Principal coordinates analysis (PCoA) of microbiota samples.

<p>Based on Jaccard index distances measuring dissimilarity of OTU-level microbiota composition between individual samples. Axis labels including fractions of variance explained.</p

OTU counts and Good’s coverage (dataset containing 1227 sequences per sample, 8 samples per sample set).

<p>OTU counts and Good’s coverage (dataset containing 1227 sequences per sample, 8 samples per sample set).</p

Distribution of OTUs among samples.

<p>Colors encode absolute OTU counts. Information on OTU classification according to RDP classifier. Numbers 1–8 are mouse identifiers. Within one mouse batch, equal numbers refer to cecum and colon samples of the same animal. Heatmap generated after subsampling to 1227 sequences per sample. The numbers on the color key correspond to untransformed OTU abundances.</p

Rarefaction curves.

<p>A–E, rarefaction curves for individual samples (n = 8 mice), grouped by sample set. F, rarefaction curves for combined data for each sample set (n = 5 sets), including 95% confidence intervals. Lci, lower bound of confidence interval; hci, higher bound of confidence interval. Each sample set consist of either the cecum or the colon samples for one batch of 8 mice. All curves generated after subsampling to 1227 sequences per sample.</p

Phylum-level composition of microbiota.

<p>A. Fraction of sequence counts in each of the individual samples, color coded by sample group. Grey boxes indicate significant differences between sample groups (unequal variances t-Test, p<0.05): a, significantly different between MIT and MHH2009 cecum samples; b, significantly different between MIT and MHH2011 cecum samples; c, significantly different between MHH2009 and MHH2011 cecum samples; d, significantly different between MIT and MHH2009 colon samples. B. Relative abundance of phyla in each of the sample groups, including standard deviation (n = 8).</p

Effects of <i>H. hepaticus</i> infection on MIT vs. MHH mice.

<p>Intestinal inflammation induced by <i>H. hepaticus</i> infection in C57BL/6J <i>Il10^−/−</i> mice reared in MIT and MHH SPF facilities. A, histological sections (H&E stain); B, Histological sections of cecum were scored separately for inflammation, epithelial defects, edema, crypt atrophy, hyperplasia and dysplasia on a scale of 0 to 4. The scores from all the different parameters were added and represented as Typhlitis Index scores as described in Burich <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070783#pone.0070783-Burich1" target="_blank">[29]</a>. P values according to nonparametric Mann-Whitney test, **<0.005.</p

MHH-specific OTUs occurring in at least 4 samples of one MHH sample set.

<p>MHH-specific OTUs occurring in at least 4 samples of one MHH sample set.</p

Distribution of OTUs occurring in at least 4 samples of the same set.

<p>A, cecum samples, B, colon samples.</p

MIT-specific OTUs occurring in at least 4 samples of one MIT sample set.

<p>MIT-specific OTUs occurring in at least 4 samples of one MIT sample set.</p