Comparison of the relative abundance of fecal microbial communities of each sample using the Yue and Clayton theta measure of dissimilarity.

<p>Dissimilarity between the relative abundance of communities was calculated with the Yue and Clayton measure of dissimilarity within Mothur and clustering performed using the UPGMA algorithm. The first numeral/letter indicates the patient or control, the last numeral indicates when the sample was obtained. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062815#pone-0062815-g001" target="_blank">Figure 1</a> legend for sample labelling.</p

Dice similarity coefficients (%) of 16S rRNA amplicon DGGE profiles for fecal samples collected pre- and post-colonoscopy bowel preparation.

†<p>1 week post-colonoscopy sample not obtained.</p>*<p>LS, last sample, obtained 1 week post-colonoscopy.</p>**<p>LS, last sample, obtained 1 month or 3–6 months post-colonoscopy.</p>***<p>Samplesobtained 3–6 months apart, patient did not undergo colonoscopy.</p>∧<p>The post-colonoscopy comparisons are invalid for technical reasons.</p

Comparison of the composition of the fecal microbial communities of each sample using the Jaccard similarity coefficient.

<p>Distances between communities, based on the presence and absence of 16S rRNA sequences, were calculated with the Jaccard coefficient (jclass) within Mothur and clustered using the UPGMA algorithim. The first numeral/letter (subjects that underwent colonoscopy/subjects who did not) corresponds to the subject, the last numeral indicates when the sample was obtained. For subjects who underwent colonoscopy: −1m, −1w, sample obtained one month, one week pre-colonoscopy, +1w, +1m, +3m, sample obtained 1 week, one month, or 3–6 months post-colonoscopy, respectively. For subjects who did not undergo colonoscopy: +3m, sample obtained 3–6 months after the first sample.</p

Summary of high-throughput sequencing parameters.

#<p>number of quality sequences obtained for a given sample.</p>*<p>number of observed operational taxonomic units.</p>**<p>Shannon diversity index.</p>$<p>Good’s coverage; C = 1 n₁/N, where n₁ is the number of OTUs that have been sampled once, and N is the total number of sequences.</p>†<p>Calculated with Mothur at the 3% distance level. Values in brackets are 95% confidence intervals as calculated by Mothur.</p>∧<p>For subjects who underwent colonoscopy: −1m, −1w, sample obtained one month, one week pre-colonoscopy, +1w, +1m, +3m, sample obtained 1 week, one month, or 3–6 months post-colonoscopy, respectively. For subjects who did not undergo colonoscopy: +3m, sample obtained 3–6 months after the first sample.</p

Relative abundance of <i>Firmicutes</i> and <i>Bacteroidetes</i> 16S rRNA sequences for all subjects’ samples analysed using high-throughput sequencing.

<p>Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062815#pone-0062815-g001" target="_blank">Figure 1</a> legend for sample labelling.</p

NMDS plot of the microbial communities of subjects’ samples using a distance matrix calculated with the Jaccard similarity coefficient.

<p>The plot of the two NMDS axes was generated using a distance matrix calculated at the 3% level, with the Jaccard similarity coefficient within Mothur for all samples. The distance between two points is directly proportional to the Jaccard similarity value for two samples such that sites positioned close together share more OTUs than samples further apart. NMDS stress = 0.15. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062815#pone-0062815-g001" target="_blank">Figure 1</a> legend for sample labelling.</p

NMDS plot of the microbial 16S rRNA communities of subjects’ samples using a distance matrix calculated with the Yue and Clayton theta similarity coefficient.

<p>The plot of the two NMDS axes was generated using a distance matrix calculated at the 3% level, with the Yue and Clayton theta similarity coefficient within Mothur for all samples. The distance between two points is directly proportional to the Yue and Clayton theta similarity value for two samples such that sites positioned close together share a similar abundance in OTUs than samples further apart. NMDS stress = 0.52. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062815#pone-0062815-g001" target="_blank">Figure 1</a> legend for sample labelling.</p

Comparison of the mean distances between samples observed in the presence/absence (Jaccard) or relative abundance (Yue and Clayton) NMDS plots using matched pairs <i>t</i>-tests.

<p>For subjects who underwent colonoscopy: −1m, −1w, sample obtained one month, one week pre-colonoscopy, +1w, +1m, +3m, sample obtained 1 week, one month, or 3–6 months post-colonoscopy, respectively. For subjects who did not undergo colonoscopy: +3m, sample obtained 3–6 months after the first sample. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062815#pone-0062815-g005" target="_blank">Figure 5</a> outlines the sample comparisons for each test. P = <0.05.</p

Summary of shifts (>32%) in the relative proportions of <i>Firmicutes</i> and <i>Bacteroidetes</i> for subjects with dissimilar samples, and all shifts observed for subjects who did not undergo colonoscopy.

*<p>Abbreviations for indications for colonoscopy: UC, ulcerative colitis, AP, abdominal pain, FHCRC, family history of colorectal cancer, PP, previous polyps, N/A, did not undergo colonoscopy; indication not applicable.</p>**<p>Sample most dissimilar to other sample(s) from the same subject.</p>***<p>Values showing shifts (%) in <i>Firmicutes</i> and <i>Bacteroidetes</i> phyla for samples obtained from the same patient at different time points, ↑, increase in <i>Firmicutes</i> relative to the first sample, ↓, decrease in <i>Firmicutes</i> relative to the first sample for each comparison. For subjects who underwent colonoscopy: −1m, −1w, sample obtained one month, one week pre-colonoscopy, and LS refers to the last sample obtained post-colonoscopy (refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062815#pone-0062815-t003" target="_blank">Table 3</a>), respectively. For subjects who did not undergo colonoscopy: +3m, sample obtained 3–6 months after the first sample.</p

The time course of activation of enhancers and promoter at the IL6 locus.

<p>The core panel shows a genome browser view of the <i>IL6</i> locus with the locations of FANTOM5 enhancers. The upper right panel shows the time course of induction of <i>IL6</i> mRNA, detected by CAGE, which peaks around 3–4 hours and declines by 12 hours. The lower panels show the transient activity of the enhancers indicated, the majority of which peak around 1–2 hours and decline rapidly. Data are expressed at TPM, and are the average of the three replicates.</p