Relative abundance of CD3^pos cells, CD8^pos -, CD4^pos -T cells and Tregs in the intestinal mucosa.

<p>A) T cells are more or less evenly distributed in the gut B) CD8^pos T cells are enriched in the human gastric corpus and antrum. C) CD3^posCD4^pos T cells are predominantly found in the lower intestinal tract. D) The relative abundance of CD4^posCD25^highCD127^low/negFOXP3 cells was highest in the appendiceal orifice region and the ascending colon. The figures represent cumulative flow cytometry data from all study participants (N=16) from all seven biopsy regions including the gastric corpus (GC), gastric antrum (GA), duodenum (DD), terminal ileum (TI), appendiceal orifice (AO), ascending colon (AC) and sigmoid colon (SC). Unless otherwise indicated, differences were not significant. *P<0.05; **P<0.01; ***P<0.001.</p

Representative gating strategy for the FACS analysis of lamina propria CD3+, CD4+, CD8+ and regulatory T-cells from pinch biopsies obtained from the appendiceal orifice region of one healthy subject.

<p>Representative gating strategy for the FACS analysis of lamina propria CD3+, CD4+, CD8+ and regulatory T-cells from pinch biopsies obtained from the appendiceal orifice region of one healthy subject.</p

Study design.

<p>Subjects were on a free diet from day –7 to day –2 and from day 4 to day 10. From day −1 to day 0 a standardized diet was ingested. Diarrhea was induced by PEG for 3 days (day 1 to day 3). One stool sample was obtained one week before induction of diarrhea. Before the first dose of PEG a second stool sample and a mucosa sample were collected. A third stool and a second mucosa sample were taken at day three of PEG administration when diarrhea was maximally pronounced. A fourth stool sample was taken one week after withdrawal of PEG.</p

Changing taxa due to diarrhea in stool samples.

#<p>Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods.</p>*<p>(M) <i>Metastats</i>, (E) <i>edgeR</i>, (V) scoring & visualization.</p>+<p>Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score.</p

Additional file 2: of Changes of intestinal microbiota composition and diversity in very low birth weight infants related to strategies of NEC prophylaxis: protocol for an observational multicentre pilot study

SPIRIT flow-chart. (DOC 53 kb

Osmotic diarrhea leads to decreased phylotype richness.

<p>(<b>A</b>) Rarefaction analysis of averaged stool samples before (time-point 2, red) and during diarrhea (time-point 3, green) shows significantly decreased richness (richness time-point 2 vs. time point 3: <i>P</i> = 0.029, Student’s t-test). (<b>B</b>) Rarefaction analysis of averaged mucosa samples before (time-point 2, red) and during diarrhea (time-point 3, green) shows a trend toward but non-significant decrease in richness (richness time-point 2 vs. time point 3: <i>P</i> = 0.08 Student’s t-test). The dotted line indicates ± SEM; OTU distance = 0.03.</p

Changing taxa due to diarrhea in mucosa samples.

#<p>Score 3, found by all 3 methods; score 2, found by 2 out of 3 methods.</p>*<p>(M) <i>Metastats</i>, (E) <i>edgeR</i>, (V) scoring & visualization.</p>+<p>Taxonomy string according to RDP classification; the number after the taxon name denotes the similarity score.</p

Consistency of measures.

<p>Congruence of <i>Metastats, edgeR</i> and <i>Viz</i> (denoted “Profile”; in at least two individuals simultaneously) for identification of significantly changing OTUs (diversity = 0.03) in stool samples (<b>A</b>) and mucosa samples (<b>B</b>).</p

Comparative overview of Genomic Islands (GIs).

<p>(<b>A</b>) VGI I (PAI) with the T4SS and putative prohage I, (<b>B</b>) VGI II with a <i>vir</i>-gene cluster and plasmid-related genes, (<b>C</b>) VGI III containing the surface array protein cluster and prohage III, (<b>D</b>) VGI IV containing the CRISPR-array and prophage IV and (<b>E</b>) FGI II with prophage-related genes (prophage II) and the CRISPR-cluster (array and <i>cas</i>-genes). The GI borders to genes shared between the subspecies (grey) are indicated with nucleotide position. Gene clusters are colored as follows: phage-related genes (orange), plasmid related genes (green), integrases and transposases (blue), T4SS (red), effector proteins (yellow), surface array proteins (purple), <i>cas</i>-genes (lavender), tRNAs (green boxes); Each x represents a hypothetical protein and their numbers in tandem are indicated above.</p

Characterization and prevalence of T4SS regions in <i>C</i>. <i>fetus</i> strains.

<p>Characterization and prevalence of T4SS regions in <i>C</i>. <i>fetus</i> strains.</p