HLA-B27 transgenic animals have significant alterations in gut microbiota by 16s rDNA sequencing.

<p>WT: wild-type Lewis rats; B27/B2M: (21–3×283–2)F1 HLA-B27/hβ2m transgenic Lewis rats; B2M: 283–2 hβ2m expressing transgenic rats; * designates p<0.05.</p

Genus level analysis differences from A, cecal lumen specimens, and B, cecal mucosal samples from cohort 3.

<p>Genus level analysis differences from A, cecal lumen specimens, and B, cecal mucosal samples from cohort 3.</p

Relative differences in <i>Bacteroides vulgatus</i> and <i>Akkermansia muciniphila</i> shown by A, quantitative PCR using the 16S rRNA gene as a reference, and B, by traditional PCR using whole cecum samples in cohort 1.

<p>Relative differences in <i>Bacteroides vulgatus</i> and <i>Akkermansia muciniphila</i> shown by A, quantitative PCR using the 16S rRNA gene as a reference, and B, by traditional PCR using whole cecum samples in cohort 1.</p

Principal coordinates analysis from combined cecal lumen and cecal mucosa samples from cohort 3.

<p>Principal coordinates analysis from combined cecal lumen and cecal mucosa samples from cohort 3.</p

16S rRNA gene sequencing principal coordinates analysis from non-co-housed rats shows significant differences in cecal microbiota between genotypes.

<p>A. Cecal lumen samples from cohort 3; B, Cecal mucosa samples from cohort 3; C, Phylum-level analysis from cecum lumen samples; D, Phylum-level analysis from cecum mucosa samples. WT: wild type rats; B2M: hβ2 microglobulin; B27/B2M: HLA-B27/hβ2 microglobulin transgenic rats.</p

Rat cohorts used in experiments.

<p>WT: wild type; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105684#pone-0105684-t001" target="_blank">Table 1</a> for genotype designations.</p

BRISK analysis of whole cecum samples from cohort 1 shows microbial diversity differences on a species level between HLA-B27/hβ2m animals and co-housed wild type animals.

<p>A. Each line on the heat map represents a different bacterial species and the color code represents the relative abundance of that organism, with yellow indicating the highest abundance. B, Specific species differences are highlighted, with a black dot indicating statistically significant differences.</p

HLA-B27/hβ2m transgenic rat lines.

<p>Adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105684#pone.0105684-Taurog2" target="_blank">[35]</a>.</p

American Gut Project fecal sOTU counts table

The Deblur sOTU counts table for the fecal samples used in the American Gut Project manuscript. The samples were trimmed to a common read length of 125nt, and processed by Deblur (Amir et al mSystems 2017). Blooms were removed (Amir et al mSystems 2017) and any sample with fewer than 1250 sequences was omitted. This table is not rarefied,

movie_s2.mp4

Placing changes in the microbiome in the context of the American Gut. We accumulated samples over sequencing runs to demonstrate the structural consistency in the data. We demonstrate that while the ICU dataset (https://www.ncbi.nlm.nih.gov/pubmed/27602409) falls within the American Gut samples, they do not fall close to most samples at any of the body sites. We then highlight samples from the United Kingdom, Australia, the United States and other countries to show that nationality does not overcome the variation in body site. We then highlight the utility of the American Gut in meta-analysis by reproducing results from (https://www.ncbi.nlm.nih.gov/pubmed/20668239) and (https://www.ncbi.nlm.nih.gov/pubmed/23861384), using the AGP dataset as the context for dynamic microbiome changes instead of the HMP dataset. We show rapid, complete recovery of C. diff patients following fecal material transplantation and also contextualized the change in an infant gut over time until it settles into an adult state. This demonstrates the power of the American Gut dataset, both as a cohesive study and as a context for other investigations