FOMC Service Report

16S rRNA Gene V1V3 Amplicon Sequencing

Version V1.41 fork

Version History

The Forsyth Institute, Cambridge, MA, USA
September 23, 2023

Project ID: 20230919_HAKU_1


I. Project Summary

Project 20230919_HAKU_1 services do not include NGS sequencing of the V1V3 region of the 16S rRNA gene amplicons from the samples. First and foremost, please download this report. These links will expire after 60 days. We cannot guarantee the availability of your data after 60 days.

Full Bioinformatics analysis service was requested.

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

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

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

 

II. Workflow Checklist

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

III. NGS Sequencing

Not available
 

IV. Complete Report Download

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

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

Complete report download link:

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

 

V. Raw Sequence Data Download

Not available
 

VI. Analysis - DADA2 Read Processing

Not available
 

Sample Meta Information

#SampleIDSampleNameGroupGROUP_AGEDRPART-SEXGROUP_SHEDEVERSHEDHIV_STATUSPriortestSEQHIV_SheddingGender_Shedding
HAKU.02057.04HAKU.02057.04CHILD-NON-SHEDDERCHILDMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.04092.05HAKU.04092.05CHILD-NON-SHEDDERCHILDFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.06449.04HAKU.06449.04CHILD-NON-SHEDDERCHILDMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.06601.03HAKU.06601.03CHILD-NON-SHEDDERCHILDFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.07991.04HAKU.07991.04CHILD-SHEDDERCHILDFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.10302.01HAKU.10302.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.12368.01HAKU.12368.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.12368.03HAKU.12368.03CHILD-SHEDDERCHILDFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.12653.01HAKU.12653.01ADULT-SHEDDERADULTMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.13254.01HAKU.13254.01ADULT-SHEDDERADULTFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.13254.03HAKU.13254.03ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.14131.01HAKU.14131.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.14131.03HAKU.14131.03CHILD-NON-SHEDDERCHILDMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.14257.05HAKU.14257.05CHILD-NON-SHEDDERCHILDFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.14257.06HAKU.14257.06CHILD-SHEDDERCHILDFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.15133.01HAKU.15133.01ADULT-SHEDDERADULTFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.15133.03HAKU.15133.03CHILD-NON-SHEDDERCHILDFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.15133.05HAKU.15133.05CHILD-SHEDDERCHILDMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.16063.02HAKU.16063.02ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.16255.04HAKU.16255.04ADULT-SHEDDERADULTMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.17022.02HAKU.17022.02CHILD-SHEDDERCHILDMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.17043.01HAKU.17043.01ADULT-SHEDDERADULTFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.17043.03HAKU.17043.03CHILD-SHEDDERCHILDFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.17251.01HAKU.17251.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.17282.03HAKU.17282.03CHILD-NON-SHEDDERCHILDFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.17575.01HAKU.17575.01ADULT-SHEDDERADULTFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.17575.08HAKU.17575.08ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.18078.01HAKU.18078.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.19356.04HAKU.19356.04CHILD-SHEDDERCHILDMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.19356.05HAKU.19356.05ADULT-SHEDDERADULTMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.21309.01HAKU.21309.01ADULT-SHEDDERADULTMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.22420.02HAKU.22420.02ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERFemale NON-SHEDDER
HAKU.22968.02HAKU.22968.02ADULT-SHEDDERADULTFemaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERFemale SHEDDER
HAKU.22968.06HAKU.22968.06CHILD-SHEDDERCHILDMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.23313.04HAKU.23313.04CHILD-NON-SHEDDERCHILDMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.24962.03HAKU.24962.03CHILD-SHEDDERCHILDMaleSHEDDERyesnegative1SEQ039HIV-Neg SHEDDERMale SHEDDER
HAKU.25095.01HAKU.25095.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnonegative1SEQ039HIV-Neg NON-SHEDDERMale NON-SHEDDER
HAKU.02057.01HAKU.02057.01ADULT-SHEDDERADULTMaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERMale SHEDDER
HAKU.05094.01HAKU.05094.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.05791.01HAKU.05791.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.06266.01HAKU.06266.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.06641.01HAKU.06641.01ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
HAKU.06912.03HAKU.06912.03ADULT-SHEDDERADULTMaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERMale SHEDDER
HAKU.06978.01HAKU.06978.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.07031.01HAKU.07031.01ADULT-SHEDDERADULTMaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERMale SHEDDER
HAKU.07102.01HAKU.07102.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.07104.01HAKU.07104.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.08146.01HAKU.08146.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.10105.01HAKU.10105.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.12128.01HAKU.12128.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.13032.01HAKU.13032.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.13051.01HAKU.13051.01ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
HAKU.13110.01HAKU.13110.01ADULT-SHEDDERADULTMaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERMale SHEDDER
HAKU.13254.02HAKU.13254.02ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.15133.08HAKU.15133.08ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.16255.01HAKU.16255.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.16255.02HAKU.16255.02ADULT-SHEDDERADULTMaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERMale SHEDDER
HAKU.17022.01HAKU.17022.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.17164.01HAKU.17164.01ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
HAKU.17164.06HAKU.17164.06ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
HAKU.17364.01HAKU.17364.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.18305.01HAKU.18305.01ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.19122.01HAKU.19122.01ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
HAKU.21294.01HAKU.21294.01ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
HAKU.22022.01HAKU.22022.01ADULT-NON-SHEDDERADULTMaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERMale NON-SHEDDER
HAKU.25284.02HAKU.25284.02ADULT-NON-SHEDDERADULTFemaleNON-SHEDDERnopositive2SEQ041HIV-Pos NON-SHEDDERFemale NON-SHEDDER
HAKU.25705.02HAKU.25705.02ADULT-SHEDDERADULTFemaleSHEDDERyespositive2SEQ041HIV-Pos SHEDDERFemale SHEDDER
 
 

ASV Read Counts by Samples

#Sample IDRead Count
HAKU.19356.0525,795
HAKU.06912.0328,475
HAKU.17282.0328,730
HAKU.06601.0328,949
HAKU.15133.0830,535
HAKU.07104.0130,920
HAKU.14257.0636,669
HAKU.17043.0338,148
HAKU.17575.0840,616
HAKU.12368.0340,676
HAKU.06449.0441,135
HAKU.07991.0441,660
HAKU.23313.0441,706
HAKU.12653.0142,335
HAKU.15133.0142,545
HAKU.17043.0142,710
HAKU.15133.0342,967
HAKU.22968.0243,087
HAKU.19356.0443,706
HAKU.22968.0643,874
HAKU.12368.0144,138
HAKU.14131.0344,184
HAKU.17575.0144,291
HAKU.25284.0244,885
HAKU.10105.0144,984
HAKU.16255.0445,918
HAKU.14257.0546,123
HAKU.10302.0146,218
HAKU.16063.0247,633
HAKU.13254.0348,235
HAKU.02057.0448,322
HAKU.14131.0148,431
HAKU.22420.0248,649
HAKU.17164.0648,690
HAKU.13254.0148,972
HAKU.21309.0149,067
HAKU.15133.0549,692
HAKU.17022.0250,011
HAKU.25095.0151,219
HAKU.04092.0551,685
HAKU.18078.0151,693
HAKU.24962.0351,720
HAKU.21294.0151,796
HAKU.17251.0152,051
HAKU.13254.0252,495
HAKU.17164.0153,230
HAKU.13032.0153,578
HAKU.17364.0156,377
HAKU.16255.0157,409
HAKU.22022.0159,817
HAKU.12128.0162,172
HAKU.25705.0263,606
HAKU.06978.0163,770
HAKU.18305.0164,705
HAKU.08146.0165,095
HAKU.16255.0267,126
HAKU.13051.0167,808
HAKU.19122.0170,404
HAKU.05094.0170,625
HAKU.06266.0171,430
HAKU.06641.0171,848
HAKU.17022.0176,274
HAKU.07102.0179,326
HAKU.02057.0180,201
HAKU.13110.0183,060
HAKU.07031.0187,315
HAKU.05791.0196,451
 
 
 

VII. Analysis - Read Taxonomy Assignment

Read Taxonomy Assignment - Methods

 

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

Version 20210310
 

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

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

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

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

3. Designations used in the taxonomy:

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

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

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

Read Taxonomy Assignment - Result Summary *

CodeCategoryMPC=0% (>=1 read)MPC=0.01%(>=334 reads)
ATotal reads3,487,9673,487,967
BTotal assigned reads3,346,6183,346,618
CAssigned reads in species with read count < MPC027,942
DAssigned reads in samples with read count < 50000
ETotal samples6767
FSamples with reads >= 5006767
GSamples with reads < 50000
HTotal assigned reads used for analysis (B-C-D)3,346,6183,318,676
IReads assigned to single species1,429,2291,409,914
JReads assigned to multiple species1,917,3891,908,762
KReads assigned to novel species00
LTotal number of species540276
MNumber of single species369192
NNumber of multi-species17184
ONumber of novel species00
PTotal unassigned reads141,349141,349
QChimeric reads00
RReads without BLASTN hits6262
SOthers: short, low quality, singletons, etc.141,287141,287
A=B+P=C+D+H+Q+R+S
E=F+G
B=C+D+H
H=I+J+K
L=M+N+O
P=Q+R+S
* MPC = Minimal percent (of all assigned reads) read count per species, species with read count < MPC were removed.
* Samples with reads < 500 were removed from downstream analyses.
* The assignment result from MPC=0.1% was used in the downstream analyses.
 
 
 

Read Taxonomy Assignment - ASV Species-Level Read Counts Table

This table shows the read counts for each sample (columns) and each species identified based on the ASV sequences. The downstream analyses were based on this table.
SPIDTaxonomyHAKU.02057.01HAKU.02057.04HAKU.04092.05HAKU.05094.01HAKU.05791.01HAKU.06266.01HAKU.06449.04HAKU.06601.03HAKU.06641.01HAKU.06912.03HAKU.06978.01HAKU.07031.01HAKU.07102.01HAKU.07104.01HAKU.07991.04HAKU.08146.01HAKU.10105.01HAKU.10302.01HAKU.12128.01HAKU.12368.01HAKU.12368.03HAKU.12653.01HAKU.13032.01HAKU.13051.01HAKU.13110.01HAKU.13254.01HAKU.13254.02HAKU.13254.03HAKU.14131.01HAKU.14131.03HAKU.14257.05HAKU.14257.06HAKU.15133.01HAKU.15133.03HAKU.15133.05HAKU.15133.08HAKU.16063.02HAKU.16255.01HAKU.16255.02HAKU.16255.04HAKU.17022.01HAKU.17022.02HAKU.17043.01HAKU.17043.03HAKU.17164.01HAKU.17164.06HAKU.17251.01HAKU.17282.03HAKU.17364.01HAKU.17575.01HAKU.17575.08HAKU.18078.01HAKU.18305.01HAKU.19122.01HAKU.19356.04HAKU.19356.05HAKU.21294.01HAKU.21309.01HAKU.22022.01HAKU.22420.02HAKU.22968.02HAKU.22968.06HAKU.23313.04HAKU.24962.03HAKU.25095.01HAKU.25284.02HAKU.25705.02
SP1Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT392113422631463523140141324571312221550941412815153948461601402863183714699911251646212719947152220446415359901719761021498
SP100Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;veroralis1805013031816868462105493532247435850256213115219191241763101365721151356147221501303922122172552111545201612810310506165
SP101Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Shuttleworthia;satelles63111202533114358270427742500235973580400282391512019269714912800410113354014412700871801328
SP120Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;micans0471300410104718600015010312010124510011210202025450005002614024619012153720281860180
SP121Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnoanaerobaculum;orale151110256141742741832396234913043951193414383172314412912777935916643494132162943210487384153134359940261466939241361703011028223213515483312587928174
SP122Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;oralis9462901178974983716351418710889911073091101951163548121470012918412616155140161338263217315394012816784710771941033543322551310458618311017224557913884951551776420118
SP127Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;fusca26523210800600084021801014000000305109600117807130946001191860100400000900430
SP137Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Megasphaera;micronuciformis17866013781514764621216925219722543141084996113622326526934767111731378121882485082271381023222081721217231109215867668292406913911444806250316170
SP138Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;dianae0620010002149400002410001111502031403001100110042403142001500651460355274300005041
SP139Bacteria;Proteobacteria;Deltaproteobacteria;Desulfobacterales;Desulfobulbaceae;Desulfobulbus;sp. HMT0410000010001611000017000001011000000030000081004824090158190850122209300004371
SP15Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;salivae1192043094972104610572824518142131197375109533831065757851021110268296113800281854967551912129506491102411667812141295723706170431552821177511292121050816619517788338
SP152Bacteria;Firmicutes;Clostridia;Negativicutes;Veillonellaceae;Veillonella;sp. HMT7802426115253189261412857600414425724729381481475696352524620800113176934242547596486031587042628012717693822100998961742402114961066039223400887493121333365490250
SP153Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT2560010003000000000300001000000000020002000000784130000064117000000240010042320
SP155Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Catonella;morbi17173223151640285032802465616762449156271617008033171111154451834796627181715451170308332600670063011139
SP156Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-1];bacterium HMT07568134180515438561461694935495819321548616818713112118078825515397120171121848283124152924246817733903915913143115127261731335914
SP159Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-3];bacterium HMT28000300170005000010490001101900003000035001050271901160002431260650046180000013520
SP16Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;actinomycetemcomitans09245000747008900002300000000000000045953388514300409800310900100059000032000000000027
SP160Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;buccalis39601213940125013501371222132111011294409134211049338921243874185271573221286540268261840111116812132615418371161610324
SP161Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Tannerella;serpentiformis33900240135035426911010240400075100505241419817501011540263005501113322274363121
SP169Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-5];bacterium HMT505003000012007000080900001600000110137015110154180346201700910640130000001200900038100
SP17Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT34519011156100281008000080004132135002219310000080011829314026158010274735331035002271171010133350
SP170Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;sp. HMT10200000000002500021000017111801230100000000420401801400001115400011218800000704
SP174Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT91412545154341424080206331104323531600310561501316127126831712613015932171210360018218038513232828047070018150110
SP175Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3092688535010021003384100101299010940441243036040013183390149320053900112122600306212410010
SP176Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;noxia659111555102752176881214680240382349994260017275725839107588376617101342351728115118584431012080967106819
SP19Bacteria;Firmicutes;Clostridia;Eubacteriales;Eubacteriaceae;Pseudoramibacter;alactolyticus6600010000003200100600114900000050000000104320221310390100410424100002400677
SP203Bacteria;Firmicutes;Clostridia;Negativicutes;Veillonellaceae;Veillonella;sp. HMT91700134013000450081209900500300882000600456111181940000103660167026400000178500120417123120000
SP204Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Peptidiphaga;gingivicola1584237822655252733051711240275376308311400028991516401500115273258800260111010128349843171825139127
SP206Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oulorum761692421151431964241846597217122722724121285072491354195233862420340410100216571792361352138341483814710274489469051101
SP208Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-8];bacterium HMT5000050050116921001858200035121002400000540011020244911201801263015001990107412008002243843
SP216Bacteria;Firmicutes;Bacilli;Lactobacillales;Aerococcaceae;Abiotrophia;defectiva6335791043703212227361205160291131132601711231212425603560226109721312790295124782741451228341046133812222370332489150574422988262197158115459522763367122
SP217Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;pleuritidis5219302750310034818214000219181040401000158013128223103033175049582056740127100941411100691110182
SP220Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;koreensis00400100000100000000004060000220000200000001005000002291910000000000001642
SP23Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT30010201509100128120000405922724026140116187020001143201211192200121102901000094005050
SP243Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Butyrivibrio;sp. HMT45514014151317003301653224753160410014165112478505001160043804020200104202111045150800163010130
SP248Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;gingivalis000006400003124006841516702590256039703005530002800047500118384104764053000016194099200112461150400301991568705
SP253Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Dialister;invisus10917116302298398242120308154013642102919432454291601518404542997363015520202016331273851518122051172623841583512916218231115862331118477
SP254Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT2251022541603152660167102104120365201309258013739813091038120702512213593331152630142032571001242190149181014390151639875
SP255Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multisaccharivorax20400100008021151490001440000690202603025101800011805062000300008000034031027420000385
SP256Bacteria;Synergistetes;Synergistia;Synergistales;Synergistaceae;Fretibacterium;fastidiosum00201129006134300061330102207100120300001300314132513840067217014403244550055038444
SP257Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;baroniae00270980019232000019481127058418502108023034041600853006923180060400242207187039891111400007928
SP266Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Stomatobaculum;longum455604105220134742148330485155624814117314523817165134831286827914805571159211763948751850167464810367132371604216461903345505115128862121037
SP267Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;pallens178672233497516841935189112871831231002508212610180558115713095113467856470051088541440816222721108542514911583152429625233352334204722193841040117169257185
SP269Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-5];[Eubacterium]_saphenum0060050005550002141210040045221144020060000404501000034199034000147823907680004718540004024828372
SP278Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT4720160491243355359291715090021317130925001149007006312401004500520016030170100005114
SP282Bacteria;Firmicutes;Clostridia;Clostridiales;Peptoniphilaceae;Parvimonas;micra381371663360158054979373121642275662610901374213241920621402875101480310185664012658151342564317611077262390107150549122719
SP283Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;gracilis2609425123596359812742824764842515141527833328172252470012122992163530261612017105181111105104327143600152142471657816535928219878
SP285Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-5];bacterium HMT507008000000000000000080123000000001001640000006178000000147000000032000006700
SP286Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT41710724124185367712721024625918901517433335585820721167709703758749351404129212552922536258643601214731271910910225287056978121149371401365280665122282254941854837164620714417516
SP290Bacteria;Firmicutes;Clostridia;Clostridiales;Peptoniphilaceae;Peptoniphilaceae_[G-1];bacterium HMT1130000000000000400000001714210000100000003000007000000002900008330000002511810
SP291Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multiformis001860083000033000000550025901370301032005057021261700259234134429300211328034781124211310081050
SP292Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;shahii25311565912723416811220913919622310015627124813241517452402050923126301318716579129816926912049411843503257436228242152974244832078105
SP293Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum30136088132251951443543884638155212111992471134671332271339363761384213569736155163219699298300661691562089761555845950602403950243648422181481693208319929697251
SP294Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;concisus701281451741398683183138117483220453812144361471091359275160194314820765641921510652459716512193223261083401012012091411559216441017822933323183252149057
SP295Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT909360012210004210200113067020120100001307010833200300015920105081712020371620
SP297Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Pseudostreptobacillus;hongkongensis01001025000000054012000201150400301047100001821200100040000000700001000300
SP298Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;valvarum0816172582413336301224702605380005101016017810811160170215111301223012101015120394671354
SP300Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;denticola498403336664011212120361063901310358102275076536446191250391444109053722918594345333492052900440432018662391012554432111524185
SP301Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-2];bacterium HMT091120224010012616230402164350611600521000022004120612901406070239016013233100001161228
SP304Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;hongkongensis61618041160267012522176221310131171082938301839135153014112281211165321511005462499310249016450313
SP307Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;intermedia002800172200269400047544312650340163010050117202028021201217066501838381517013550131526136604530730115261003020216064
SP310Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Granulicatella;adiacens2903521065940546757221163408434689389113114469728181751192645688854241211711513144153689412822555219779936727161190145458285116913289214712831267911395164273849068420261710762115428361252176836479341282483801168629
SP313Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Ottowia;sp. HMT8940001133270128385060121030026000480000001400030480000210001001942400090007450
SP323Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;sp. HMT0782086110162551541051140032421284937205112101121119131230121503113110217260201055500128702537921402509
SP328Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Atopobium;sp. HMT1992100404350149527801804105343230110128914002010162301007113192924748030616118325103148950007117016275
SP329Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Rothia;aeria147182789305104252571328665319102711198082821735561592409106108160320566050941138331841329131101950263612101217482414829521584827432783930125
SP330Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidales_[F-2];Bacteroidales_[G-2];bacterium HMT27458329252036964951984325916631390020012418833322681970471443321032934610912175028278450139622707802431628000187232922
SP332Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Kingella;oralis35975441142323472811432610917018253017023287323012262114962493413896106612383805623610264072111571701345182274010542
SP333Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT25700146040025107400305931401013970001390001210266003794449474033000015105485011900027534200063132110
SP337Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sp. HMT9018000012000004930000000000000010101001000003000000000000400300300100000001
SP338Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;parvum114811474023503812104791641139082844171425921230083603913803703251562011221235101533700224119059006930
SP342Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;sp. HMT01800048220017400132022031203000311136641000261311402000021000030001101502700109162301000
SP343Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT443010003100207200051381330210214225030696000017190081009666911004373168235025040461320000021842291
SP344Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;shahii131404165801283480121215900103500026096002124213072132101860051021198120349000124018205681
SP345Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;intermedius14112180065112139281692672961115151918240350545110152133505945240164220861190204011731648230110851980124
SP346Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3136274292247199247134530168113128911621264873610167101383051371214450323001313925010829214416251773494332120651330281721910333926130466750097315148161
SP347Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;tannerae02043171539797133323210510703961865928150147113139652070183268797598013712327066445302103912386227304639068358039254082229501819373912117122
SP355Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;socranskii3127110428109411814271011062714022918428018483152156500241031551813295462140122231731120733314630022524345751
SP357Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;sp. HMT0442052120401801023224401096691300041450000141057004127115100250455951100341613591440035142460100222336
SP36Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;melaninogenica22417120471036876413618134165095223921344184529613305823982254169517120239668153620725556959943153358314059314689155647987021348123045352319815329817716886467936059038261109114862094435812125619616564
SP365Eukaryota;Streptophyta;Pinopsida;Pinales;Pinaceae;Pinus;sylvestris101244044063106219021006420010930101120007027254358037201318900200311193110610053020201018049181300
SP366Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;periodonticum3983361545155352516018152170966413813257119513823782182217003522407994625687565691080696105838705719643942035891949947240134010823486652774217155731194336925402563373625515317525845424217931027596291378429
SP37Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;histicola4224929891023317709263034021209564415146782401197136610981710401344224210091914455368692013242019049413200312131259102199686432218125917318922411977729186012115437881152442275
SP381Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT231015400201002504001022307025001501020072008447002100371020102200144400107006246
SP389Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;nucleatum_subsp._vincentii211217918671624500332222961485025223731514721315827127205291930518438207325551521682985211631136096315240426575264115827164257400207422523431552051407417174593971837
SP39Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Johnsonella;sp. HMT16600300130008000009300000120190441010000000020087709000146020100000414600000165414
SP391Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Mogibacterium;timidum001002700176017031400001713233000030200900022013213010102201001170321434000020388956
SP392Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-1];[Eubacterium]_sulci11316174114410274664965331504024296270114056134112150422864100112903665814116930665104674799021018642427843714621051880
SP400Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;lingnae_[Not_Validly_Published]523914344800298619125173514771517452806115116162342398110090124511501329014183710539501045660647012170629311440027198
SP401Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;durum1441743733311271272251381428332749202833618619601284616713258281892346345369812917271994212291248022101212224153419147110333040
SP402Bacteria;Actinobacteria;Actinomycetia;Corynebacteriales;Corynebacteriaceae;Corynebacterium;matruchotii1481198613394773911539348350199343134141391284126431315815155504128132952433452172421882358733838434110242872298199241352471528412921244298
SP407Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT942926143701652114810020140014446011001000601500020603010001301112110800864290240012052001922102441741
SP409Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Peptidiphaga;sp. HMT1831827011842130118225951510100045502112012015152348100000560416001000173119036700107001522
SP418Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;sp. HMT930139571021129216983003136466475088210327182863369086331526541261810264168810051219217618322889104682468203645142052322430251848702794163403
SP419Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Streptobacillus;felis000001724000050000037000040463000000000000000002571310000017033010750000176000005232580
SP42Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-3];bacterium HMT10053542902361230656691291106417335616152127166200127182728215541135230460342107396504604351688538709102085360
SP420Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Mitsuokella;sp. HMT5211582470027012004001120000441110400200121354001010102139030001001001300260730009
SP421Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT91283541117678000203308011000124310021320007041701144913042831021014681600140380035031541
SP424Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT498754308441124205197050224866431357451831841205975426999141685156303593374166761416227940193723553611503102519905391222284651139213
SP425Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT262013000900038000023201071150000060000092001030001170190000381217300000052000611870
SP427Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;sinus108504004185983820701947535435121144542115123183331496511349161038945452679012132352313648287306928351171542110471173887971431426332311335801
SP428Bacteria;Bacteroidetes;Bacteroidetes_[C-1];Bacteroidetes_[O-1];Bacteroidetes_[F-1];Bacteroidetes_[G-5];bacterium HMT5110053000002262552003161660133840000140440000122028410400145162413310118127223170000124928
SP429Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3174288615261145511538132828105012935131673141962163515391043521271311422141515104816017342045105696102112153214131
SP44Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;sp. HMT172128534002255527015088524650137423493031841834436460756495944125531170140054947301744071541056210620176166271113212141312250626302718751831816633014171550
SP455Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Solobacterium;moorei1523636902015719088720374475486117849238611013833397199928125647101300379111234231217525832281139818329123102711474782312181322542968137257901017
SP456Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT874070370613211052261167022400190207006716610034612096153405600281102027510074104554100213177150
SP457Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Kingella;sp. HMT0120231735702970015021611100441000038160131270148410200828700123018301080623601900285241170
SP46Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae;Erysipelotrichaceae_[G-1];bacterium HMT90500101380044210002140220019200600020001010131010174200908016002240012330490
SP464Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT2121044429732372643718242411082423515013331311920105551611072405233949104268702114941268203157591548772122676191401014076139181117923
SP468Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sputigena14352634382843512735212510291917261211131414641006291713926546313514080106181743161910163010815561389354517102317213611172282631
SP469Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;leadbetteri3655539131647954363252784217816591182723121314535194393125811610312213320237646914612473764440942118342325104571335357426
SP470Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT2170000000033013200007000011720007534320000000000640030012908852100000001500004410
SP477Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Butyrivibrio;sp. HMT0800000001200706004131320101901001930000041100001001162301800432018003013300400251863
SP478Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;flueggei92200113050011600050001741234000006111201113329000113547000000700770002100043
SP479Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Rothia;mucilaginosa898603125513075283141011655397031660139072140346599129412969187068051548551417162713105017590178428301174379536144513365671509364318022089258311115341273287841052283641343373145198180731263274477165290134215271070205039328185295612891855
SP48Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3040000010600005500000500160204010500008405400000010066980240000660200025101101817730000190316366
SP487Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-9];[Eubacterium]_brachy42102509103562861502164201221241021018214020207110210636813416211401252202879020125120307351682615100054052154147
SP490Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;denticola25010002360340242700158115902024901460632057056012901521813192744353010701343171226028004601327620923048443153
SP491Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT305009532760011097021231005721340004310100230170050007065000018168260000041000101020000020
SP492Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Veillonellaceae_[G-1];bacterium HMT1555028101100111166020000060486210200001800702510021177100080270400149310002610162
SP493Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Anaeroglobus;geminatus1161300000900155212025575115110294480620320211501800012166313559151034704471213104110143711293402258319
SP494Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT5260000010000120001260530001618000017000011300000262104000011235015200004100002269
SP495Bacteria;Firmicutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;faucium00440357006721001010278000065200008201223414001859011368200000112700104020637000606172200
SP509Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Atopobium;sp. HMT416000000000001000000000002000200000020000010001000000000000000000059000108
SP51Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Eikenella;corrodens819711112520364615912028234010671220155041625461430330144658133026422917691249340153911115141625101623308
SP511Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;hongkongensis154511062367232103039310131181643028844156381415423128538127103109114444469558018643030231113825910613820463186894631453171212523537627753216170
SP513Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Eikenella;halliae457375412823854316211681271721312131322900213684314859378320710197449411210311228112247269141013722113883612183354820497
SP517Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-2];bacterium HMT096664438442021018042371108015262537524958419072020284193132001329149746228112114256022114128268513514377327722124016549111693914200019092215525
SP518Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;hofstadii3596812362638253016054318730115434681474604758451842241227552960574330761289217255910152963061104119257854968154516542
SP519Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Romboutsia;timonensis110121273002161117233022901000051024240000200070241002400069101301016901402501000063
SP520Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;amylovorum0020011700015200012000000140000012753221200340010014812000570091360008700700303730102365
SP521Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT2190001182230214318011203001297060014480040751222362017800070202903540059495178117127632
SP534Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;saccharolytica447100601404120251320111015160002703214345001016032131624701057010206210035113113
SP535Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;sanguinis18081606925436957531561028342587196677352812814223815115929546144473209717512444718058343413947094522652465203913579373569802662861522468021673081841018649148188109155780108747115214
SP537Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;oris57257803819553658921954107149105108111950141933521224446242631513764836185846376342423166843563544310725648932231975142232546073118944062415571034354387142
SP540Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT931311435251011001447158297711280141010005014725011003012992898012011174920430810000191301201904
SP543Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;sp. HMT3961502221890025137909061550291231340541315001200216240109414493832018211210010018002230
SP553Bacteria;Synergistetes;Synergistia;Synergistales;Synergistaceae;Fretibacterium;sp. HMT360002041501540000204000010114312013210000090181301510902006103047002048000306465
SP554Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;wadei260669131999991296444454436313171571055050379571378305232172821412178904315440151122216121510141215531201724731231326914637075151
SP567Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;anginosus193090022600784522790014139151126130846109713835194007213421880123190756531012313006164036322693926366662317192012108257
SP568Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;nanceiensis35171391411217237272617733267127136223149524136017358363937431566176456003915364831510279771519725477742420648533711949524133596301736259142
SP570Bacteria;Firmicutes;Clostridia;Negativicutes;Veillonellaceae;Veillonella;dispar331861111693546153715615519228626913761683463411038746233390668127394281442171458128951211707763204594734409601452111541011652306137711228919143537154457112291872208461444105198556343710
SP58Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Lautropia;mirabilis29565001309431268903312090261508889334149691671511771421168224203217531332131673914149725413267238054419272146130566056195698135214505516439151457639353511401486023156367
SP598Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Ruminococcaceae_[G-2];bacterium HMT0855210355120923121891316735141041561218915890301173110522136917934274092145610229251324714301192153804020154218131311295323311
SP599Bacteria;Firmicutes;Clostridia;Eubacteriales;Peptostreptococcaceae;Clostridioides;difficile16001830800165121324401640200006102401310000000201515011000580019000141000702200000071
SP606Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-6];[Eubacterium]_nodatum001001000030000001480000300000001000011001200103511141002001019031000168510000090167108
SP607Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;sp. HMT2488481134008000052308053827420005251180490071630110050000027896170002260135172027073200128000258411000
SP612Bacteria;Actinobacteria;Coriobacteriia;Eggerthellales;Eggerthellaceae;Cryptobacterium;curtum5930001201070050005514081114341000600100201500010142600000001300190000211502013
SP613Bacteria;Absconditabacteria_(SR1);Absconditabacteria_(SR1)_[C-1];Absconditabacteria_(SR1)_[O-1];Absconditabacteria_(SR1)_[F-1];Absconditabacteria_(SR1)_[G-1];bacterium HMT8754001610838013012005501012000008111000641310000003508031919000840204012000100021620000351100
SP614Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Stomatobaculum;sp. HMT0978214017841602129220698481523561672210770164490257104761851105002043305017319498969230411356333004724241135755531330313610926680639321330
SP619Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Oribacterium;asaccharolyticum93177032148110048659061232552126201645348691874426205225150148613129221050258198645744410104108622025129818680399010118
SP623Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT32213111158467910123337469751910934651868134142104994615393129831246242111985374321019179941451915617677651816264596091033021514
SP624Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT9070640001011008210020210171280082171101507230001331510003439008809010848004912154
SP663Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT84759928280324811411250000370232510553653031871164495905013017627221203810329171410551594601140
SP682Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;gingivalis21717612953332947428855111782671413391341711055201783420416191331342424105713498098010313813181391803823167
SP687Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnoanaerobaculum;saburreum1635051466301540191062086140112345490171511230045755621253931058093808981108201315780164131558232602911
SP691Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;rava30116749982193911264124803522331920483673501054321125302516493103031311306631827532843108268161120819100013147121591213343841763069132
SP693Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcus;stomatis30353508491221908226683438571375618310829223182533320752267619962390201064178321291537031271326101862592211281914149916872332474697164701510105619407149
SP695Bacteria;Proteobacteria;Gammaproteobacteria;Cardiobacteriales;Cardiobacteriaceae;Cardiobacterium;hominis0781125582359123233917702408155029011511211012303931760166391744461652233161700613245615411111581102
SP71Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT47341483493449029561122910235698327146419001281183462851022133117165012628503398977476078273100164520756224791214480131729611512104497355172922546086592824911310888223134331
SP716Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Scardovia;wiggsiae112622444171141321400603003419413020540219000623300010010920890617400205540500009172208
SP717Bacteria;Firmicutes;Negativicutes;Veillonellales;Veillonellaceae;Dialister;pneumosintes170250076240316351790419382053270695718701451260301776402303004472331207401104425014503878382005361231163140
SP75Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT21542817320850511385139796240371119770942364165186858458259120299530226537601576142317443461185186203671974722291513051442716481171061990272277741147964168401012740145180
SP756Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;sp. HMT332311613812300313030400027250031902329153220102901210304137002700263018791302241498
SP76Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;mutans159342113011324307841511220915054519163918100215889554165976527200121060050001810872231906001028003292
SP78Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT21840748572987259778120192200385807169033604380147054751144758717295759337103050401291715858512509215109506810609601762932825301585
SP785Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;sp. HMT3087141771198454881314775787116554078832655423432618139157626939051234013572222024205123218821306013141241962303421713
SP794Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;nigrescens23375488712357411111124252719203132011219115463421040321611696063482590173123540841012586125151221610410863191098349141938248
SP795Bacteria;Firmicutes;Erysipelotrichia;Erysipelotrichales;Erysipelotrichaceae;Bulleidia;extructa006012260031600019319101020193000114000915403001107061123011029054000533300018054567
SP798Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Capnocytophaga;granulosa3331011463023373517249541054282342192391921220306538338373172932730464546341720356373273014482060116637111232117523
SP804Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Limosilactobacillus;mucosae18600020072007005000110010035051100001006010130006000900004370007900005530010318
SP807Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;maculosa341781648546271197641911615011131110308521540385161315101441912234727282091529016115941041627642621
SP809Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT23800570000000000002400000000011900000016230003700491500000016505900000076000140822050
SP810Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Tannerella;forsythia009077901093908142431030250675655051133012013510170727315254136191221086538101290442517830000101175249
SP816Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;parainfluenzae5251238424572733644245683914037128199425252542436187026827814414189161221842769849938203671644161470219334871151051329259126911106201814412041177535555852428225791101225064033695903311915939529044761304120812291933152718895409809226451233441658523785
SP821Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;parahaemolyticus1140007800200002579043619211001052790022561871436709551000832300050901520130806884815000025046500330029411877200
SP823Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Bergeyella;sp. HMT206539031110001168181100342009336900006000003553050263001010000015459042050136000000000372269144406760200
SP825Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;aurantiaca0391043000135161115002302441743757002101120028117303061611302474161160130551731631162602300104114250041220
SP828Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Rothia;dentocariosa64941463145507485621153190701566032818958171115425044642942821422681078408738222271891054132404117310643644251898122426514221630163114819052705143448122881671509494628871255
SP853Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT951007007300016000222001901120000000030000001216803200000003712047000300004038130
SP854Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-4];bacterium HMT369000001000010180001632000042060000100001311007001533700010111143097015722500000104635
SP857Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Peptostreptococcaceae_[XI][G-1];[Eubacterium]_infirmum10252102923024271453613093213100254514000010202121040101521642439900532390751410502501311022794
SP858Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;graevenitzii6914256171585091547949696086319911944364672171310224149812921400005542641728235035113373226861378024359816171572238853198116170214314657
SP869Eukaryota;Streptophyta;Magnoliopsida;Poales;Poaceae;Triticum;aestivum005020580360045722700000000200000020008316021500200100000300000000000002201040
SP877Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Filifactor;alocis30230118170137900003706034401301200222002010104043019571619255718562241770049015175476473704232127232500030513397700
SP881Bacteria;Firmicutes;Clostridia;Eubacteriales;Lachnospiraceae;Lachnospiraceae_[G-2];bacterium HMT08800000011000010400140230000026000500000013000010000000009142001070018010048600
SP89Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;lecithinolyticum00200121900512510001820002205014400015041031100212222911133012300261160123040364006422001485
SP892Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Granulicatella;elegans3563149526568147590516081721611350323382106904211794130489715924302680663147834290100410330215332297344730272813721546393318218622781906272210374355227910230441310169421136014521446819128209201017995229229917769042301961
SP893Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;sp. HMT2212624734882985381092865967829074411121992471377319382264062959817356513646783219023252871921331114413819262344717112810519174193110585149107816065342813434099115
SP96Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;sp. HMT246350390000000000010000108321500000200000275701330010111600000001800000055000111135470
SP98Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Centipeda;periodontii321401130120414839201032415110050037388330536011850214102161011130016351016518920
SP99Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;trevisanii3221010815277872112370314001598300212120876151060700575220584506000162560235213110014
SPP1Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp1_2121305517437605440749731870157137403014665270526935041151309138295085127291934280019342813615610107133210106
SPP100Bacteria;Firmicutes;Clostridia;Clostridiales;Peptostreptococcaceae_[XI];Mogibacterium;multispecies_spp100_4237161915248111350975512224213067163173819082192607141581012162310317112118781214072202041013150905161101251571311163761532421815557445527
SPP101Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;multifamily;multigenus;multispecies_spp101_21343310238125403274114328139917048230263476171745354409916982591912881175063041384181918899633305444311512127147464671831215055696290281363591888336413169270
SPP103Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;multigenus;multispecies_spp103_271273601023207285121220150321001120586010268132363510272104010029040160033023140220051206
SPP106Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;multispecies_spp106_957319686518221518064732204531981864766322586101125457323103415016243181081731262642126915182183941214713273050
SPP107Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;multispecies_spp107_58033327431320355611106509194927931391208327218111809413168970556362934831827836171596157813310772253105309059838087103884061029621117755172146812615143133743942269572458360848758048444365488783143280146422599
SPP11Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;multigenus;multispecies_spp11_3861653010012861007010040882915801900001231481030700030520818503101200006100243
SPP111Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;multigenus;multispecies_spp111_21400000000009030412020530190031000000000005014221033007873502700311181000010322
SPP112Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp112_242330211304185146283021162309209901341280915132813876910221014067551013122156013218189318037262796412143651444487
SPP113Bacteria;Firmicutes;Clostridia;Negativicutes;Veillonellaceae;Veillonella;multispecies_spp113_210359374588551227421686213222229922233619581173230146047916911210762439729610614519694259130619925791107497210669217021265832792163606174389313328778381511153861709152177245423731326581205866911203403413806967668801031
SPP115Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Lautropia;multispecies_spp115_2997081336139110176710012029391182740083181601454153720086370121218834641507723760223032199575128517967213378
SPP116Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Schaalia;multispecies_spp116_31644189910773170814104256308772728215944223334913171635119351216123458911214664010216531312411141804232326571941436721274100932218196854197104013023227464
SPP118Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;multispecies_spp118_6726290290548280862802257843395854851035627479168601485112713511613032687910921165625536736980472344895875112243171827789185711754117196174861654337150
SPP119Bacteria;Actinobacteria;Actinomycetia;Actinomycetales;Actinomycetaceae;Actinomyces;multispecies_spp119_475207332928171282222174321313611113009091079530310628154385410054141124290316100226226822634111136413731
SPP121Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;multispecies_spp121_23521002130101900011061106013014000030420163009525343481077362022063990233000983001601555912
SPP122Bacteria;Actinobacteria;Actinomycetia;Micrococcales;Micrococcaceae;Kocuria;multispecies_spp122_202100072000000100000000000000012660001000000000000000000029000000012000
SPP123Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;multigenus;multispecies_spp123_705130001330000005001307141200011011161451051611090090111261020708990041309031159672100
SPP125Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;multigenus;multispecies_spp125_200100120010936001210702052431001094022015008426261813013000223700720013060001033124116
SPP129Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;multispecies_spp129_20101000540507000250050104160009104002161016030153004658820017822246180634650204513305231410
SPP130Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;multispecies_spp130_34449258281910943983202282868611570623174397840143245522882001611218818135453874682615014413023242913149
SPP134Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;goodfellowii3094314317234653001751101412111164000386352106122070151503846134192992221502211016391416196202221
SPP135Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Tannerella;multispecies_spp135_2204152143635412461315158212243728432132154637801561645112705310219115114841172412634641281117014011431210191612152746192406
SPP139Bacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;multispecies_spp139_2282843927424228217476631349196060581751017512956615132673012192520112011071784481935018528234114228193872501810151381486439237168253109
SPP14Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Catonella;multispecies_spp14_247100181112185010040420227646001603160126360033180161541016975321537101113108105014721081521
SPP145Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;multispecies_spp145_229102022239212108141333235336464327195202301216138530378526101633666231093437371116310371320239103838341321900168125053363132098
SPP147Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;multispecies_spp147_20012122671000763174200114846375060031293892453412580212073419332823439309347533142396864831321815841521052201101664743006718641110728
SPP153Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Aggregatibacter;multispecies_spp153_313613919668213969564137256529252333777112932360395518863144325571820111137051041120792132916993492064305570937162229778118355731931771161617387636516654961580112660114105914287250925640562701324981103338
SPP154Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;multigenus;multispecies_spp154_5286930562522127101122811406588315818121311926739952734587912757493328649685512192912105621300484490266514456246281681342536551521686007507322493887711751504083348734313630212281129038431278495361895267080732196673131323230059314091223
SPP155Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp155_319165180491155614906704162028175956168144406402458913445123442910512091365796470672819482327901031179267334272619951257465657743280432813528313713525130108263917972780120108466114363756773153205841042
SPP156Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;multifamily;Atopobium;rimae20112521018224946000200031791180164696516101401013171751509261116112117600162011226112543310424562335
SPP16Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;multispecies_spp16_2137201106217219072356006911020793119051516714241621921931263561951614140432482102853826016812784732311
SPP160Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;multispecies_spp160_32927781340960265104001271502533358722015024516423146918922031470152141600101110134521501129007813928400037693541949911359114110653116019
SPP167Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;multigenus;multispecies_spp167_271014220178838611023525424562041364839125096326354171117850730171108118722822887202032841906209341001938612348017761011786914790572471057230245828157248812516
SPP169Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Bifidobacterium;multispecies_spp169_2910000001800271000010005950460157300000100950400073090020000011000019231600288637000715
SPP170Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp170_21459786343622015447293182031012421195025675109238180832143326314013399398102888136906451246077035210591114110390180653822
SPP171Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp171_22221084323779241420490111111221651214140805146752011461921119313332542421328104951221113904244160148161533139334582814204735
SPP2Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp2_18152903428795699332180915040100467636848762078256136662311610105751023844700533631968379481224580449479110211321176355596562740531317123468102619476771005962203147767669751331019864116732462662863216890660444136841745515298565156051318383015163693390541230787009392239313160111286808767720410
SPP25Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;multispecies_spp25_31490000000000000000011000000317000000000001200000005000000000207000057800000
SPP28Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;multispecies_spp28_435210000510130057400001590000130100004700255902052010510121270350014212000311005
SPP3Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp3_3932101022216511241401139144499366441006938108236563461431019165341204104133217331035301740578915637521013581267109793190255217972996735522132443414924485241938143216621645570136922223384271388453410591866711142
SPP31Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae_[XIV];Lachnoanaerobaculum;multispecies_spp31_2389520174378418841925122236545727332674538691022551310761144102182703241638188542286423846189286928338464178692546415310152602563721045316871301415
SPP33Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp33_10353204158244453177282113161345257241201821262216258725111814758741075261211968624748344664931775454475134111612161804002191218369365280292158210589185170551191266108171268
SPP34Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp34_73462821030798551107332309177912999725527672735262954364833532810477305110345656651064607326435870310461362534455912431136124187615153932779378615322208693032226102161432278989656731196918150537914431
SPP35Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp35_3131210204821253716940016111960607512397643603110038234551010529239413211902101382118436267714100528171110
SPP39Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria;multispecies_spp39_4449618105838955743173547024658852623965495244749381403355167853123875263764102834041795751323582175860322956514221178252315942034280668464337173765223844802388314824432005491517660431270225464219206563741326015264236112219841163120425967960267
SPP44Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp44_25468100151111900021622410241211120000420132123112300931312521120328793220180554025018115522608
SPP45Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;multispecies_spp45_2441991351636277134633586091535752452314743947985803414202387928018070911035579962751184168151581351945628715086261841195978131109274174244126154818164036418351649204912661858131743957822841
SPP46Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;multispecies_spp46_35216128537142526001107274147137015310039915113305570004396153421860021841690740224009699147103664046339840491131723253946500
SPP47Bacteria;Firmicutes;Clostridia;Clostridiales;multifamily;multigenus;multispecies_spp47_433200045120187254323100880872785508136795502233892214033244180111331016323504916261214662011655902690227233320302139323320
SPP5Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp5_4151858023672563796992623281364321433896229321625116923570314381826158319911514741041279173552121339109185818362005581857814386502164196622694572979217749069210134111765141814183518049977214292491435917
SPP51Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp51_311691246300194232811634212582938193279819410917101852261023490134615383651324172220105121414136025913104821226891874136651230
SPP52Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp52_6134124712522013432027823461492916024162118140158861912396107701271526364427161724021913554910471118102755102346471286651
SPP53Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp53_4303566762647928647156691481111209496212334124541578316560397135244489467755210112197491371174282561127131521051264829328946810030136552128959799143127401643074374378665564
SPP54Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp54_33590163163038115197228226587287309130221318180173037948114960343232642204110019086125172983148116212132719340919854297121364302464533316510015295116322112254
SPP55Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp55_268038612122282331851055287132325126432942481217129241198299192106211404067751623694981112360911409826354749894481608410136342432208743712236228852779124463012961
SPP57Bacteria;Firmicutes;Clostridia;Negativicutes;Veillonellaceae;Veillonella;multispecies_spp57_3298252842544903846587712053825431175620111236594422804105411206359869601270143243322140185737182436826644108108126650910677914039711252721312309855729819385321874333256131646785713852332349854156
SPP60Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp60_63212211415426238101719228230376139100015802522771616186919130451094251318394281963602098239351315061231502527443551878117377111515832052432133137
SPP61Bacteria;Fusobacteria;Fusobacteria;Fusobacteriales;Fusobacteriaceae;Fusobacterium;multispecies_spp61_21355852244193422332112828160023114091714620725119186158994734417145152520791652531296616420243113187712173471413103905655010626233201211361758241738380315212
SPP62Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp62_237250621312092993842640615261654841050226498172323026311147782711011638186291552102254705712688741011239823268921497154114745111127940319583336152068
SPP63Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp63_717285610272800290445625208904505053384523452210102405831281421284121115610005201442010010612160500
SPP66Bacteria;Firmicutes;Clostridia;Clostridiales;Peptococcaceae;Peptococcus;multispecies_spp66_2524315115110515242521213122030196101110022134002435932171120472128230014049003102182414
SPP67Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp67_313301242510131116001158001502209200481000608190171100700183965326366084952158002631682102
SPP69Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp69_20188802511119509833020000619016008042014017003270141113022069310026150193301370272174
SPP70Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp70_6351144131628013106962433429281913261239117302744203193792160152217341411594221219819502459101508424127141493534042245723
SPP71Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp71_2623696952181340507250382874958927061195285214133141902877608122254047046876341302081893392391419668299691037448290111825217331702657221006752241014793847
SPP72Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp72_4362454788150256111027924718698938581427020509260185670831041261428803264077349111616138091112322371765212238333
SPP73Bacteria;Firmicutes;Negativicutes;Selenomonadales;Selenomonadaceae;Selenomonas;multispecies_spp73_274216201719161425637298334916279714348480216123385717273219178153999633319382829347893114820557013581550946460037110252377152
SPP74Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella;multispecies_spp74_400016000000000000100000000020249518000000020870300000410082533000014000000005100
SPP75Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Kingella;multispecies_spp75_2061150328032280060702003011223012100030040224041202023540231823314021073174196010
SPP76Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp76_2940264295721000091016011223737042335770150862561341164748050911014243595540376249118514802825292582324058752569589
SPP77Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp77_313312641235541461740636488342891159390458753351782657051831278872142414915177757464254267174239303010431886281395628193292893894967259823355954899121610153214015817818829157727041112
SPP8Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp8_700021901600723402660000038600007017450000000000092640261100060201000102900000110
SPP80Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;multispecies_spp80_4113121027814811825322651203298580002011003301143101471620490300116806340082592014008132920
SPP81Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Treponemataceae;Treponema;multispecies_spp81_200100100011000016100001401101005042003003422042409010010434603800283470000026288
SPP82Bacteria;Synergistetes;Synergistia;Synergistales;Synergistaceae;Fretibacterium;multispecies_spp82_40060120000100002110000330170000100002400360155270102001300330238001622910000127852
SPP84Bacteria;Firmicutes;Clostridia;multiorder;multifamily;multigenus;multispecies_spp84_2001000800400000007100060910040303001200013000125091910116394001912018200071050100
SPP86Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;multispecies_spp86_214121600504400630110103111021712212094100104311004228248065110180018279060560271100170427133
SPP9Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;multispecies_spp9_316015769231901217719054066271106500114014280000011930039336500123607402104302271811119
SPP91Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;multigenus;multispecies_spp91_202709221001203287000413604530061310010191409301168111120501030063411410122731920081430
SPP92Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;multispecies_spp92_38240200001380150020002061007000000163160304700102120192600010200730402004530110018
SPP94Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;multispecies_spp94_300000100912750000247100000000612000000006100584700012091527006000012500000000
SPP96Bacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Leptotrichiaceae;Leptotrichia;multispecies_spp96_24500010050612000023530302120631900001060411161012100303039020057200004810
SPP97Bacteria;Firmicutes;Bacilli;Bacillales;Gemellaceae;Gemella;multispecies_spp97_4430561053723683964596354392916758152074743968781589204653863901176659688117721458385829241350230925621540202136926754555754130506887619326093702196490049941787259238122134658219493810113293952485638575101280612922385378445176313027184937334615816225
SPP98Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;multigenus;multispecies_spp98_66123742021801084900015000452041101001140188551302316752160036000700139005126577600
 
 
Download OTU Tables at Different Taxonomy Levels
PhylumCount*: Relative**: CLR***:
ClassCount*: Relative**: CLR***:
OrderCount*: Relative**: CLR***:
FamilyCount*: Relative**: CLR***:
GenusCount*: Relative**: CLR***:
SpeciesCount*: Relative**: CLR***:
* Read count
** Relative abundance (count/total sample count)
*** Centered log ratio transformed abundance
;
 
The species listed in the table has full taxonomy and a dynamically assigned species ID specific to this report. When some reads match with the reference sequences of more than one species equally (i.e., same percent identiy and alignmnet coverage), they can't be assigned to a particular species. Instead, they are assigned to multiple species with the species notaton "s__multispecies_spp2_2". In this notation, spp2 is the dynamic ID assigned to these reads that hit multiple sequences and the "_2" at the end of the notation means there are two species in the spp2.

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

Taxonomy Bar Plots for All Samples

 
 

Taxonomy Bar Plots for Individual Comparison Groups

 
 
Comparison No.Comparison NameFamiliesGeneraSpecies
Comparison 1CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 2CHILD vs ADULTPDFSVGPDFSVGPDFSVG
Comparison 3Male vs FemalePDFSVGPDFSVGPDFSVG
Comparison 4NON-SHEDDER vs SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 5no vs yesPDFSVGPDFSVGPDFSVG
Comparison 6negative vs positivePDFSVGPDFSVGPDFSVG
Comparison 7HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 8Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERPDFSVGPDFSVGPDFSVG
 
 

VIII. Analysis - Alpha Diversity

 

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


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

 

Alpha Diversity Analysis by Rarefaction

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


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

 
 
 

Boxplot of Alpha-diversity Indices

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

 
Alpha Diversity Box Plots for All Groups
 
 
 
 
 
 
 
Alpha Diversity Box Plots for Individual Comparisons
 
Comparison 1CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERView in PDFView in SVG
Comparison 2CHILD vs ADULTView in PDFView in SVG
Comparison 3Male vs FemaleView in PDFView in SVG
Comparison 4NON-SHEDDER vs SHEDDERView in PDFView in SVG
Comparison 5no vs yesView in PDFView in SVG
Comparison 6negative vs positiveView in PDFView in SVG
Comparison 7HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERView in PDFView in SVG
Comparison 8Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERView in PDFView in SVG
 
 
 

Group Significance of Alpha-diversity Indices

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

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

 
 
Comparison 1.CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERObserved FeaturesShannon IndexSimpson Index
Comparison 2.CHILD vs ADULTObserved FeaturesShannon IndexSimpson Index
Comparison 3.Male vs FemaleObserved FeaturesShannon IndexSimpson Index
Comparison 4.NON-SHEDDER vs SHEDDERObserved FeaturesShannon IndexSimpson Index
Comparison 5.no vs yesObserved FeaturesShannon IndexSimpson Index
Comparison 6.negative vs positiveObserved FeaturesShannon IndexSimpson Index
Comparison 7.HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERObserved FeaturesShannon IndexSimpson Index
Comparison 8.Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERObserved FeaturesShannon IndexSimpson Index
 
 

IX. Analysis - Beta Diversity

 

NMDS and PCoA Plots

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

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

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

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

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

 
 
NMDS and PCoA Plots for All Groups
 
 
 
 
 

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

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

 
 
 
 
 
 
 
NMDS and PCoA Plots for Individual Comparisons
 
 
Comparison No.Comparison NameNMDAPCoA
Bray-CurtisCLR EuclideanBray-CurtisCLR Euclidean
Comparison 1CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 2CHILD vs ADULTPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 3Male vs FemalePDFSVGPDFSVGPDFSVGPDFSVG
Comparison 4NON-SHEDDER vs SHEDDERPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 5no vs yesPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 6negative vs positivePDFSVGPDFSVGPDFSVGPDFSVG
Comparison 7HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERPDFSVGPDFSVGPDFSVGPDFSVG
Comparison 8Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERPDFSVGPDFSVGPDFSVGPDFSVG
 
 
 
 
 

Interactive 3D PCoA Plots - Bray-Curtis Dissimilarity

 
 
 

Interactive 3D PCoA Plots - Euclidean Distance

 
 
 

Interactive 3D PCoA Plots - Correlation Coefficients

 
 
 

Group Significance of Beta-diversity Indices

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

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

 
 
Comparison 1.CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERBray–CurtisCorrelationAitchison
Comparison 2.CHILD vs ADULTBray–CurtisCorrelationAitchison
Comparison 3.Male vs FemaleBray–CurtisCorrelationAitchison
Comparison 4.NON-SHEDDER vs SHEDDERBray–CurtisCorrelationAitchison
Comparison 5.no vs yesBray–CurtisCorrelationAitchison
Comparison 6.negative vs positiveBray–CurtisCorrelationAitchison
Comparison 7.HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERBray–CurtisCorrelationAitchison
Comparison 8.Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERBray–CurtisCorrelationAitchison
 
 
 

X. Analysis - Differential Abundance

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

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

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

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


References:

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

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

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

 
 

ANCOM Differential Abundance Analysis

 
ANCOM Results for Individual Comparisons
Comparison No.Comparison Name
Comparison 1.CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDER
Comparison 2.CHILD vs ADULT
Comparison 3.Male vs Female
Comparison 4.NON-SHEDDER vs SHEDDER
Comparison 5.no vs yes
Comparison 6.negative vs positive
Comparison 7.HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDER
Comparison 8.Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDER
 
 

ANCOM-BC Differential Abundance Analysis

 

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

Starting with version V1.43, ANCOM-BC2 is used instead of ANCOM-BC, So that multiple pairwise directional test can be performed (if there are more than two gorups in a comparison). When performing pairwise directional test, the mixed directional false discover rate (mdFDR) is taken into account. The mdFDR is the combination of false discovery rate due to multiple testing, multiple pairwise comparisons, and directional tests within each pairwise comparison. The mdFDR is adopted from (Guo, Sarkar, and Peddada 2010; Grandhi, Guo, and Peddada 2016). For more detail explanation and additional features of ANCOM-BC2 please see author's documentation.

References:

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

 
 
ANCOM-BC Results for Individual Comparisons
 
Comparison No.Comparison Name
Comparison 1.CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDER
Comparison 2.CHILD vs ADULT
Comparison 3.Male vs Female
Comparison 4.NON-SHEDDER vs SHEDDER
Comparison 5.no vs yes
Comparison 6.negative vs positive
Comparison 7.HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDER
Comparison 8.Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDER
 
 
 

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.

 
CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDER
 
 
 
 
 
 
 
LEfSe Results for All Comparisons
 
Comparison No.Comparison Name
Comparison 1.CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDER
Comparison 2.CHILD vs ADULT
Comparison 3.Male vs Female
Comparison 4.NON-SHEDDER vs SHEDDER
Comparison 5.no vs yes
Comparison 6.negative vs positive
Comparison 7.HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDER
Comparison 8.Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDER
 
 

XI. Analysis - Heatmap Profile

 

Species vs Sample Abundance Heatmap for All Samples

 
 
 

Heatmaps for Individual Comparisons

 
A) Two-way clustering - clustered on both columns (Samples) and rows (organism)
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 1CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 2CHILD vs ADULTPDFSVGPDFSVGPDFSVG
Comparison 3Male vs FemalePDFSVGPDFSVGPDFSVG
Comparison 4NON-SHEDDER vs SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 5no vs yesPDFSVGPDFSVGPDFSVG
Comparison 6negative vs positivePDFSVGPDFSVGPDFSVG
Comparison 7HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 8Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERPDFSVGPDFSVGPDFSVG
 
 
B) One-way clustering - clustered on rows (organism) only
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 1CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 2CHILD vs ADULTPDFSVGPDFSVGPDFSVG
Comparison 3Male vs FemalePDFSVGPDFSVGPDFSVG
Comparison 4NON-SHEDDER vs SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 5no vs yesPDFSVGPDFSVGPDFSVG
Comparison 6negative vs positivePDFSVGPDFSVGPDFSVG
Comparison 7HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 8Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERPDFSVGPDFSVGPDFSVG
 
 
C) No clustering
Comparison No.Comparison NameFamily LevelGenus LevelSpecies Level
Comparison 1CHILD-NON-SHEDDER vs CHILD-SHEDDER vs ADULT-SHEDDER vs ADULT-NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 2CHILD vs ADULTPDFSVGPDFSVGPDFSVG
Comparison 3Male vs FemalePDFSVGPDFSVGPDFSVG
Comparison 4NON-SHEDDER vs SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 5no vs yesPDFSVGPDFSVGPDFSVG
Comparison 6negative vs positivePDFSVGPDFSVGPDFSVG
Comparison 7HIV-Pos SHEDDER vs HIV-Pos NON-SHEDDER vs HIV-Neg SHEDDER vs HIV-Neg NON-SHEDDERPDFSVGPDFSVGPDFSVG
Comparison 8Female SHEDDER vs Female NON-SHEDDER vs Male SHEDDER vs Male NON-SHEDDERPDFSVGPDFSVGPDFSVG
 
 

XII. Analysis - Network Association

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


References:

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

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

 

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

 

 

 

Association Network Inference by SparCC

 

 

 
 

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