160340000000000000000000000000000
SPN625Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-3];bacterium HMT351 nov_95.067%0000000000000000000000000001530000000000000033000260000102000000000000000000000000000
SPN626Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Megamonas;funiformis_nov_97.854%0000000000000000000000000000000000000000000000000000018000000000000366000000000000
SPN627Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;maculosa_nov_89.633%00000000000000000000000000000000000000000000000000005440000000000000000000000000
SPN628Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerostipes;butyraticus_nov_96.380%0000000000000000000000000000000000000000000000000000000000000010500000000133000000
SPN629Bacteria;Proteobacteria;Deltaproteobacteria;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;sp. HMT040 nov_92.918%0000000000000000000000000000000000000000000000000000000000108001020000003549115000059060
SPN63Bacteria;Lentisphaerae;Lentisphaeria;Victivallales;Victivallaceae;Victivallis;vadensis_nov_84.163%00000000000000000000000000000000000000000000000000000000000000000008700002800000
SPN630Bacteria;Firmicutes;Firmicutes_[C];Firmicutes_[O];Firmicutes_[F];Firmicutes_[G];sp._Oral_Taxon_A55_nov_88.651%000000200000000600001300000720560200300000480711020000007600110000000000000000000000000000
SPN631Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;sp. HMT018 nov_97.645%0000000000000000012639500000000000000000000000000000000000000000000000000000000000
SPN632Bacteria;Elusimicrobia;Elusimicrobia;Elusimicrobiales;Elusimicrobiaceae;Elusimicrobium;minutum_nov_95.740%00000000000000000000000000000000000000000000000000000000000000112023001030000000000
SPN633Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides_nov_97.959%000000000000000000000000000000000000000000000000000000000000000000018900048000000
SPN634Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;species5_nov_87.234%006404000000014900053000000000021002200000409000000000000000000000000000000000000000
SPN635Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_92.584%00000000000000000000000000000000000000000000000000030600480000001292210000341001170351025803150
SPN636Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Eubacterium;siraeum_nov_93.878%00000000000000000000000000000000000000000000000000000012500900000000000028519000000
SPN637Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Breznakia;pachnodae_nov_85.225%0000000000000000000000000000000000000000000000000000000000000000000420000000441490
SPN638Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Rhodospirillum;rubrum_nov_88.565%00000000000000000000000000000000000000000000000000000023400000000000000000000000
SPN639Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Kineothrix;alysoides_nov_97.059%000000000000000000000000000000000000000000000000000000000000000000000076000001570
SPN64Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminoclostridium;methylpentosum_nov_89.462%000000000000000000000000000000000000000000000000000002280168000780300089001071251891961292870440011
SPN640Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;minuta_nov_88.143%00000000000000000000000000000000000000000000000000000000000000000000000000002290
SPN641Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Barnesiellaceae;Coprobacter;fastidiosus_nov_89.805%000000000000000000000000000000000000000000000000000410000000000000004000001840000
SPN642Bacteria;Tenericutes;Mollicutes;Acholeplasmatales;Acholeplasmataceae;Acholeplasma;parvum_nov_87.738%000000000000000000000000000000000000000000000000000000000000024320000150017067065000
SPN643Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Caproiciproducens;galactitolivorans_nov_92.793%0000000000000000000000000000000000000000000000000000000000000360120000640000000000
SPN644Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotellamassilia;timonensis_nov_95.011%00000000000000000000000000000000000000000000000000000000000000000000000000021700
SPN645Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Clostridium;sp._str._NML04A032_nov_89.238%0000000000000000000000000000000000000000000000000000000000000106000000000010800000
SPN646Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Faecalicatena;orotica_nov_97.959%00000000000000000000000000000000000000000000000000000000002730000002900006600004100
SPN647Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Anaerotignum;faecicola_nov_97.978%00000000000000000000000000000000000000000000000000000000000000000000000000002100
SPN648Bacteria;Lentisphaerae;Lentisphaeria;Victivallales;Victivallaceae;Victivallis;vadensis_nov_95.475%0000000000000000000000000000000000000000000000000005712600000000000000000000001330
SPN649Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Blautia;faecis_nov_97.959%000000000000000000000000000000000000000000000000000001340000000000000000000730000
SPN65Bacteria;Tenericutes;Mollicutes;Acholeplasmatales;Acholeplasmataceae;Acholeplasma;brassicae_nov_86.797%000000000000000000000000000005425000000000000003500000000000000000000000000000000
SPN650Bacteria;Firmicutes;Bacilli;Turicibacterales;Turicibacteraceae;Turicibacter;sanguinis_nov_86.266%000000000000000000000000000000000000000000000000000000000000000000000000021001820
SPN651Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-2];bacterium HMT091 nov_93.213%00000000000000000000000000000000000000000000000000001519003300001200000228022000019530
SPN652Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Faecalitalea;cylindroides_nov_92.241%000000000000000000000000000000000000000000000000000000000000043100000000110011003300
SPN653Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-2];bacterium HMT402 nov_90.337%00000000000000000000000000000000000000000000000000048000000000000000015304805500000
SPN654Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;sp._SS3/4_nov_97.727%00000000000000000000000000000000000000000000000000000000193000000000000000000000
SPN655Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;sinus_nov_95.909%00000000000000000000000000000000000000000000000000000000000000000000000000019100
SPN656Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Eubacterium;coprostanoligenes_nov_92.551%000000000000000000000000000000000000000000000000000000000000086000003200000000000
SPN66Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;unclassified_Ruminococcaceae;sp._str._D16_nov_93.454%00000000000000000000000000000000000000000000000000065001200000021000007400007301701310
SPN67Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Flavonifractor;plautii_nov_91.441%000000000000000000000000000000000000000000000000000810000000000000000000012000190
SPN68Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acetobacter;orleanensis_nov_87.133%00000000000000000000000000000000000000000000000000000000000000009000210000000000
SPN69Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Fastidiosipila;sanguinis_nov_89.238%00000000000000000000000000000000000000000000000000051000000000000000000000000600
SPN7Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Eggerthella;lenta_nov_93.424%00000000000000000000000000000000000000000000000000001000000000000000160000430018980
SPN70Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT436 nov_88.503%00000000000000000000000000000000000000000000000000000000000000000001090000000000
SPN71Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Raoultibacter;timonensis_nov_91.610%00000000000000000000000000000000000000000000000000029000068000000000000000800000
SPN72Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Sporobacter;termitidis_nov_90.562%000000000000000000000000000000000000000000000000000330000000000005700013000000000
SPN73Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Papillibacter;cinnamivorans_nov_93.034%00000000000000000000000000000000000000000000000000000000000000530000000490000000
SPN74Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XIII. Incertae Sedis;Emergencia;timonensis_nov_93.468%000000000000000000000000000000000000000000000000000380000000000000004100000002200
SPN75Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_92.809%000000000000000000000000000000000000000000000000000000790000000037010800130000577009203130
SPN76Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT305 nov_97.619%00000000000000000000000000000000000000000000010100000000000000000000000000000000
SPN77Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_94.344%0000000000000000000000000000000000000000000000000000000099000000000000000000000
SPN78Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes;indistinctus_nov_96.529%00000000000000000000000000000000000000000000000000072000000002600000000000000000
SPN79Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT365 nov_89.655%0000000000000000000000000000000000000000000000000000000000000000000000000000098
SPN8Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Coprococcus;catus_nov_96.154%000000000000000000000000000000000000000000000000000000001290000000000000000000560
SPN80Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Anaerotruncus;colihominis_nov_93.850%00000000000000000000000000000000000000000000000000000000000003800000590000000000
SPN81Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Acetivibrio;clariflavus_nov_90.745%00000000000000000000000000000000000000000000000000000000000000500005300003900000
SPN82Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT085 nov_92.411%00000000000000000000000000000000000000000000000000000000000000600000000000000370
SPN83Plantae;Angiosperms;Magnoliids;Laurales;Calycanthaceae;Calycanthus;floridus_Oral_Taxon_D07_nov_97.297%0000000000950000000000000000000000000000000000000000000000000000000000000000000
SPN84Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospira;eligens_nov_97.959%0000000000000000000000000000000000000000000000000000009500000000000000000000000
SPN85Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;zoogleoformans_nov_92.625%000000000000000000000000030000014000060320000000040000000000000000000000000000000
SPN86Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Fournierella;massiliensis_nov_95.455%000000000000000000000000000000000000000000000000000000000000066108000011100000000960
SPN87Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Agathobaculum;desmolans_nov_97.738%0000000000000000000000000000000000000000000000000000000043600003700002141181531786812200003170
SPN88Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Butyricicoccus;pullicaecorum_nov_94.382%00000000000000000000000000000000000000000000000000000000000000062000000002600060
SPN89Bacteria;Proteobacteria;Deltaproteobacteria;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;sp. HMT040 nov_92.521%0000000000000000000000000000000000000000000000000008500000000000080000000000000
SPN9Bacteria;Firmicutes;Firmicutes_[C];Firmicutes_[O];Firmicutes_[F];Firmicutes_[G];sp._Oral_Taxon_A55_nov_91.880%000000000000000000000000000000000000000000000000000000000000000000000027000001530
SPN90Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Muribaculum;intestinale_nov_90.043%0000000000000000000000000000000000000000000000000000000000093000000000000000000
SPN91Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Hespellia;porcina_nov_95.238%000000000000000000000000000000000000000000000000000001000300000000000000000000520
SPN92Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Breznakia;pachnodae_nov_83.512%0000000000000000000000000000000000000000000000000000000000000000000000000000910
SPN93Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptococcaceae;Desulfohalotomaculum;tongense_nov_87.696%00000000000000000000000000000000000000000000000000000000000000041000490000000000
SPN94Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;copri_nov_97.174%0000000000000000000000000000000000000000000000000000000000000010022000014000028034
SPN95Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;massiliensis_nov_88.739%0000000000000000000000000000000000000000000000000000000000000671190000650033052032900
SPN96Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;ruminantium_nov_92.601%0000000000000000000000000000000000000000000000000004312961939793340000195337088004641841992293853930216270321150
SPN97Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Coprococcus;catus_nov_96.136%000000000000000000000000000000000000000000000000000000000000000000000000310019390
SPN98Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Holdemanella;biformis_nov_97.854%00000000000000000000000000000000000000000000000000000198020500000141000428004501660178170109000
SPN99Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XIII. Incertae Sedis;Ihubacter;massiliensis_nov_96.606%0000000000000000000000000000000000000000000000000000000008900000000000000000000
SPP1Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;multispecies_spp1_2000000000000000000000000000000000000000000000000000200233023702253713371172140000783868001520000020334
SPP103Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;multispecies_spp103_200000000000000000000000000000000000000000000000000011600000001820045000000023002500000
SPP104Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp104_3000000000000000000000000000000000000000000000000000000265000480402003828300000000000950
SPP105Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;ruminis000000000000000000000000000000000000000000000000000006900001910007601950100971090000362400
SPP109Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;multispecies_spp109_2000960283279015004122932140000276326008724400014000150000000001901306008813200820128222820267000000000000030000000000000
SPP11Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp11_20312934484153285415915092110484526653118227143062202327635754754310229733768334889557356982356723214744537480565656175596414029892183140649934856084442417610347055471115724631180442475390355744600000000000047700000000000000
SPP111Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;multispecies_spp111_230700000000128000162000991900000048901590000001970000000750167000320256879000000000000000000000000000
SPP113Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp113_2470110258946241197418924920162019169520029015100127000020525000002536410000000000000000000000000000000000
SPP115Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;coprocola0000000000000000000000000000000000000000000000000001220000000000000000002670000000
SPP117Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp117_2000000000000000000000000000000000000000000000000000000285018206300000000000220000000366
SPP118Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;multifamily;multigenus;multispecies_spp118_20289134187326251105080023690011605044007911000244299122170260327213393024540695276021074496284156024018831233900133000000000000000000000000000
SPP12Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Roseburia;multispecies_spp12_200000000000000000000000000000000000000000000000000002951920208227258374038402430217013901642169120606500014
SPP127Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp127_3000000000000000000000000014600000003000000000000000000000000000000000000000000000
SPP134Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Granulicatella;multispecies_spp134_257437934343520832323042137529048733334241329027723528021037936813525440320433723613542324921226532957427319643503542011321783983683381962553571813391091200000000000000000000000000
SPP135Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;multigenus;multispecies_spp135_20710000000000000000942110001980000000350091000036000000001700740000000000000000000000000000
SPP136Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;multispecies_spp136_200000000000000000000000000000000000000000000000000000000000800000000000000200000
SPP137Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp137_2000000000000000000000000000000000000000000000000000000000114098500000003600000026600000
SPP138Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];multigenus;multispecies_spp138_20000000000000000000000000000000000000000000000000003080084000136391250003850000001250000000
SPP14Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;multispecies_spp14_20000000000000000000000000000000000000000000000000009410208003595733350524011902681940000013000000280
SPP15Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;multigenus;multispecies_spp15_5000000000000000000000000000000000000000000000000000022201200021100000000419000000000870
SPP17Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp17_418700176280297262025101891930148032001110000003682230300000027315713226902207125522702952451690014900000000000000000000000000000
SPP18Bacteria;Firmicutes;Clostridia;Clostridiales;Peptoniphilaceae;Parvimonas;multispecies_spp18_300196135003235141580133031970000191117000113333032615737001450022213132001912590022802890514179901010000000000000000000000000000
SPP19Bacteria;Actinobacteria;Actinomycetia;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;multispecies_spp19_2000000000000000000000000000000000000000000000000000013100007212200003952143240057251018102410000
SPP2Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp2_20000002800000002407000000110000000009210000930120024319707300000000000000000000000000000000
SPP20Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;multispecies_spp20_20000000050000000000000014000000009300170000004300199320000000000000000000000000000000
SPP21Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;multispecies_spp21_3000000000270009000000000000105000000000000000000141021805151000000000000000000000000000
SPP25Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp25_23516000028030124100210000000001801700009001100590510000550000000000000000000000000000000000
SPP26Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;multigenus;multispecies_spp26_500005000000000000000000000000000000000000000000000093111850002100057141852518123705501600312036701170
SPP27Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Gemella;multispecies_spp27_200000000350037000007759009001750055810015221128813513411334303251480750936512316520301270000000000000000000000000000
SPP28Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;coprophilus00000000000000000000000000000000000000000000000000002350000000000000000000000000
SPP29Bacteria;Firmicutes;Clostridia;multiorder;Lachnospiraceae_[XIVa];Blautia;multispecies_spp29_200000000000000000000000000000000000000000000000000030600001472841971553541021741281870215112059273146680471164360
SPP3Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp3_200000000000000000000000000000000000000153002800000158000000000000007113400000000000000
SPP30Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp30_2000000122000000000000000000000000000000000000000005400000000000000000000000000000
SPP39Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;multispecies_spp39_50000000001370000000000000000000000000170009001120025301862650301330000000000000000000000000000
SPP4Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;multigenus;multispecies_spp4_30000000181366000017600000000000610000000000000000000000000000000000000000000000000000
SPP41Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Enterobacter;multispecies_spp41_40000000000000000000037000000000000000000000000000000000000210000000000000430000000
SPP42Bacteria;Proteobacteria;Gammaproteobacteria;multiorder;multifamily;multigenus;multispecies_spp42_400000000000000000000000000000000000000000000000000000000000000000000000036900000
SPP43Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;multispecies_spp43_2000000000000000000000000000000000000000000000000000050000027540000000540000000000320
SPP46Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp46_400000000024100000000000000000000000000000000000000000000000000000000000000000000
SPP47Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp47_3000000000000000000240000148000000000000000000011900570000000000000000000000000000000
SPP48Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp48_4000000000000000000000000000020000000000000217000000000000000000000000000000000000
SPP49Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp49_200000000000000000129000000000000270000000000001240000000000000000000000000000000000
SPP5Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;multigenus;multispecies_spp5_2039903434282750001231582350455282003719218000004272640043013102360224367518269086527035205205370424012500000000000000000000000000000
SPP50Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp50_20000091000000000000000000900000000000000000000000000000000000000000000000000000
SPP51Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;multispecies_spp51_200000000000000000000000000000000000000000000000000000000043030371537206500796125010101040000
SPP52Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Klebsiella;multispecies_spp52_200000000000000000000000000000000000000000000082000000000021900000000000001410000000
SPP53Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Klebsiella;multispecies_spp53_20000000000000000000000000000000000000000000000000000000000000000000000850000000
SPP54Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Alcaligenaceae;multigenus;multispecies_spp54_2000000000000000000000000000000000000000000000000000470092001713031693000055000097000005317
SPP55Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;multispecies_spp55_20000000000024000090310027314502300000000000000000000290000000000000000000000000000000
SPP56Bacteria;Firmicutes;multiclass;multiorder;Selenomonadaceae;Selenomonas;multispecies_spp56_2000001684177800000873280000000002161580030701020016100107018000233000200850000000000000000000000000000000
SPP57Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;salivarius00000000000000000000000000000000000000000000000000000000000000000187000000000000
SPP59Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp59_20000000000000000000000000000000000000027500000018100000000000000000000000000000000
SPP60Bacteria;Firmicutes;multiclass;Clostridiales;Veillonellaceae;Veillonella;multispecies_spp60_2760046042400000172000000000007500083001300003540000000000000000000021000000000000000000000
SPP62Bacteria;Firmicutes;multiclass;multiorder;Peptostreptococcaceae_[XIII];Peptoniphilus;multispecies_spp62_2041000000000000000000000000000400000000000000000000000000000000041300000000000000
SPP63Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp63_30000000000000000000000000000389000000043100000000000000000000000000000000000000000
SPP64Bacteria;Firmicutes;multiclass;multiorder;Acidaminococcaceae;Acidaminococcus;multispecies_spp64_20000000000000000000000000000000000000000000000000000000001002210000000000004800000
SPP65Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;multispecies_spp65_200000000020600000000000000000000000000000000000000000000000000000000000000000000
SPP67Bacteria;Actinobacteria;Actinomycetia;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;multispecies_spp67_200000000000000000000000000000000000000000000000000000000228000399000031850000001030096451
SPP68Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;multispecies_spp68_2000000000000000000000000000000000000000000000000000000990159020204830510000000294310760000
SPP69Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;multispecies_spp69_300000000000000000000000000000000000000000000000000000000011418026000000000000000000
SPP7Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp7_22205658910505416016141106281200020101524012021421010170380161881728407002220000000000000000000000000000
SPP70Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonella;multispecies_spp70_2000020427700002890012100023837000000000100000106000630001910000000000000000000000097000000000000
SPP71Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonella;multispecies_spp71_2000000344000000000000000000595014900000018600010400000000000000000000000000258000000000000
SPP73Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Atopobiaceae;Olsenella;multispecies_spp73_2000000000000000000000000035000000000370000062000000000000000000000000000000000000
SPP74Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;plebeius00000000000000000000000000000000000000000000000000018720311900642000000250000002180000000
SPP75Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp75_3000000000000000000000003300000000000140040000000000000000000000000000000000000000
SPP76Bacteria;Firmicutes;Clostridia;multiorder;Lachnospiraceae;Lachnoanaerobaculum;multispecies_spp76_20102000104944805504400000000000220137048000000783800230000380007000000000000000000000000000000
SPP77Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;multigenus;multispecies_spp77_30000000000000000000000000000000000000000000000000000000000000000010000015000279000
SPP78Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Mobiluncus;multispecies_spp78_20550000000000000000000000000000000560000000000000000000000000000323300000000000000
SPP79Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Oribacterium;multispecies_spp79_202280000000000062380000000000960003000049007201970000000073000000000000000000000000000000
SPP8Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Mogibacterium;multispecies_spp8_3000000160001960066000000300148003553634933035271589111190023322001101340000000000000000000000000000000
SPP80Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;multispecies_spp80_20000000000000000000000000000000000000089000000000000000000000000000000000000000
SPP81Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;odontolyticus00000000000232000000000000000000000000000000000000000000000000000000000000000000
SPP82Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;multispecies_spp82_200000000000000000000000000000000000000319000000000000000000000000000000000000000
SPP83Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp83_700000000000000000000000000001150000000000000000000000000000000000000000000000000
SPP84Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp84_3000003700000001400000400000128000000060000000170290000000000000000000000000000000000
SPP85Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp85_600000000000000000000000000004500000000000000000000000000000000000000000000000000
SPP87Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;multispecies_spp87_200000000058229316900000192000000027700000000000000011403160000000000000000000000000000000000
SPP88Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;multispecies_spp88_2000005600007600000000000000000000000000000000970000000000000000000000000000000000
SPP9Bacteria;Firmicutes;Clostridia;multiorder;Lachnospiraceae[14];Shuttleworthia;multispecies_spp9_200000000000000000000000035000900000181034096000201350000009000000000000000000000000000
SPP92Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;multigenus;multispecies_spp92_60000000000000000000000000000000000000000000000000000000000000000000010513400000000
SPP93Bacteria;Firmicutes;multiclass;multiorder;Veillonellaceae;Selenomonas;multispecies_spp93_300000000000000000000000000000000000000000147000000000000000000000000000000000000
SPP94Bacteria;Firmicutes;multiclass;Clostridiales;Veillonellaceae;Veillonellaceae_[G-1];multispecies_spp94_30000000000000000000000000000002600000130000116000000000000000000000000000000000000
SPP95Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp95_400000134530290376207900033000002266990000609804795000326012113301555872550000000000000000000000000000000
SPP96Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp96_30000000000000000000000000000000000000000000000000000000002170000000018500000000000
SPP97Bacteria;Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus;multispecies_spp97_60000000000000000000000000000000000000000000000000000000000000000068000180000047350
SPP98Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;multifamily;Atopobium;rimae0000000000000000000000000000027200000000000142000000000000004000000000000000000000
SPP99Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;multifamily;multigenus;multispecies_spp99_30000000000000000000000000000000000000000000222001890000000000000000000000000000000
SPPN1Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus;multispecies_sppn1_2_nov_95.023%00000000000000000000000000000000000000000000000000043024404132613390874323603261570000026932725927402165600116
SPPN10Bacteria;Firmicutes;Clostridia;Eubacteriales;Defluviitaleaceae;Defluviitalea;multispecies_sppn10_2_nov_92.135%000000000000000000000000000000000000000000000000000420000000000240000800000399000
SPPN102Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;multigenus;multispecies_sppn102_2_nov_95.692%0000000000000000000000000000000000000000000000000000460000004400000000841050727075001710
SPPN103Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;multifamily;multigenus;multispecies_sppn103_2_nov_94.631%00000000000000000000000000000000000000000000000000000620050000000325000001800610630039
SPPN104Bacteria;Actinobacteria;Actinomycetia;Cryptosporangiales;Cryptosporangiaceae;Cryptosporangium;multispecies_sppn104_4_nov_84.978%00000000000000000000000000000000000000000000000000000000000005730000000000000000
SPPN105Bacteria;Actinobacteria;Actinomycetia;Streptomycetales;Streptomycetaceae;Streptomyces;multispecies_sppn105_2_nov_83.929%00000000000000000000000000000000000000000000000000000000000000000000000000002150
SPPN106Bacteria;Firmicutes;Clostridia;multiorder;Lachnospiraceae;Roseburia;multispecies_sppn106_3_nov_96.833%000000000000000000000000000000000000000000000000000017601060990007500008603760000164000000
SPPN11Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_sppn11_3_nov_96.606%00000000000000000000000000000000000000000000000000000000000000000000000001150000
SPPN12Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;multigenus;multispecies_sppn12_2_nov_95.692%00000000000000000000000000000000000000000000000000000000000000000000000037000660
SPPN13Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_sppn13_2_nov_91.775%00000000000000000000000000000000000000000000000000003920000000000000000000000000
SPPN14Bacteria;Actinobacteria;Actinomycetia;multiorder;multifamily;multigenus;multispecies_sppn14_8_nov_84.615%0000000000000000000000000000000000000000000000000000000000000000000920000000000
SPPN15Bacteria;Actinobacteria;Actinomycetia;Bifidobacteriales;Bifidobacteriaceae;Alloscardovia;multispecies_sppn15_2_nov_97.753%0000000000000000000000000000000000000092000000000000000000000000000000000000000
SPPN2Bacteria;Firmicutes;Clostridia;Eubacteriales;Christensenellaceae;Christensenella;multispecies_sppn2_2_nov_91.216%000000000000000000200000000000000000000000000000000003300000003344100003610013602150282637339
SPPN27Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;multispecies_sppn27_2_nov_97.959%0000000000000000000000000000000000000000000000000000000033300004411940472068000000037000
SPPN3Bacteria;Actinobacteria;Actinomycetia;Geodermatophilales;Geodermatophilaceae;Modestobacter;multispecies_sppn3_4_nov_83.408%000000000000000000000000000000000000000000000000000000000000000000014500000027000
SPPN34Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Mobiluncus;multispecies_sppn34_2_nov_97.817%05790056043000300001080000000000310012800000001080000000253000000000000000000000000000000000
SPPN36Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Clostridium;multispecies_sppn36_2_nov_91.723%00000000000000000000000000000000000000000000000000000000000000000000000034900000
SPPN4Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;multispecies_sppn4_6_nov_97.210%00000000000000000000000000000000000000000000000016700000000000000000000000000000
SPPN46Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_sppn46_2_nov_92.568%000000000000000000000000000000000000000000000000000167000000000033700001680000980003020
SPPN5Bacteria;Actinobacteria;Actinomycetia;Geodermatophilales;Geodermatophilaceae;Modestobacter;multispecies_sppn5_4_nov_83.408%00000000000000000000000000000000000000000000000000000155000000000000000000000000
SPPN52Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Roseburia;multispecies_sppn52_2_nov_97.072%00000000000000000000000000000000000000000000000000002570167000000013000000000004310000
SPPN6Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_sppn6_2_nov_91.910%00000000000000000000000000000000000000000000000000019000000000000000002900002713650
SPPN68Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;multispecies_sppn68_2_nov_97.279%00000000000000000000000000000000000000000000000000030000006400113000000000630940000117129
SPPN7Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;multigenus;multispecies_sppn7_2_nov_88.964%0000000000000000000000000000000000000000000000000000000000000012000000023000330730
SPPN70Bacteria;Firmicutes;Clostridia;Eubacteriales;multifamily;multigenus;multispecies_sppn70_2_nov_88.288%00000000000000000000000000000000000000000000000000000000000002720000000000000000
SPPN74Bacteria;Firmicutes;Clostridia;multiorder;multifamily;Bacteroides;capillosus00000000000000000000000000000000000000000000000000014733000000740000000000000000014
SPPN75Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Odoribacteraceae;Butyricimonas;multispecies_sppn75_2_nov_97.391%0000000000000000000000000000000000000000000000000000930000000002330000008010631000026
SPPN79Bacteria;Actinobacteria;Actinomycetia;Kineosporiales;Kineosporiaceae;Kineosporia;multispecies_sppn79_2_nov_83.445%00000000000000000000000000000000000000000000000000000105000000007523400000002670000850
SPPN8Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Phocaeicola;coprocola00000000000000000000000000000000000000000000000000000000000000000000071000000600
SPPN9Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;multigenus;multispecies_sppn9_2_nov_95.023%00000000000000000000000000000000000000000000000000000000000000127000000000000000
SPPN91Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;multispecies_sppn91_2_nov_97.732%0000000000000000000000000000000000000000000000000000081001021380000580001830000000000146
SPPN96Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIVa];Lacnoclostridium;multispecies_sppn96_2_nov_97.732%0000000000000000000000000000000000000000000000000001290105002120063120000000000500000000
 
 
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 1Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 2Saliva Healthy Control vs Saliva PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 3Saliva Healthy Control vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 4Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 5Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 6Feces Healthy Control vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 7Feces Healthy Control vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 8Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 9Saliva Healthy Control vs Feces Healthy ControlPDFSVGPDFSVGPDFSVG
Comparison 10Saliva Periodontitis vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 11Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 12Saliva vs FecesPDFSVGPDFSVGPDFSVG
 
 

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 1Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisView in PDFView in SVG
Comparison 2Saliva Healthy Control vs Saliva PeriodontitisView in PDFView in SVG
Comparison 3Saliva Healthy Control vs Saliva Parkinson + PeriodontitisView in PDFView in SVG
Comparison 4Saliva Periodontitis vs Saliva Parkinson + PeriodontitisView in PDFView in SVG
Comparison 5Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisView in PDFView in SVG
Comparison 6Feces Healthy Control vs Feces PeriodontitisView in PDFView in SVG
Comparison 7Feces Healthy Control vs Feces Parkinson + PeriodontitisView in PDFView in SVG
Comparison 8Feces Periodontitis vs Feces Parkinson + PeriodontitisView in PDFView in SVG
Comparison 9Saliva Healthy Control vs Feces Healthy ControlView in PDFView in SVG
Comparison 10Saliva Periodontitis vs Feces PeriodontitisView in PDFView in SVG
Comparison 11Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisView in PDFView in SVG
Comparison 12Saliva vs FecesView 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 1.Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 2.Saliva Healthy Control vs Saliva PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 3.Saliva Healthy Control vs Saliva Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 4.Saliva Periodontitis vs Saliva Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 5.Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 6.Feces Healthy Control vs Feces PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 7.Feces Healthy Control vs Feces Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 8.Feces Periodontitis vs Feces Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 9.Saliva Healthy Control vs Feces Healthy ControlObserved FeaturesShannon IndexSimpson Index
Comparison 10.Saliva Periodontitis vs Feces PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 11.Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisObserved FeaturesShannon IndexSimpson Index
Comparison 12.Saliva vs FecesObserved 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 1Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2Saliva Healthy Control vs Saliva PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 3Saliva Healthy Control vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 4Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 5Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 6Feces Healthy Control vs Feces PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 7Feces Healthy Control vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 8Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 9Saliva Healthy Control vs Feces Healthy ControlPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 10Saliva Periodontitis vs Feces PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 11Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 12Saliva vs FecesPDFSVGPDFSVGPDFSVGPDFSVG
 
 
 
 
 

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 1.Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 2.Saliva Healthy Control vs Saliva PeriodontitisBray–CurtisCorrelationAitchison
Comparison 3.Saliva Healthy Control vs Saliva Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 4.Saliva Periodontitis vs Saliva Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 5.Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 6.Feces Healthy Control vs Feces PeriodontitisBray–CurtisCorrelationAitchison
Comparison 7.Feces Healthy Control vs Feces Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 8.Feces Periodontitis vs Feces Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 9.Saliva Healthy Control vs Feces Healthy ControlBray–CurtisCorrelationAitchison
Comparison 10.Saliva Periodontitis vs Feces PeriodontitisBray–CurtisCorrelationAitchison
Comparison 11.Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisBray–CurtisCorrelationAitchison
Comparison 12.Saliva vs FecesBray–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 1.Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + Periodontitis
Comparison 2.Saliva Healthy Control vs Saliva Periodontitis
Comparison 3.Saliva Healthy Control vs Saliva Parkinson + Periodontitis
Comparison 4.Saliva Periodontitis vs Saliva Parkinson + Periodontitis
Comparison 5.Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + Periodontitis
Comparison 6.Feces Healthy Control vs Feces Periodontitis
Comparison 7.Feces Healthy Control vs Feces Parkinson + Periodontitis
Comparison 8.Feces Periodontitis vs Feces Parkinson + Periodontitis
Comparison 9.Saliva Healthy Control vs Feces Healthy Control
Comparison 10.Saliva Periodontitis vs Feces Periodontitis
Comparison 11.Saliva Parkinson + Periodontitis vs Feces Parkinson + Periodontitis
Comparison 12.Saliva vs Feces
 
 

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.Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + Periodontitis
Comparison 2.Saliva Healthy Control vs Saliva Periodontitis
Comparison 3.Saliva Healthy Control vs Saliva Parkinson + Periodontitis
Comparison 4.Saliva Periodontitis vs Saliva Parkinson + Periodontitis
Comparison 5.Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + Periodontitis
Comparison 6.Feces Healthy Control vs Feces Periodontitis
Comparison 7.Feces Healthy Control vs Feces Parkinson + Periodontitis
Comparison 8.Feces Periodontitis vs Feces Parkinson + Periodontitis
Comparison 9.Saliva Healthy Control vs Feces Healthy Control
Comparison 10.Saliva Periodontitis vs Feces Periodontitis
Comparison 11.Saliva Parkinson + Periodontitis vs Feces Parkinson + Periodontitis
Comparison 12.Saliva vs Feces
 
 
 

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.

 
Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + Periodontitis
 
 
 
 
 
 
 
LEfSe Results for All Comparisons
 
Comparison No.Comparison Name
Comparison 1.Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + Periodontitis
Comparison 2.Saliva Healthy Control vs Saliva Periodontitis
Comparison 3.Saliva Healthy Control vs Saliva Parkinson + Periodontitis
Comparison 4.Saliva Periodontitis vs Saliva Parkinson + Periodontitis
Comparison 5.Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + Periodontitis
Comparison 6.Feces Healthy Control vs Feces Periodontitis
Comparison 7.Feces Healthy Control vs Feces Parkinson + Periodontitis
Comparison 8.Feces Periodontitis vs Feces Parkinson + Periodontitis
Comparison 9.Saliva Healthy Control vs Feces Healthy Control
Comparison 10.Saliva Periodontitis vs Feces Periodontitis
Comparison 11.Saliva Parkinson + Periodontitis vs Feces Parkinson + Periodontitis
Comparison 12.Saliva vs Feces
 
 

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 1Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 2Saliva Healthy Control vs Saliva PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 3Saliva Healthy Control vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 4Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 5Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 6Feces Healthy Control vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 7Feces Healthy Control vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 8Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 9Saliva Healthy Control vs Feces Healthy ControlPDFSVGPDFSVGPDFSVG
Comparison 10Saliva Periodontitis vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 11Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 12Saliva vs FecesPDFSVGPDFSVGPDFSVG
 
 
B) One-way clustering - clustered on rows (organism) only
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 1Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 2Saliva Healthy Control vs Saliva PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 3Saliva Healthy Control vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 4Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 5Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 6Feces Healthy Control vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 7Feces Healthy Control vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 8Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 9Saliva Healthy Control vs Feces Healthy ControlPDFSVGPDFSVGPDFSVG
Comparison 10Saliva Periodontitis vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 11Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 12Saliva vs FecesPDFSVGPDFSVGPDFSVG
 
 
C) No clustering
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 1Saliva Healthy Control vs Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 2Saliva Healthy Control vs Saliva PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 3Saliva Healthy Control vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 4Saliva Periodontitis vs Saliva Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 5Feces Healthy Control vs Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 6Feces Healthy Control vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 7Feces Healthy Control vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 8Feces Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 9Saliva Healthy Control vs Feces Healthy ControlPDFSVGPDFSVGPDFSVG
Comparison 10Saliva Periodontitis vs Feces PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 11Saliva Parkinson + Periodontitis vs Feces Parkinson + PeriodontitisPDFSVGPDFSVGPDFSVG
Comparison 12Saliva vs FecesPDFSVGPDFSVGPDFSVG
 
 

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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