Figure

<p><b>5. </b><b>Phylogenetic trees of 3 selected OTUs.</b> (A) Unclassified_Ruminococcaceae_442, (B) <i>Ruminococcus</i>_1290 OTU and (C) <i>Prevotella</i>_2172. Branches are labelled with the sample from which the sequence originated (labelled as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054783#pone-0054783-g001" target="_blank">Figure 1</a>). Branch labels in bold are where an identical sequence was obtained from samples from more than one host species. Scale bars indicate the number of base substitutions per site.</p

Distribution of the most abundant OTUs (>0.5% of total abundance) in humans, chimpanzees and cattle.

a<p>Probability that the OTU is non-randomly distributed between humans, chimpanzees and cattle, calculated using the G test of independence after correction for the ‘False Discovery Rate’. All probabilities of <0.05 are shown. Where no values are shown there is not considered to be a significant non-random distribution.</p

Figure

<p><b>4. </b><b>Phylogenetic tree showing the most abundant OTUs within the Firmicutes phylum.</b> Phylogeny is based on 400 bp alignment of the V4–V5 of the 16S rRNA gene showing, together with the closest matches from the Ribosomal Database Project. Together these 8 OTUs comprise 12.3% of the total sequences and 33.2% of those within the Firmicutes phylum. RDP sequences are labelled with their “S” accession number and taxonomic assignment. Coloured symbols indicate the distribution of OTUs (defined as 97% sequence similarity) that are shared between hosts; (green ▪) humans, cattle and chimpanzees, (blue ♦) humans and chimpanzees, (lilac ▾) humans only. Each OTU name consists of its taxonomic assignment and a unique numerical identifier. Scale bars indicate the number of base substitutions per site.</p

Figure

<p><b>3. </b><b>Phylogenetic tree showing the most abundant OTUs within the Bacteroidetes phylum.</b> Phylogeny is based on 400 bp alignment of the V4–V5 of the 16S rRNA gene, together with the closest matches from the Ribosomal Database Project. Together these 17 OTUs comprise 37.7% of the total sequences and 75.3% of those within the Bacteroidetes phylum. RDP sequences are labelled with their “S” accession number and taxonomic assignment. Coloured symbols indicate the distribution of OTUs (defined as 97% sequence similarity) that are shared between hosts; (green ▪) humans, cattle and chimpanzees, (blue ♦) humans and chimpanzees, (orange •) chimpanzees only, and (red ▴) cattle only. Each OTU name consists of its taxonomic assignment and a unique numerical identifier. Scale bars indicate the number of base substitutions per site.</p

Relative abundance of the Bacteroidetes and Firmicutes phyla in each host species.

<p>Relative abundance of the Bacteroidetes and Firmicutes phyla in each host species.</p

Distribution of bacterial species across patients.

<p>Given is occupancy, (the number of samples for which each bacterial species was observed), plotted against mean species abundance (log₁₀ scale) across all 21 samples (<i>r</i>² = 0.084, <i>F</i>_1,234 = 1.38, <i>P</i> = 0.242).</p

Phyla represented by 16S rRNA gene sequences obtained.

<p>Phyla represented by 16S rRNA gene sequences obtained.</p

Box plot comparisons of bacterial diversity, bacterial community membership, and bacterial community structure for the 21 cross-sectional samples (A, B, and C, respectively).

<p>Richness was calculated with a uniform re-sample size of 1901 sequences following 1000 iterations. Community membership and structure were calculated using the Sørensen (presence/absence) and Bray-Curtis (quantitative) indices of similarity, respectively. The top and bottom boundaries of each box plot indicate the 75^th and 25^th quartile values, respectively, and lines within each box represent the 50^th quartile (media) values. Ends of whiskers represent interquartile range and open circles mark the lowest and highest values in each instance.</p

Patient information for the 25 patients enrolled in the study.

<p>Asterisks denote samples for which no sequencing data was obtained. “cef” - cefuroxime, “met” - metronidazole, “nor” - norfloxacin, “cip” - ciprofloxacin, ALD- Alcoholic liver disease. NASH- Non Alcoholic SteatoHepatitis, HCV- Hepatitis C virus.</p>†<p>- denotes ascitic PMN >250 cells/mm³.</p

FISH of murine lungs.

<p>Lung sections from germ free C57BL/6 (A), SPF C57BL/6 (B), non-SPF C57BL/6 (C and D, higher magnification of the area in the white box in C), and wild-derived mice (E and F) were analyzed by FISH. Nuclei were stained with DAPI (blue). Bacteria were identified by hybridization with the broad-range bacterial probe EUB338 (red). White bars indicate 10 µm.</p