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
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
XIII.	Disclaimer

(Click to navigate)

FOMC Service Report

16S rRNA Gene V1V3 Amplicon Sequencing

Version V1.11

The Forsyth Institute, Cambridge, MA, USA

March 13, 2023

Project ID: FOMC9099_Rerun

I. Project Summary

Project FOMC9099_Rerun 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 (service not requested)
☐	10.	Bioinformatics Analysis - Alpha Diversity Analysis (service not requested)
☐	11.	Bioinformatics Analysis - Beta Diversity Analysis (service not requested)
☐	12.	Bioinformatics Analysis - Differential Abundance Analysis (service not requested)
☐	13.	Bioinformatics Analysis - Heatmap Profile (service not requested)
☐	14.	Bioinformatics Analysis - Network Association (service not requested)

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.

Absolute Abundance Quantification*: A quantitative real-time PCR was set up with a standard curve. The standard curve was made with plasmid DNA containing one copy of the 16S gene and one copy of the fungal ITS2 region prepared in 10-fold serial dilutions. The primers used were the same as those used in Targeted Library Preparation. The equation generated by the plasmid DNA standard curve was used to calculate the number of gene copies in the reaction for each sample. The PCR input volume (2 µl) was used to calculate the number of gene copies per microliter in each DNA sample.
The number of genome copies per microliter DNA sample was calculated by dividing the gene copy number by an assumed number of gene copies per genome. The value used for 16S copies per genome is 4. The value used for ITS copies per genome is 200. The amount of DNA per microliter DNA sample was calculated using an assumed genome size of 4.64 x 10⁶ bp, the genome size of Escherichia coli, for 16S samples, or an assumed genome size of 1.20 x 10⁷ bp, the genome size of Saccharomyces cerevisiae, for ITS samples. This calculation is shown below:

Calculated Total DNA = Calculated Total Genome Copies × Assumed Genome Size (4.64 × 10⁶ bp) ×
Average Molecular Weight of a DNA bp (660 g/mole/bp) ÷ Avogadro’s Number (6.022 x 10²³/mole)

* Absolute Abundance Quantification is only available for 16S and ITS analyses.

The absolute abundance standard curve data can be viewed in Excel here:

The absolute abundance standard curve is shown below:

Absolute Abundance Standard Curve

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 ID Original Sample ID Read 1 File Name Read 2 File Name
F9099.S1 zr9099_1V1V3_R1.fastq.gz zr9099_1V1V3_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”.

Quality plots for all samples:

XXXXXX

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 -

Create a random subset of each sample consisting of 5,000 R1 and 5,000 R2 (to reduce computation time)
Trim 10 bases at a time from the ends of both R1 and R2 up to 50 bases
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
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/R2	281	271	261	251	241	231
321	49.92%	47.30%	47.44%	50.84%	50.58%	50.72%
311	50.72%	48.00%	48.70%	50.26%	50.08%	46.76%
301	51.42%	48.68%	49.80%	51.68%	47.80%	23.14%
291	50.30%	47.30%	47.86%	47.72%	25.30%	14.92%
281	50.76%	48.16%	44.76%	24.42%	15.48%	5.66%
271	50.44%	44.96%	23.98%	14.72%	5.62%	3.82%

Based on the above result, the trim length combination of R1 = 301 bases and R2 = 251 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 ID	F9099.S1	Row Sum	Percentage
input	104,749	104,749	100.00%
filtered	98,446	98,446	93.98%
denoisedF	96,720	96,720	92.34%
denoisedR	96,189	96,189	91.83%
merged	89,466	89,466	85.41%
nonchim	42,103	42,103	40.19%

This table can be downloaded as an Excel table below:

5. DADA2 Amplicon Sequence Variants (ASVs). A total of 1027 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:

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

Code	Category	MPC=0% (>=1 read)	MPC=0.01%(>=4 reads)
A	Total reads	42,103	42,103
B	Total assigned reads	41,597	41,597
C	Assigned reads in species with read count < MPC	0	31
D	Assigned reads in samples with read count < 500	0	0
E	Total samples	1	1
F	Samples with reads >= 500	1	1
G	Samples with reads < 500	0	0
H	Total assigned reads used for analysis (B-C-D)	41,597	41,566
I	Reads assigned to single species	21,319	21,319
J	Reads assigned to multiple species	0	0
K	Reads assigned to novel species	20,278	20,247
L	Total number of species	180	168
M	Number of single species	35	35
N	Number of multi-species	0	0
O	Number of novel species	145	133
P	Total unassigned reads	506	506
Q	Chimeric reads	0	0
R	Reads without BLASTN hits	113	113
S	Others: short, low quality, singletons, etc.	393	393
	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

* MC = Minimal Count per species, species with total read count < MC were removed.

* The assignment result from MC=100 was used in the downstream analyses.

Read Taxonomy Assignment - Sample Meta Information

Download Sample Meta Information

#SampleID	SampleName	Group
F9099.S1	Sample S1	Group1

Read Taxonomy Assignment - ASV Read Counts by Samples

#Sample ID	Read Count
F9099.S1	42103

Read Taxonomy Assignment - ASV 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.

SPID	Taxonomy	F9099.S1
SP1	Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;animaloris	199
SP10	Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;canifelinum	354
SP11	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gingivicanis	248
SP12	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;denticola	321
SP13	Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;freiburgense	107
SP14	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT490	57
SP15	Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum	116
SP16	Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Bradyrhizobiaceae;Bradyrhizobium;japonicum	27
SP17	Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Frederiksenia;canicola	211
SP18	Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Gordoniaceae;Gordonia;polyisoprenivorans	11
SP19	Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;fryi	4
SP2	Bacteria;Proteobacteria;Deltaproteobacteria;Desulfovibrionales;Desulfomicrobiaceae;Desulfomicrobium;orale	802
SP20	Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sputigena	92
SP21	Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;catuli	13
SP22	Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;rectus	64
SP23	Bacteria;Actinobacteria;Actinobacteria;Propionibacteriales;Propionibacteriaceae;Propionibacteriaceae_[G-2];bacterium HMT192	55
SP24	Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Buchananella;hordeovulneris	35
SP25	Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-4];bacterium HMT355	6
SP26	Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;dumasiana	107
SP27	Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;bowdenii	46
SP28	Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;zoohelcum	69
SP29	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Vandammella;animalimorsus	47
SP3	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;cangingivalis	1357
SP30	Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;canis	51
SP31	Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;canimorsus	18
SP32	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Paraburkholderia;bryophila	9
SP33	Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;canis	40
SP34	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;heparinolyticus	13
SP35	Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Pasteurella;canis	52
SP4	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gulae	14172
SP5	Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Filifactor;villosus	256
SP6	Bacteria;Firmicutes;Clostridia;Clostridiales;Peptoniphilaceae;Peptoniphilaceae_[G-2];bacterium HMT790	360
SP7	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;canoris	1754
SP8	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Franklinella;schreckenbergeri	74
SP9	Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;cynodegmi	172
SPN1	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XII. Incertae Sedis;Fusibacter;fontis_nov_88.178%	68
SPN10	Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Dysgonomonadaceae;Fermentimonas;caenicola_nov_92.060%	57
SPN100	Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella;osloensis_nov_90.078%	2491
SPN101	Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;canis_nov_97.839%	20
SPN102	Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Alkaliphilus;transvaalensis_nov_86.019%	205
SPN103	Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;rectus_nov_96.593%	184
SPN104	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT473 nov_93.137%	177
SPN105	Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Conchiformibius;steedae_nov_95.720%	175
SPN106	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT239 nov_95.712%	166
SPN107	Bacteria;Actinobacteria;Actinomycetia;Propionibacteriales;Propionibacteriaceae;Tessaracoccus;bendigoensis_nov_92.137%	162
SPN108	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT473 nov_92.955%	152
SPN109	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT232 nov_95.322%	150
SPN11	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;denticola_nov_96.780%	16
SPN110	Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;naeslundii_nov_93.578%	145
SPN111	Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Weeksellaceae;Weeksellaceae_[G_1];bacterium_MOT-126_nov_94.932%	19
SPN112	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidales_[F-2];Bacteroidales_[G-2];bacterium HMT274 nov_92.292%	747
SPN113	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XII. Incertae Sedis;Fusibacter;paucivorans_nov_86.095%	144
SPN114	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT473 nov_89.412%	141
SPN115	Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Alkaliphilus;transvaalensis_nov_85.742%	139
SPN116	Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Catonella;sp. HMT164 nov_92.958%	137
SPN117	Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Catonella;sp. HMT164 nov_91.784%	130
SPN118	Bacteria;Synergistetes;Synergistia;Synergistales;Synergistaceae;Fretibacterium;sp. HMT362 nov_95.397%	127
SPN119	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT914 nov_94.303%	121
SPN12	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Mobilisporobacter;senegalensis_nov_84.423%	56
SPN120	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-8];bacterium HMT500 nov_95.344%	121
SPN121	Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Anaerorhabdus;furcosa_nov_88.615%	109
SPN122	Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;valvarum_nov_92.126%	17
SPN123	Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Acetoanaerobium;sticklandii_nov_76.854%	725
SPN124	Bacteria;Bacteroidota;Bacteroidia;Marinilabiliales;Prolixibacteraceae;Prolixibacter;denitrificans_nov_82.376%	104
SPN125	Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae;Anaerolineae_[G-1];bacterium HMT439 nov_95.966%	104
SPN126	Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT875 nov_97.727%	103
SPN127	Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-7];bacterium HMT081 nov_91.984%	102
SPN128	Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnoanaerobaculum;orale_nov_89.515%	100
SPN129	Bacteria;Proteobacteria;Betaproteobacteria;Rhodocyclales;Rhodocyclaceae;Propionivibrio;dicarboxylicus_nov_93.529%	100
SPN13	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT490 nov_95.703%	56
SPN130	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT227 nov_97.266%	99
SPN131	Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae_[XV];Eubacterium;oxidoreducens_nov_84.363%	99
SPN132	Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Anaerorhabdus;furcosa_nov_85.981%	98
SPN133	Bacteria;Firmicutes;Bacilli;Lactobacillales;Aerococcaceae;Globicatella;sanguinis_nov_90.485%	17
SPN134	Bacteria;Actinobacteria;Actinomycetia;Propionibacteriales;Propionibacteriaceae;Tessaracoccus;massiliensis_nov_92.585%	90
SPN135	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;canoris_nov_97.154%	506
SPN136	Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Conchiformibius;steedae_nov_97.292%	90
SPN137	Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Granulicatella;elegans_nov_93.494%	90
SPN138	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XII. Incertae Sedis;Guggenheimella;bovis_nov_86.822%	86
SPN139	Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Rikenellaceae;Acetobacteroides;hydrogenigenes_nov_82.530%	85
SPN14	Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Acetoanaerobium;pronyense_nov_90.927%	56
SPN140	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp._MOT-131_nov_95.543%	81
SPN141	Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Acetoanaerobium;pronyense_nov_89.960%	79
SPN142	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;denticola_nov_93.156%	69
SPN143	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp._MOT-131_nov_92.969%	68
SPN144	Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiales_[F-1];Clostridiales_[F-1][G-2];bacterium HMT402 nov_93.496%	16
SPN15	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Tannerella;forsythia_nov_97.697%	477
SPN16	Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Helicobacteraceae;Wolinella;succinogenes_nov_97.947%	55
SPN17	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-8];bacterium HMT500 nov_95.749%	55
SPN18	Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;rectus_nov_95.382%	52
SPN19	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;xylanisolvens_nov_90.116%	49
SPN2	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Tannerella;forsythia_nov_89.464%	67
SPN20	Bacteria;Firmicutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;feliminutum_nov_85.328%	49
SPN21	Bacteria;Gracilibacteria_(GN02);Gracilibacteria_(GN02)_[C-1];Gracilibacteria_(GN02)_[O-1];Gracilibacteria_(GN02)_[F-1];Gracilibacteria_(GN02)_[G-1];bacterium HMT872 nov_94.340%	48
SPN22	Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Arcobacteraceae;Aliarcobacter;thereius_nov_96.215%	15
SPN23	Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Proteocatella;sphenisci_nov_90.524%	47
SPN24	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;denticola_nov_95.085%	47
SPN25	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-8];bacterium HMT500 nov_96.154%	46
SPN26	Bacteria;Actinobacteria;Actinomycetia;Micromonosporales;Micromonosporaceae;Salinispora;pacifica_nov_86.733%	43
SPN27	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;catoniae_nov_91.321%	359
SPN28	Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-3];bacterium HMT366 nov_89.243%	42
SPN29	Bacteria;Proteobacteria;Betaproteobacteria;Rhodocyclales;Rhodocyclaceae;Propionivibrio;dicarboxylicus_nov_94.314%	39
SPN3	Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Alkaliphilus;transvaalensis_nov_85.185%	488
SPN30	Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Buchananella;hordeovulneris_nov_94.411%	35
SPN31	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT236 nov_96.078%	35
SPN32	Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-7];bacterium HMT081 nov_93.173%	35
SPN33	Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;valvarum_nov_92.110%	15
SPN34	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-8];bacterium HMT500 nov_94.929%	34
SPN35	Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;canis_nov_97.250%	34
SPN36	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gulae_nov_97.082%	33
SPN37	Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;valvarum_nov_91.304%	33
SPN38	Bacteria;Firmicutes;Clostridia;Eubacteriales;Clostridiaceae;Wukongibacter;baidiensis_nov_86.573%	31
SPN39	Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;gastrosuis_nov_97.347%	349
SPN4	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales_[F-1];Eubacteriales_[G-1];bacterium_MOT-144_nov_86.640%	65
SPN40	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT490 nov_96.863%	31
SPN41	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lacrimispora;xylanolytica_nov_89.883%	30
SPN42	Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Canicola;haemoglobinophilus_nov_94.687%	28
SPN43	Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-1];bacterium HMT957 nov_95.513%	27
SPN44	Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Pseudoleptotrichia;goodfellowii_nov_92.629%	292
SPN45	Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;bowdenii_nov_97.410%	27
SPN46	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XII. Incertae Sedis;Fusibacter;fontis_nov_85.493%	27
SPN47	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales_[F-1];Eubacteriales_[G-1];bacterium_MOT-144_nov_84.466%	26
SPN48	Bacteria;Bacteroidota;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Flavobacterium;suaedae_nov_93.424%	25
SPN49	Bacteria;Gracilibacteria_(GN02);Gracilibacteria_(GN02)_[C-1];Gracilibacteria_(GN02)_[O-1];Gracilibacteria_(GN02)_[F-1];Gracilibacteria_(GN02)_[G-1];bacterium HMT871 nov_93.895%	25
SPN5	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;fusca_nov_86.867%	65
SPN50	Bacteria;Actinobacteria;Actinomycetia;Propionibacteriales;Propionibacteriaceae;Raineyella;fluvialis_nov_93.574%	22
SPN51	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;vincentii_nov_97.070%	14
SPN52	Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-1];bacterium HMT075 nov_93.018%	14
SPN53	Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriales Family XII. Incertae Sedis;Fusibacter;fontis_nov_86.154%	13
SPN54	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Lautropia;dentalis_nov_95.800%	13
SPN55	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT473 nov_92.745%	13
SPN56	Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Rhodanobacteraceae;Chiayiivirga;flava_nov_93.077%	13
SPN57	Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum_nov_97.217%	4718
SPN58	Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Actinobacillus;succinogenes_nov_94.129%	12
SPN59	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;catoniae_nov_91.509%	11
SPN6	Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;valvarum_nov_93.491%	63
SPN60	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;bivia_nov_86.466%	10
SPN61	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Brachymonas;chironomi_nov_94.208%	10
SPN62	Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;canis_nov_92.549%	288
SPN63	Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Dysgonomonadaceae;Proteiniphilum;acetatigenes_nov_88.805%	8
SPN64	Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae;Luteimonas;notoginsengisoli_nov_93.143%	7
SPN65	Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Sneathia;sanguinegens_nov_90.297%	7
SPN66	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gulae_nov_91.571%	7
SPN67	Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum_nov_89.421%	7
SPN68	Bacteria;Proteobacteria;Deltaproteobacteria;Desulfobacterales;Desulfobulbaceae;Desulfobulbus;propionicus_nov_94.403%	299
SPN69	Bacteria;Saccharibacteria_(TM7);Saccharibacteria_(TM7)_[C-1];Saccharibacteria_(TM7)_[O-1];Saccharibacteria_(TM7)_[F-1];Saccharibacteria_(TM7)_[G-4];bacterium HMT355 nov_95.565%	7
SPN7	Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Pseudoleptotrichia;goodfellowii_nov_92.742%	61
SPN70	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT258 nov_97.461%	6
SPN71	Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;parainfluenzae_nov_96.402%	5
SPN72	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT258 nov_97.065%	5
SPN73	Bacteria;Synergistetes;Synergistia;Synergistales;Synergistaceae;Fretibacterium;sp. HMT362 nov_94.340%	287
SPN74	Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Alysiella;crassa_nov_94.061%	4
SPN75	Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Filifactor;villosus_nov_96.378%	4
SPN76	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gingivicanis_nov_95.636%	4
SPN77	Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae;Luteimonas;chenhongjianii_nov_91.304%	4
SPN78	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Brachymonas;chironomi_nov_93.462%	4
SPN79	Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT365 nov_86.193%	21
SPN8	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;catoniae_nov_90.772%	60
SPN80	Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Actinobacillus;capsulatus_nov_93.130%	4
SPN85	Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Catonella;sp. HMT164 nov_92.000%	286
SPN9	Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;valvarum_nov_91.897%	58
SPN90	Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Paludibacteraceae;Paludibacter;propionicigenes_nov_87.452%	21
SPN95	Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp._MOT-131_nov_92.996%	272
SPN96	Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;rectus_nov_97.610%	256
SPN97	Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Brachymonas;chironomi_nov_93.462%	239
SPN98	Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella;nonliquefaciens_nov_93.846%	233
SPN99	Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Mobilisporobacter;senegalensis_nov_91.489%	230
SPPN1	Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;multispecies_sppn1_2_nov_96.660%	148

Download Read Count Tables at Different Taxonomy Levels
domain
phylum
class
order
family
genus
species

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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.

Sample Taxonomy Bar Plots

VIII. Analysis - Alpha Diversity


Results unavailable

IX. Analysis - Beta Diversity

Results unavailable


X. Analysis - Differential Abundance

Results unavailable

XI. Analysis - Heatmap Profile

Results unavailable


XII. Analysis - Network Association

Results unavailable


XIII. Disclaimer
The results of this analysis are for research purpose only. They are not intended to diagnose, treat, cure, or prevent any disease. Forsyth and FOMC are not responsible for use of information provided in this report outside the research area.