FOMC Service Report (SAMPLE)

16S rRNA Gene V1V3 Amplicon Sequencing

Version V1.1

The Forsyth Institute, Cambridge, MA, USA
March 25, 2021

Project ID: FOMC0000


I. 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
 

II. 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

 

III. 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.

 

IV. 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 IDRead 1 File NameRead 2 File Name
S10zr4083_10V1V3_R1.fastq.gzzr4083_10V1V3_R2.fastq.gz
S11zr4083_11V1V3_R1.fastq.gzzr4083_11V1V3_R2.fastq.gz
S12zr4083_12V1V3_R1.fastq.gzzr4083_12V1V3_R2.fastq.gz
S13zr4083_13V1V3_R1.fastq.gzzr4083_13V1V3_R2.fastq.gz
S14zr4083_14V1V3_R1.fastq.gzzr4083_14V1V3_R2.fastq.gz
S15zr4083_15V1V3_R1.fastq.gzzr4083_15V1V3_R2.fastq.gz
S16zr4083_16V1V3_R1.fastq.gzzr4083_16V1V3_R2.fastq.gz
S17zr4083_17V1V3_R1.fastq.gzzr4083_17V1V3_R2.fastq.gz
S18zr4083_18V1V3_R1.fastq.gzzr4083_18V1V3_R2.fastq.gz
S19zr4083_19V1V3_R1.fastq.gzzr4083_19V1V3_R2.fastq.gz
S01zr4083_1V1V3_R1.fastq.gzzr4083_1V1V3_R2.fastq.gz
S20zr4083_20V1V3_R1.fastq.gzzr4083_20V1V3_R2.fastq.gz
S02zr4083_2V1V3_R1.fastq.gzzr4083_2V1V3_R2.fastq.gz
S03zr4083_3V1V3_R1.fastq.gzzr4083_3V1V3_R2.fastq.gz
S04zr4083_4V1V3_R1.fastq.gzzr4083_4V1V3_R2.fastq.gz
S05zr4083_5V1V3_R1.fastq.gzzr4083_5V1V3_R2.fastq.gz
S06zr4083_6V1V3_R1.fastq.gzzr4083_6V1V3_R2.fastq.gz
S07zr4083_7V1V3_R1.fastq.gzzr4083_7V1V3_R2.fastq.gz
S08zr4083_8V1V3_R1.fastq.gzzr4083_8V1V3_R2.fastq.gz
S09zr4083_9V1V3_R1.fastq.gzzr4083_9V1V3_R2.fastq.gz
S01zr4106_1V1V3_R1.fastq.gzzr4106_1V1V3_R2.fastq.gz
S02zr4106_2V1V3_R1.fastq.gzzr4106_2V1V3_R2.fastq.gz
S03zr4106_3V1V3_R1.fastq.gzzr4106_3V1V3_R2.fastq.gz
S04zr4106_4V1V3_R1.fastq.gzzr4106_4V1V3_R2.fastq.gz
S05zr4106_5V1V3_R1.fastq.gzzr4106_5V1V3_R2.fastq.gz
S06zr4106_6V1V3_R1.fastq.gzzr4106_6V1V3_R2.fastq.gz
S07zr4106_7V1V3_R1.fastq.gzzr4106_7V1V3_R2.fastq.gz
S08zr4106_8V1V3_R1.fastq.gzzr4106_8V1V3_R2.fastq.gz
S09zr4106_9V1V3_R1.fastq.gzzr4106_9V1V3_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:

 

V. 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
32132.55%43.72%45.51%46.47%48.42%44.12%
31133.04%45.27%47.10%48.47%45.65%29.30%
30132.83%45.63%47.16%43.90%29.24%11.86%
29133.39%45.89%43.28%27.76%12.66%11.36%
28134.62%42.35%27.83%12.26%11.94%9.12%
27129.22%28.17%12.23%10.91%9.07%3.26%

Based on the above result, the trim length combination of R1 = 311 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 bulding 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 IDF4083.S01F4083.S02F4083.S03F4083.S04F4083.S05F4083.S06F4083.S07F4083.S08F4083.S09F4083.S10F4083.S11F4083.S12F4083.S13F4083.S14F4083.S15F4083.S16F4083.S17F4083.S18F4083.S19F4083.S20F4106.S01F4106.S02F4106.S03F4106.S04F4106.S05F4106.S06F4106.S07F4106.S08F4106.S09Row SumPercentage
input19,73128,10626,83124,79329,33020,89616,72226,28521,82125,39227,37825,42527,85123,14523,56524,94123,72824,74931,00021,43830,57533,77036,60539,28739,55737,58035,73239,78829,892815,913100.00%
filtered14,55621,72220,64519,27122,67216,07612,75320,54716,50119,69321,19119,32521,70917,81018,10218,88417,75919,08424,02116,36124,09228,17030,38732,32732,23430,76329,24531,55523,056640,51178.50%
denoisedF13,73520,91219,49718,52621,91115,24111,92319,57815,66118,61820,46218,77920,60916,94917,11418,09017,03518,20822,90815,78123,27027,32129,61531,34931,20329,61128,07530,44522,345614,77175.35%
denoisedR13,89521,39819,96418,77922,19215,51112,29620,11915,91419,25020,73019,02421,04817,21717,61718,42617,21118,59423,51715,95923,49727,55729,93731,51731,72829,82028,43130,82722,549624,52476.54%
merged10,62619,16316,68916,15419,44412,6959,86317,12313,18416,59418,60617,40617,75814,63414,36315,90415,28715,82020,58014,21720,47424,48127,27127,42627,73625,05423,05125,21619,262536,08165.70%
nonchim6,1819,1149,1458,5048,5246,7085,3417,4436,9257,0108,3688,2868,9198,2047,7116,9136,5647,2609,6526,9419,75011,28212,78715,05114,24014,59213,52513,13511,241269,31633.01%

This table can be downloaded as an Excel table below:

 

5. DADA2 Amplicon Sequence Variants (ASVs). A total of 5634 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:

 
 
 
 

VI. 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

CodeCategoryRead Count (MC=1)*Read Count (MC=100)*
ATotal reads1,315,9201,315,920
BTotal assigned reads1,308,1011,308,101
CAssigned reads in species with read count < MC011,504
DAssigned reads in samples with read count < 50000
ETotal samples1717
FSamples with reads >= 5001717
GSamples with reads < 50000
HTotal assigned reads used for analysis (B-C-D)1,308,1011,296,597
IReads assigned to single species788,335787,712
JReads assigned to multiple species37,62537,575
KReads assigned to novel species482,141471,310
LTotal number of species788462
MNumber of single species6342
NNumber of multi-species52
ONumber of novel species720418
PTotal unassigned reads7,8197,819
QChimeric reads3,3403,340
RReads without BLASTN hits1,6691,669
SOthers: short, low quality, singletons, etc.2,8102,810
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

#SampleIDGroup
pool1.10.1-6Oral_JAX
pool1.2040-1.5-6Fecal
pool1.2040-2.0-7Fecal
pool1.2092.1-7Fecal
pool1.2093-1.2-7Fecal
pool1.22.2-6Oral_JAX
pool1.490.0-6Oral
pool1.60.3-6Oral_JAX
pool1.69.4-6Oral_JAX
pool2.2040-3.0-8Fecal
pool2.2093-1-W1.0-2Oral
pool2.2093-3.0-9Fecal
pool2.47.0-7Oral_JAX
pool2.483.0-3Oral
pool2.488.0-4Oral
pool2.489.0-5Oral
pool2.492.0-6Oral
 
 

Read Taxonomy Assignment - ASV Read Counts by Samples

#Sample IDRead Count
pool2.483.0-332586
pool1.490.0-637017
pool2.489.0-547026
pool2.2093-3.0-949261
pool2.2040-3.0-855737
pool2.2093-1-W1.0-256804
pool1.60.3-663945
pool1.69.4-666453
pool2.488.0-467114
pool2.492.0-669777
pool1.22.2-687600
pool1.2040-2.0-789410
pool2.47.0-7108336
pool1.2040-1.5-6110639
pool1.2093-1.2-7114439
pool1.2092.1-7118677
pool1.10.1-6141099
 
 

Read Taxonomy Assignment - ASV Read Counts Table

SPIDTaxonomypool1.10.1-6pool1.2040-1.5-6pool1.2040-2.0-7pool1.2092.1-7pool1.2093-1.2-7pool1.22.2-6pool1.490.0-6pool1.60.3-6pool1.69.4-6pool2.2040-3.0-8pool2.2093-1-W1.0-2pool2.2093-3.0-9pool2.47.0-7pool2.483.0-3pool2.488.0-4pool2.489.0-5pool2.492.0-6
SP1k__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum;s__rodentium0592812240287207000032800047000
SP10k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Muribacter;s__muris00000045700047000438415631278775
SP12k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia;s__coli1841000012570486930000640000
SP14k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__thoraltensis0000004640001710041542244852
SP15k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__pseudolongum04371353181914630220005660202500377790
SP16k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__sciuri136078000080605055395410001037570000
SP17k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__acidifaciens0480300209013740000196031100000
SP18k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__intestinalis0127969011446240360041302730376252110
SP2k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__danieliae0001600753100053324001421269061992122910
SP20k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Propionibacteriaceae;g__Propionibacterium;s__acnes0000001000089002192707684
SP21k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Gemellaceae;g__Gemella;s__species1_MOT330000002000012200366631673
SP22k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__mastitidis0000001510001448001416515496
SP23k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__muciniphila0000001930000000138110
SP24k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__murinus083531752688333024400131590999802389368510
SP25k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__ganmani05021932893800910012901190042000
SP26k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Acutalibacter;s__muris02100130000000000000
SP27k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas;s__gingivalis0000000000227000000
SP28k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__Romboutsia;s__ilealis0279194000000014970000000
SP29k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__caecimuris06363219114000000000000
SP3k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__casseliflavus00000100300000000000
SP30k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__johnsonii23085008142782030117808380058040217030710961910
SP31k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__cohnii00000000000007540310
SP32k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__acidominimus0000005946000109005766155214467965
SP33k__Bacteria;p__Tenericutes;c__Mollicutes;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma;s__muris00012312200000013300000
SP35k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Parabacteroides;s__distasonis01210461927137100001330270029600
SP38k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale0795104941635900002890260011300
SP39k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Enterorhabdus;s__muris03008944000000000004
SP40k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__hepaticus03658757042000002206500000
SP42k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__goldsteinii0900060000000000800
SP44k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__saprophyticus0000000000000102000
SP48k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium;s__acnes00000000001150017500102
SP5k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__reuteri5654170766033873143014700312507070261330480
SP50k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__agalactiae00000000029376000000
SP51k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Enterorhabdus;s__caecimuris014818132422200000014700000
SP58k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__uniformis0120000000000000000
SP59k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichidae;g__Ileibacterium;s__valens0000000000000200000
SP6k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Rodentibacter;s__pneumotropicus0000006120000007852175351376
SP60k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__hirae0009700000002600000
SP64k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Pasteurella;s__caecimuris000000481000000079318121
SP7k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__sartorii01623132629042709000070705390027500
SP8k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__animalis000000006591200000000
SP9k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__gallinarum00000230800000025650000
SPN1k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__Catabacter;s__hongkongensis00067433000000000000
SPN10k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Millionella;s__massiliensis01520136186000000000000
SPN100k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichidae;g__Dubosiella;s__newyorkensis0101083840000001200000
SPN101k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis;g__Ihubacter;s__massiliensis00064213000000000000
SPN102k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelatoclostridium;s__sp._str._HGF2000000000000096018156
SPN103k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__loescheii091045127000000000000
SPN104k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Sutterella;s__sp._str._cont1.66030018246000000000000
SPN105k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__senegalensis0001197160500000011000000
SPN106k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__timonensis0853246480000400000000
SPN107k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis;g__Anaerovorax;s__odorimutans02040188505000000000000
SPN108k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__merdae09512838988823732100043740731300000
SPN109k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__producta011807655000000000000
SPN11k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__shahii01222213422150000670000000
SPN110k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Murimonas;s__intestini00091157000000000000
SPN111k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Culturomica;s__massiliensis0957430370000110000000
SPN112k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Negativibacillus;s__massiliensis010405390000000000000
SPN113k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Paraprevotella;s__clara093065680000601200000
SPN114k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Mordavella;s__massiliensis000123990000002100000
SPN115k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__Peptococcus;s__sp._Oral_Taxon_16700060182000000000000
SPN116k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__Peptostreptococcaceae_[G];s__sp._Oral_Taxon_B610111992816846700001710000000
SPN117k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Acutalibacter;s__muris0103315947000000000000
SPN118k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Raoultibacter;s__timonensis0003714900000003000000
SPN119k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Olsenella;s__sp._Oral_Taxon_8070001011050000003200000
SPN12k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Mucispirillum;s__schaedleri01200192156000000000000
SPN120k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Gordonibacter;s__pamelaeae000106000000012600000
SPN121k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Coprococcus;s__comes000154550000002000000
SPN122k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__acidophilus010681350000000000000
SPN123k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__ultunensis000985101500000005800
SPN124k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae_[XV];g__Anaerofustis;s__stercorihominis0002210000000000000
SPN125k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__johnsonii00012991000000000000
SPN126k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__mesocricetorum05606696000000000000
SPN127k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__sp._str._M62/100068149000000000000
SPN128k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospira;s__multipara00000046470000003170379428539782
SPN129k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminoclostridium;s__thermocellum035215202101160012000023400
SPN13k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Muribaculum;s__intestinale016063128116000000000000
SPN130k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__rodentium000871163200000014400000
SPN131k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__Sporosarcina;s__pasteurii00061155000000000000
SPN132k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Eggerthella;s__timonensis048072840000001000000
SPN133k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Faecalicatena;s__contorta00122000000910000000
SPN134k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__champanellensis042077790000001300000
SPN135k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__unclassified_Lachnospiraceae;s__sp._str._cont1.81046053870000220000000
SPN136k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__marasmi0000000000000207000
SPN137k__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longibaculum;s__muris065033108000000000000
SPN138k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Dorea;s__longicatena018103114950000004400000
SPN139k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerostipes;s__hadrus093019210000006700000
SPN14k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Anaerorhabdus;s__furcosa0945231077343827000032440665100000
SPN140k__Bacteria;p__Tenericutes;c__Mollicutes;o__Mycoplasmatales;f__Mycoplasmataceae;g__Ureaplasma;s__urealyticum000930136900000019100000
SPN141k__Bacteria;p__Tenericutes;c__Mollicutes;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma;s__axanthum000479300002403600000
SPN142k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__amygdalinum0001980000000000000
SPN143k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter;s__massiliensis01752200000000000000
SPN144k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Agathobaculum;s__desmolans035060890000001200000
SPN145k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__sp._str._L2_5000056140000000000000
SPN146k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Harryflintia;s__acetispora016401500000150000000
SPN147k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminiclostridium;s__cellobioparum010404743000000000000
SPN148k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Eubacterium;s__siraeum012615329517500005406700000
SPN149k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__tarantellae089014260000006200000
SPN15k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans0001634156000000068000000
SPN150k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__casseliflavus0018900000000000000
SPN151k__Bacteria;p__Tenericutes;c__Mollicutes;o__Entomoplasmatales;f__Spiroplasmataceae;g__Spiroplasma;s__velocicrescens03130653113400000038200000
SPN152k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter;s__bifida08505846000000000000
SPN153k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Clostridium;s__sp._str._NML04A032010403252000000000000
SPN154k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Falcatimonas;s__natans05008253000000000000
SPN155k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus_nov_90.957%03308072000000000000
SPN156k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__bolteae_nov_92.857%00040510000009400000
SPN157k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis_nov_93.529%03505099000000000000
SPN158k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella;s__species1_MOT32_nov_95.593%0000002609000000116157912663
SPN159k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelatoclostridium;s__sp._str._HGF2_nov_91.264%00095690200000000000
SPN16k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__NA;g__Intestinimonas;s__butyriciproducens01590176124000000000000
SPN160k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis_nov_92.657%01110071000000000000
SPN161k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__Catabacter;s__hongkongensis_nov_86.710%011101853000000000000
SPN162k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.409%0121761485531000028608000000
SPN163k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__massiliensis_nov_85.704%09704342000000000000
SPN164k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__bolteae_nov_92.724%00047440000009000000
SPN165k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus;s__rubiinfantis_nov_92.153%00074106000000000000
SPN166k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_86.306%08404353000000000000
SPN167k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__saccharolyticum_nov_91.427%04137065000000000000
SPN168k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae_[XV];g__Eubacterium;s__ventriosum_nov_92.133%01040074000000000000
SPN169k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Odoribacter;s__splanchnicus_nov_91.594%026501494170000002200500
SPN17k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__bolteae000251205000000000000
SPN170k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus_nov_95.311%0008988000000000000
SPN171k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella;s__majae_nov_85.666%04700129000000000000
SPN172k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelatoclostridium;s__sp._str._HGF2_nov_91.132%00011264000000000000
SPN173k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_91.767%000113796600000011900000
SPN174k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Butyricicoccus;s__pullicaecorum_nov_94.232%00013144000000000000
SPN175k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__oxidoreducens_nov_89.300%0001750000000000000
SPN176k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella;s__majae_nov_85.598%04730125000000000000
SPN177k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus;s__rubiinfantis_nov_94.343%0007797000000000000
SPN178k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis_nov_92.657%01120061000000000000
SPN179k__Bacteria;p__Firmicutes;c__Clostridia;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Moorella;s__thermoacetica_nov_85.797%05603224370000003700000
SPN18k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__asparagiforme0283238169000000000000
SPN180k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__unclassified_Erysipelotrichaceae;s__sp._str._cont1.113_nov_90.186%070185035000000000000
SPN181k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__putredinis_nov_96.841%063214642000000000000
SPN182k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Acetivibrio;s__cellulolyticus_nov_86.786%0000000001720000000
SPN183k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Olsenella;s__sp._Oral_Taxon_807_nov_93.166%0379141239340540093000019300
SPN184k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Marvinbryantia;s__formatexigens_nov_89.535%00058113000000000000
SPN185k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_91.455%0810880000000000000
SPN186k__Plantae;p__Pinophyta;c__Pinopsida;o__Pinales;f__Pinaceae;g__Pinus;s__thunbergii_Oral_Taxon_D30_nov_95.661%0000000000000164000
SPN187k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes_nov_96.366%03405672000000000000
SPN188k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Butyricicoccus;s__pullicaecorum_nov_93.964%0990061000000000000
SPN189k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__sciuri_nov_97.250%000004220000004290000
SPN19k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__minuta0660243145000000000000
SPN190k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Crocinitomicaceae;g__Wandonia;s__haliotis_nov_83.766%00037111000000800000
SPN191k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis_nov_93.329%03002897000000000000
SPN192k__Bacteria;p__Saccharibacteria_(TM7);c__Saccharibacteria_(TM7)_[C-1];o__Saccharibacteria_(TM7)_[O-1];f__Saccharibacteria_(TM7)_[F-1];g__Saccharibacteria_(TM7)_[G-3];s__bacterium_HMT_351_nov_95.185%000287500001104000000
SPN193k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_91.656%011032109000000000000
SPN194k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_91.307%08986728639200001330900000
SPN195k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__senegalensis_nov_96.214%000476200002002200000
SPN196k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_93.640%05203762000000000000
SPN197k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes_nov_93.826%0006982000000000000
SPN198k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__timonensis_nov_85.898%0980053000000000000
SPN199k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella;s__species1_MOT32_nov_97.755%000000730001080022904370
SPN2k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis0885916291793000070602420010500
SPN20k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__NA;g__Colidextribacter;s__massiliensis000245206000000000000
SPN200k__Bacteria;p__Cyanobacteria;c__Gloeobacterophycideae;o__Gloeobacterales;f__Gloeobacteraceae;g__Gloeobacter;s__violaceus_nov_83.401%05336062000000000000
SPN201k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__luti_nov_91.454%0001500000000000000
SPN202k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__timonensis_nov_85.898%07302254000000000000
SPN203k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Crocinitomicaceae;g__Wandonia;s__haliotis_nov_83.699%00043105000000000000
SPN204k__Plantae;p__Pinophyta;c__Pinopsida;o__Pinales;f__Pinaceae;g__Pinus;s__thunbergii_Oral_Taxon_D30_nov_95.661%0000000000000147000
SPN205k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Butyrivibrio;s__crossotus_nov_91.264%02008441000000000000
SPN206k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.806%0375601517486000051012700000
SPN207k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_91.261%00010934000000000000
SPN208k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus;s__rubiinfantis_nov_94.343%0004696000000000000
SPN209k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Phocea;s__massiliensis_nov_92.537%0790061000000000000
SPN21k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__NA;g__Pseudoflavonifractor;s__phocaeensis012521128173000000000000
SPN210k__Bacteria;p__Candidatus Melainabacteria;c__NA;o__NA;f__NA;g__Vampirovibrio;s__chlorellavorus_nov_83.414%08701875290000004200000
SPN211k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__mesocricetorum_nov_97.750%09554441371361000018010230700000
SPN212k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae;g__Catabacter;s__hongkongensis_nov_86.710%0960044000000000000
SPN213k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__amygdalinum_nov_93.103%03102188000000000000
SPN214k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes_nov_96.172%03400105000000000000
SPN215k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__minuta_nov_82.420%027000000010101000000
SPN216k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus;s__rubiinfantis_nov_91.365%03604161000000000000
SPN217k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Acetivibrio;s__cellulolyticus_nov_86.786%0000000001360000000
SPN218k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_88.223%02806345000000000000
SPN219k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.231%017416772558406000380960030180
SPN22k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Butyricicoccus;s__pullicaecorum000004330000005210000
SPN220k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis_nov_91.773%02608000000300000000
SPN221k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__Sporosarcina;s__pasteurii_nov_97.261%0000000000000135000
SPN222k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_91.048%019041726500000074006200
SPN223k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__wadsworthia_nov_93.981%0006963000000000000
SPN224k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_91.455%0660650000000000000
SPN225k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_96.324%05002258000000000000
SPN226k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Phocea;s__massiliensis_nov_92.469%0780052000000000000
SPN227k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Butyricicoccus;s__pullicaecorum_nov_94.094%0009335000000000000
SPN228k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__intestinalis_nov_90.236%0490079000000000000
SPN229k__Bacteria;p__Bacteroidetes;c__Bacteroidetes_[C-1];o__Bacteroidetes_[O-1];f__Bacteroidetes_[F-1];g__Bacteroidetes_[G-3];s__bacterium_HMT_365_nov_87.518%0585736945300000400124008100
SPN23k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bergeyella;s__porcorum01540179970000001600000
SPN230k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis;g__Ihubacter;s__massiliensis_nov_95.932%0008235000000800000
SPN231k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Olsenella;s__sp._Oral_Taxon_807_nov_93.835%023314624000000000000
SPN232k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Coprococcus;s__comes_nov_92.292%05250129940000650000000
SPN233k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__putredinis_nov_94.504%02207130000000000000
SPN234k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_88.200%02605936000000000000
SPN235k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_96.319%0450075000000000000
SPN236k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Butyrivibrio;s__crossotus_nov_91.347%0001180000000000000
SPN237k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__massiliensis_nov_85.704%0900270000000000000
SPN238k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__intestinalis_nov_88.978%03803642000000000000
SPN239k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Muribacter;s__muris_nov_97.295%00000040900000002963390226879325
SPN24k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__desulfuricans01060197140000000000000
SPN240k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_94.240%000809118100000013300000
SPN241k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter;s__massiliensis_nov_90.422%02482617327300005502900000
SPN242k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_87.483%0006254000000000000
SPN243k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__oxidoreducens_nov_88.673%0005458000000000000
SPN244k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.579%02803146000000000500
SPN245k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__intestinalis_nov_90.147%05401937000000000000
SPN246k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis;g__Anaerovorax;s__odorimutans_nov_91.293%01102474000000000000
SPN247k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis_nov_91.706%0001080000000000000
SPN248k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes_nov_93.960%0004464000000000000
SPN249k__Bacteria;p__Firmicutes;c__Firmicutes_[C];o__Firmicutes_[O];f__Firmicutes_[F];g__Firmicutes_[G];s__sp._Oral_Taxon_A55_nov_84.676%024013500000002000000
SPN25k__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelatoclostridium;s__saccharogumia03736700000000000000
SPN250k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_84.462%038192890000001300000
SPN251k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella;s__massiliensis_nov_91.385%01183220050206500002400040
SPN252k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_90.608%00024843800000011100000
SPN253k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Adlercreutzia;s__equolifaciens_nov_91.984%0005249040000000000
SPN254k__Bacteria;p__Saccharibacteria_(TM7);c__Saccharibacteria_(TM7)_[C-1];o__Saccharibacteria_(TM7)_[O-1];f__Saccharibacteria_(TM7)_[F-1];g__Saccharibacteria_(TM7)_[G-3];s__bacterium_HMT_351_nov_95.044%021001700003103600000
SPN255k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis;g__Ihubacter;s__massiliensis_nov_96.000%001155250000001400000
SPN256k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Acetatifactor;s__muris_nov_89.374%0003075000000000000
SPN257k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.650%0600045000000000000
SPN258k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis_nov_90.963%0004658000000000000
SPN259k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_84.451%0272120130000230000000
SPN26k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Phocea;s__massiliensis000129309000000000000
SPN260k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Clostridium;s__sp._str._NML04A032_nov_91.349%0004361000000000000
SPN261k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis_nov_88.535%01403455000000000000
SPN262k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__minuta_nov_82.420%0190000000830000000
SPN263k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__senegalensis_nov_95.203%0430013190000012102300000
SPN264k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__senegalensis_nov_95.476%0310724972000000205001500
SPN265k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__unclassified_Ruminococcaceae;s__sp._str._D16_nov_95.244%0530460000000300000
SPN266k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_90.435%0001686000000000000
SPN267k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Negativibacillus;s__massiliensis_nov_91.432%02704332000000000000
SPN268k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes_nov_95.366%0004358000000000000
SPN269k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus_nov_94.263%05200250000000002300
SPN27k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_[F-1];g__Clostridiales_[F-1][G-1];s__bacterium_HMT_0930673124575858502900432000011500
SPN270k__Bacteria;p__Saccharibacteria_(TM7);c__Saccharibacteria_(TM7)_[C-1];o__Saccharibacteria_(TM7)_[O-1];f__Saccharibacteria_(TM7)_[F-1];g__Saccharibacteria_(TM7)_[G-3];s__bacterium_HMT_351_nov_96.521%0013111400002503700000
SPN274k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas;s__pasteri_nov_93.988%0000001099000000199027353777
SPN276k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__senegalensis_nov_95.679%042077286400000026300000
SPN28k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Faecalicatena;s__orotica0261770000005100004800
SPN285k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis_nov_92.508%045210095000001320000000
SPN287k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__luti_nov_88.963%0007631159000000000000
SPN29k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Robinsoniella;s__peoriensis0205094131000000000000
SPN296k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.085%01453141211250000580000000
SPN299k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.431%002218123920000213027500000
SPN3k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__murinus072839435000082013300000
SPN30k__Bacteria;p__Saccharibacteria_(TM7);c__Saccharibacteria_(TM7)_[C-1];o__Saccharibacteria_(TM7)_[O-1];f__Saccharibacteria_(TM7)_[F-1];g__Saccharibacteria_(TM7)_[G-3];s__bacterium_HMT_35107495891440000000002300
SPN307k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__coccoides_nov_88.704%01780256322000000000000
SPN31k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella;s__massiliensis013938811460000000001600
SPN311k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella;s__massiliensis_nov_91.385%0112301663760530000240016700
SPN318k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__polysaccharolyticum_nov_88.889%04112130724400002501400000
SPN319k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes_nov_95.363%02280195598000000000000
SPN32k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Muribacter;s__muris0007022300000000001500
SPN324k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichidae;g__Dubosiella;s__newyorkensis_nov_91.039%00000019100000086160200
SPN33k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__gallinarum0317203545000000000000
SPN330k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__swellfunianum_nov_85.944%001520000005860000000
SPN336k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Culturomica;s__massiliensis_nov_91.957%00045185800000056800000
SPN34k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__unclassified_Ruminococcaceae;s__sp._str._D160002091740000002500000
SPN347k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_92.107%06206331166000000000000
SPN35k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotaenia;s__torta0059291190000003700000
SPN351k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_88.120%0003283820000001800000
SPN359k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.086%0387839467641493083001749016905657500
SPN36k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Oscillospiraceae;g__Oscillibacter;s__valericigenes06590176330000410000000
SPN360k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.140%0579955824920000450000000
SPN362k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__unclassified_Ruminococcaceae;s__sp._str._D16_nov_97.049%0510264387000000000000
SPN37k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Bacteroides;s__capillosus0101281071520000000001600
SPN372k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.292%01539457254005600230820022200
SPN373k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus_nov_95.177%0613390360100000000000
SPN38k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__guttoideum0102458784070600001820310005800
SPN384k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.868%013910527112600000038001400
SPN385k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Mucispirillum;s__schaedleri_nov_96.266%01880737785000000000000
SPN39k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__putredinis0460111237000000000000
SPN395k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__mesocricetorum_nov_97.750%0590401857559000011160199800000
SPN397k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_92.600%088333414718800004206800000
SPN4k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Crocinitomicaceae;g__Wandonia;s__haliotis04415400000000000000
SPN40k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__scindens000225163000000000000
SPN406k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_[F-1];g__Clostridiales_[F-1][G-1];s__bacterium_HMT_093_nov_87.726%058973000000280000000
SPN409k__Bacteria;p__Candidatus Melainabacteria;c__NA;o__NA;f__NA;g__Vampirovibrio;s__chlorellavorus_nov_84.116%049128729746500000011900000
SPN41k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__scindens0158086144000000000000
SPN417k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__swellfunianum_nov_85.934%00810000006050000000
SPN42k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Clostridium;s__glycyrrhizinilyticum01000129158000000000000
SPN421k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.820%030757933725500001140000000
SPN428k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_93.057%01340302249000000000000
SPN429k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__rodentium_nov_96.709%0430166942690000360000000
SPN43k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__glycyrrhizinilyticum09971047219470403500722010680016700
SPN434k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_86.788%0164484269359000021808900000
SPN44k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcaceae_[G-2];s__bacterium_HMT_0850885665176000000000000
SPN440k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__senegalensis_nov_95.203%0342710171000011704400000
SPN445k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.517%001826453460000184022200000
SPN45k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Adlercreutzia;s__equolifaciens08801601250000001200000
SPN450k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_94.314%0002933590000003000000
SPN455k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.229%028641440136000008500002300
SPN46k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Asaccharobacter;s__celatus031497171038000000012300
SPN460k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_90.763%02360214230000000000000
SPN466k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Mucispirillum;s__schaedleri_nov_96.334%01510584816000000000000
SPN47k__Bacteria;p__Firmicutes;c__Clostridia;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Moorella;s__thermoacetica0271163355000000600000
SPN471k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_90.818%000318361000000000000
SPN478k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.086%0394834667861196080001521012002048400
SPN479k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__luti_nov_88.963%00069175000000011000000
SPN48k__Plantae;p__Pinophyta;c__Pinopsida;o__Pinales;f__Pinaceae;g__Pinus;s__thunbergii_Oral_Taxon_D30039028158000000000000
SPN482k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__merdae_nov_95.512%03916985132000000000000
SPN49k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__intestinalis06600138000013702900700
SPN490k__Bacteria;p__Bacteroidetes;c__Bacteroidetes_[C-1];o__Bacteroidetes_[O-1];f__Bacteroidetes_[F-1];g__Bacteroidetes_[G-3];s__bacterium_HMT_365_nov_87.518%030480275624000000140008500
SPN493k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.159%050353761930000001900000
SPN5k__Bacteria;p__Firmicutes;c__Firmicutes_[C];o__Firmicutes_[O];f__Firmicutes_[F];g__Firmicutes_[G];s__sp._Oral_Taxon_A550000000000000049400
SPN50k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaeromassilibacillus;s__senegalensis000000480000000205803392150
SPN501k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_92.107%0570526892000000000000
SPN502k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Beduini;s__massiliensis_nov_89.786%0311643821200006000001100
SPN51k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__luti000271104000000000000
SPN510k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospira;s__multipara_nov_90.454%0436962154840000108012700000
SPN512k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Sutterella;s__sp._str._cont1.66_nov_95.947%05661834792546000057904620014000
SPN52k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__symbiosum013501219200001301300000
SPN521k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospira;s__multipara_nov_90.387%06417216839700009109400000
SPN523k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.085%09824813412500001203400000
SPN53k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Odoribacter;s__splanchnicus0210114239000000000000
SPN532k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__loescheii_nov_89.780%0260011082400000025300000
SPN534k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus_nov_94.712%000331320000000000000
SPN535k__Bacteria;p__Saccharibacteria_(TM7);c__Saccharibacteria_(TM7)_[C-1];o__Saccharibacteria_(TM7)_[O-1];f__Saccharibacteria_(TM7)_[F-1];g__Saccharibacteria_(TM7)_[G-3];s__bacterium_HMT_351_nov_96.662%0880198466000015022600000
SPN54k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__phytofermentans000706320340000580013300
SPN545k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_86.788%03064003051680000155010400000
SPN546k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Mordavella;s__massiliensis_nov_92.642%0445075950000000003000
SPN55k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__phytofermentans0112097160000000000000
SPN557k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__saccharolyticum_nov_91.206%01350213291000000000000
SPN558k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.069%042976456474000000000000
SPN56k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__merdae0185277575000000000000
SPN568k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_91.767%0120475936000000000000
SPN57k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__algidixylanolyticum0222962630380015028009500
SPN577k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella;s__species1_MOT32_nov_97.755%00000051000720016003454
SPN58k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Neglecta;s__timonensis0001561450000004900000
SPN580k__Bacteria;p__Candidatus Melainabacteria;c__NA;o__NA;f__NA;g__Vampirovibrio;s__chlorellavorus_nov_84.141%0531238108391000034010200000
SPN588k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_92.824%00075550000000000000
SPN59k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis0118508394000000000000
SPN591k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Bariatricus;s__massiliensis_nov_90.013%0900274200000011880000000
SPN592k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.018%09202390135000049014003200
SPN598k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_[F-1];g__Clostridiales_[F-1][G-1];s__bacterium_HMT_093_nov_88.000%00068326000000171005800
SPN6k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminiclostridium;s__alkalicellulosi000031800000000017100
SPN60k__Bacteria;p__Cyanobacteria;c__Gloeobacterophycideae;o__Gloeobacterales;f__Gloeobacteraceae;g__Gloeobacter;s__violaceus01501102030000001700000
SPN602k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichidae;g__Dubosiella;s__newyorkensis_nov_90.971%0000000000000601265510
SPN607k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.535%0000000000000062300
SPN61k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae_[XV];g__Eubacterium;s__ventriosum06905967777550000399016602412300
SPN612k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__sp._str._L2_50_nov_91.165%0009124250000003000000
SPN62k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_[F-1];g__Clostridiales_[F-1][G-2];s__bacterium_HMT_4020720159113000000000000
SPN623k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__putredinis_nov_95.445%04800221383000057021200000
SPN627k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.669%094699110067100100053602510012000
SPN63k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__swellfunianum03209517700001202600000
SPN630k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Culturomica;s__massiliensis_nov_92.024%00057962600000010700000
SPN631k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.820%0193483287191040010803700000
SPN632k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__putredinis_nov_95.445%0421203984070000560000000
SPN633k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__polysaccharolyticum_nov_88.302%00019185500000024900000
SPN634k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.168%01173746456300000064004800
SPN635k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__desulfuricans_nov_92.485%02873032848500000076006000
SPN636k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Bariatricus;s__massiliensis_nov_90.013%07674139500000014330000000
SPN637k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.282%0000428027000000016300
SPN638k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.168%0792936542800000049003800
SPN639k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Olsenella;s__sp._Oral_Taxon_807_nov_93.239%03436133926059000000016700
SPN64k__Bacteria;p__Bacteroidetes;c__Bacteroidetes_[C-1];o__Bacteroidetes_[O-1];f__Bacteroidetes_[F-1];g__Bacteroidetes_[G-3];s__bacterium_HMT_36504417331130200003205500000
SPN640k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_91.048%03761553362000038087008500
SPN641k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Odoribacter;s__splanchnicus_nov_94.054%0470025638500004205100000
SPN642k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.871%000477573000000109004300
SPN643k__Bacteria;p__Saccharibacteria_(TM7);c__Saccharibacteria_(TM7)_[C-1];o__Saccharibacteria_(TM7)_[O-1];f__Saccharibacteria_(TM7)_[F-1];g__Saccharibacteria_(TM7)_[G-3];s__bacterium_HMT_351_nov_96.662%0138027746500000030200000
SPN644k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bergeyella;s__porcorum_nov_93.918%000000650000001130382617
SPN645k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_91.980%000000185000000098500
SPN646k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__rodentium_nov_96.707%041021313733100004400003000
SPN647k__Bacteria;p__Firmicutes;c__Clostridia;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Moorella;s__thermoacetica_nov_85.797%077184435740000004600000
SPN648k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_92.530%065926590820000006200000
SPN649k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_84.758%03151800000001200000000
SPN65k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__vulgaris000205126000000900000
SPN650k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotellamassilia;s__timonensis_nov_89.467%090013732809117804900799010140015200
SPN651k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bergeyella;s__porcorum_nov_93.914%0000005800000021094409387
SPN652k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.871%00045553908000087004200
SPN653k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Odoribacter;s__splanchnicus_nov_93.948%0426022834300003805400000
SPN654k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_87.018%071220456110000000000000
SPN655k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__xylanophilum_nov_91.409%000371529032000043009800
SPN656k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__desulfuricans_nov_92.419%0247029639000000072005300
SPN657k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_91.928%000000185000000087200
SPN658k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__shahii_nov_91.110%04071661400166000000030100
SPN659k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter;s__massiliensis_nov_90.489%032434227321000063040002100
SPN66k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__sp._str._A4064171331140000001100000
SPN660k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Bacteroides;s__capillosus_nov_95.047%01450131336000000000000
SPN661k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__polysaccharolyticum_nov_88.235%002115463200000021600000
SPN662k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__gallinarum_nov_96.447%000003450000002530000
SPN663k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Mordavella;s__massiliensis_nov_92.642%0402053790000000004900
SPN664k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus_nov_95.177%05480034000000000000
SPN665k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__bolteae_nov_93.311%0130023417600001502200000
SPN666k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__gallinarum_nov_95.197%000002960000002710000
SPN667k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__coccoides_nov_88.977%01370214216000000000000
SPN668k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Beduini;s__massiliensis_nov_89.786%0391142925401000570000000
SPN669k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella;s__species1_MOT32_nov_95.593%0000001340000000165745021877
SPN67k__Bacteria;p__Candidatus Melainabacteria;c__NA;o__NA;f__NA;g__Vampirovibrio;s__chlorellavorus0140074125000000000000
SPN670k__Bacteria;p__Candidatus Melainabacteria;c__NA;o__NA;f__NA;g__Vampirovibrio;s__chlorellavorus_nov_83.241%07601666480000008900800
SPN671k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_90.818%000286274000000000000
SPN672k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_90.470%0280370148000040000000
SPN673k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis_nov_91.293%0003271860000003300000
SPN674k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.426%042087417000000000000
SPN675k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_92.991%011502381660000002100000
SPN676k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Roseburia;s__faecalis_nov_90.629%02220148167000000000000
SPN677k__Bacteria;p__Bacteroidetes;c__Bacteroidetes_[C-1];o__Bacteroidetes_[O-1];f__Bacteroidetes_[F-1];g__Bacteroidetes_[G-3];s__bacterium_HMT_365_nov_87.279%036109481000000000000
SPN678k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.633%03201100000005300005200
SPN679k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_89.868%01198722999000000000000
SPN68k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__sciuri0123013480000000000000
SPN680k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis_nov_92.364%059613197000001490000000
SPN681k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum;s__intestinale_nov_90.586%010587059688480000227038800000
SPN682k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__unclassified_Ruminococcaceae;s__sp._str._D16_nov_97.116%0360196300000000000000
SPN683k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__merdae_nov_95.512%03205455101000000000000
SPN684k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerotignum;s__lactatifermentans_nov_84.758%02571500000001210000000
SPN685k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__shahii_nov_91.030%000000129000000039800
SPN686k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_[F-1];g__Clostridiales_[F-1][G-1];s__bacterium_HMT_093_nov_87.726%04685300000000000000
SPN687k__Bacteria;p__Tenericutes;c__Mollicutes;o__Mycoplasmatales;f__Mycoplasmataceae;g__Ureaplasma;s__urealyticum_nov_91.069%08410584330000103011100000
SPN688k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales_[F-1];g__Clostridiales_[F-1][G-1];s__bacterium_HMT_093_nov_88.000%00048294000000129004000
SPN689k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__saccharolyticum_nov_91.339%0990183226000000000000
SPN69k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Enterorhabdus;s__caecimuris000174157000000000000
SPN690k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__shahii_nov_91.290%000000144000000035900
SPN691k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Coprococcus;s__comes_nov_92.292%063501611170000600000000
SPN7k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminoclostridium;s__alkalicellum07613117740014003701200000
SPN70k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__oxidoreducens0124072134000000000000
SPN71k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Acetivibrio;s__cellulolyticus0676061142000000000000
SPN72k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella;s__majae000592030000006600000
SPN73k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Lacnoclostridium;s__saccharolyticum0001129160200000064000000
SPN74k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__saccharolyticum000150173000000000000
SPN75k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__unclassified_Erysipelotrichaceae;s__sp._str._cont1.113000004380000004760000
SPN76k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Acetatifactor;s__muris030020785000000000000
SPN77k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Blautia;s__gnavus000180140000000000000
SPN78k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__xylanophilum0720801400000000002700
SPN79k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotellamassilia;s__timonensis0001281350700004800000
SPN8k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__massiliensis0230096154000000000000
SPN80k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Beduini;s__massiliensis000641640000008300000
SPN81k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Butyrivibrio;s__crossotus0600133118000000000000
SPN82k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus;s__rubiinfantis0129072910000001800000
SPN83k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminiclostridium;s__hungatei0026252160000001600000
SPN84k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__coccoides02191190395428000042903810011300
SPN85k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella;s__species1_MOT3203220200388000000000000
SPN86k__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum;s__rodentium034023241000000000000
SPN87k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Mailhella;s__massiliensis000104201000000000000
SPN88k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__wadsworthia04200135000010801900000
SPN89k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Atopostipes;s__suicloacalis0450136122000000000000
SPN9k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas;s__pasteri05425250151000000000000
SPN90k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Marvinbryantia;s__formatexigens0129011551000000000600
SPN91k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Bariatricus;s__massiliensis0120084760000001800000
SPN92k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Defluviitaleaceae;g__Defluviitalea;s__saccharophila052014298000000000000
SPN93k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__polysaccharolyticum0000000000000108033149
SPN94k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__NA;g__NA;s__pectinophilus0783111100000000006700
SPN95k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae_[XIVa];g__Coprococcus;s__pectinophilus0109011364000000000000
SPN96k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__acidominimus000450460000000000000
SPN97k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae;g__Oxalobacter;s__vibrioformis011111196016940000405011200000
SPN98k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter;s__fetus011509179000000000000
SPN99k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruthenibacterium;s__lactatiformans014506969000000000000
SPP1k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Muribacter;s__muris00000024900000009311262066336234
SPP2k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__multigenus;s__multispecies_spp2_2307000026709713000000000
SPPN1k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lacnoclostridium;s__scindens014515155105000000000000
SPPN10k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Coprococcus;s__pectinophilus0008092000000000000
SPPN11k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__NA;s__pectinophilus0007184000000000000
SPPN12k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lachnoclostridium;s__glycyrrhizinilyticum06411060000000000000
SPPN13k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lachnoclostridium;s__scindens0550660000000000000
SPPN14k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__NA;s__pectinophilus0430740000000000000
SPPN15k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lacnoclostridium;s__phytofermentans01505361280000005100000
SPPN2k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lacnoclostridium;s__saccharolyticum0118516749000060000000
SPPN22k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lachnoclostridium;s__scindens04526103300006603001800
SPPN27k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lacnoclostridium;s__phytofermentans000504690000004600000
SPPN29k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lacnoclostridium;s__scindens03904730240000510000000
SPPN3k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Clostridium;s__glycyrrhizinilyticum000121199000000000000
SPPN4k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__multigenus;s__multispecies_sppn4_2_nov_85.322%0180611080000005800000
SPPN5k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lachnoclostridium;s__phytofermentans00012887000000000000
SPPN6k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Coprococcus;s__pectinophilus06009260000000000000
SPPN7k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__multigenus;s__multispecies_sppn7_2_nov_85.302%021051730000005000000
SPPN8k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lachnoclostridium;s__glycyrrhizinilyticum071030700000140000000
SPPN9k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__multifamily;g__Lachnoclostridium;s__scindens06901080000000000000
 
 
Download Read Count Tables at Different Taxonomy Levels
domain
phylum
class
order
family
genus
species
;
 

Sample Taxonomy Bar Plots

 

VII. 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

 

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 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.

 
 

VIII. 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-dimentional 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 seperately. The results are shown below:

 
 
 
 
 

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:

 
 
 
 
 

Interative 3D PCoA Plots - Bray-Curtis Dissimilarity

 
 
 

Interative 3D PCoA Plots - Euclidean Distance

 
 
 

Interative 3D PCoA Plots - Correlation Coefficients

 
 
 

IX. 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

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.

 

ANCOM differetial abundance analysis

 
View ANCOM results
Comparison No.Comparison Name
Comparison 1.Oral vs Oral_Jax vs Fecal
 
 
 

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.

 
Oral vs Oral_Jax vs Fecal
 
 
 
 
 

X. Analysis - Heatmap Profile

 

Species vs sample abundance heatmap

 
 
 

XI. Analysis - Network Association

To analyze the co-occurrence or co-exclusion between microbial species among different samples, network correlation analysis tools are ususally 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., grahical 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)

 

 

 

SPIEC-EASI network inference by inverse covariance selection (GLASSO method)

 

 

 

Association network inference by SparCC

 

 

 
 

Copyright FOMC 2021