MOESM6 of Fecal microbiota transplantation against intestinal colonization by extended spectrum beta-lactamase producing Enterobacteriaceae: a proof of principle study

Additional file 6: Table S3. Abundances of taxa in responders vs nonresponders. Relative abundances of significantly different taxa (only < 0.9 or > 1.1 fold shown) between responders and nonresponders at baseline. Median relative abundance (percentage) is shown, also the ratio between the medians of responders and nonresponders and the p-value are given

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Additional file 4: Table S2. Characteristics of successful FMTs vs unsuccessful FMTs. Characteristics of successful FMTs vs unsuccessful FMTs

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Additional file 2: Table S4. Culture results in decolonized subjects. Rectal and urine cultures at follow-up (baseline, 1, 2 and 4 weeks after FMT)

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Additional file 5: Figure S1. Heat map of change in responders vs nonresponders. Heatmap showing fold change in microbiota abundance of significantly different species between responders and non-responders before versus after FMT. FMTs are shown, therefore patients who have received 2 FMTs are shown twice. Faecalibacterium 1 and 2 are both subgroups of the Faecalibacterium genus. Faecalibacterium 1 is the genus in the strict sense, whereas the Faecalibacterium 2 group includes uncultured bacteria related to the phylotypes Eldhufec289, Eldhufec276 and Eldhufec259

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Additional file 3: Table S1. Characteristics of responders vs nonresponders. Characteristics of responders vs nonresponders

Additional file 1 of Effect of prebiotic oligosaccharides on bowel habit and the gut microbiota in children with functional constipation (Inside study): study protocol for a randomised, placebo-controlled, multi-centre trial

Additional file 1. informed consent

Additional file 1: of Sex and strain dependent differences in mucosal immunology and microbiota composition in mice

Method and results RT qPCR for validation microarray. (DOCX 27 kb

Consensus Signature Groups systematically characterize patterns of time-dependent microbiota changes in response to infection.

<p>Consensus Signature Groups (CSGs) represent sets of taxa that share similar dynamics within a tissue, providing a means to identify common behaviors among taxa regardless of their phylogenetic relationships. Representative signatures of individual Operational Taxonomic Units (OTUs) from CSGs are shown. Horizontal axis indicates days post-inoculation with the pathogen; vertical axis shows normalized sequencing counts for the OTU. Dashed or dotted lines indicate median signature shapes for OTUs. Shaded regions indicate 95% credible intervals for signatures; regions of overlap indicate time-periods during which changes were not detected. Phases of infection are E  =  early, A  =  acute, R  =  recovery, C  =  convalescence. (<b>A</b>) The pathogen, <i>Citrobacter rodentium</i> (OTU#6) in colon. (<b>B</b>) <i>Mucispirillum</i> (OTU#1) in colon, rapidly decreases and does not return to baseline until the convalescent phase. (<b>C</b>) <i>Parabacteroides</i> (OTU#8) in colon, decreases during early infection, but returns to baseline by the recovery phase. (<b>D</b>) <i>Parabacteroides</i> (OTU#8) in cecum had no detectable change between cohorts. (<b>E–F</b>) Two <i>Lactobacilli</i> in ileum, showing different dynamics: OTU#3 increases during acute infection, while OTU#13 decreases. (<b>G–H</b>) <i>Clostridium</i> (OTU#24) in ileum and cecum, has a delayed increase that persists into the convalescent phase. (<b>I–J</b>) Representative OTUs in colon and ileum showing no detectable changes between cohorts.</p

Effect of age and sex on T cell differentiation in the spleens.

<p>Percentage of CD62L⁺CD44^- naive CD4⁺ (A) and CD8⁺ (D), CD62L⁺CD44⁺ central memory CD4⁺ (B) and CD8⁺ (E), CD62L^-CD44⁺ effector memory CD4⁺ (C) and CD8⁺ (F), T helper 1 (G), T helper 2 (H), T helper 17 (I), FoxP3⁺CD25^- T regulatory cells (J), and FoxP3⁺CD25⁺ T regulatory cells (K) in the spleen of young (3 months) and old (19 months) male and female B6 mice. T helper and T cytotoxic cells are expressed as the frequency of CD4⁺ and CD8⁺ cells within the CD3⁺ population respectively. Results are expressed as dot plots + means and were tested using Two-way ANOVA, followed by a Bonferroni post-test for comparison between groups. Significant age effects are indicated with dashed lines and significant sex effects are indicated with solid lines (p<0.05). An additional group of ovariectomized (ovx) old females was added and compared with the old females with a t-test to determine the effect of a loss of female sex hormones (human menopause).</p

Effect of age and sex on T lymphocytes in the Peyer’s patches.

<p>Percentage of CD3⁺ T lymphocytes (A), the percentage of T helper cells (CD4⁺) (B), T cytotoxic cells (CD8⁺) (C), and the percentage of expression of CD69⁺CD4⁺ (D) and CD69⁺CD8⁺ (E) in the Peyer’s patches (PP) of young (3 months) and old (19 months) male and female B6 mice. T helper and T cytotoxic cells are expressed as the frequency of CD4⁺ and CD8⁺ cells within the CD3⁺ population respectively. Results are expressed as dot plots + means and were tested using a Two-way ANOVA for overall age and sex effects, followed by a Bonferroni post-test for comparison between groups. Significant age effects are indicated with dashed lines and significant sex effects are indicated with solid lines (p<0.05). An additional group of ovariectomized (ovx) old females was added and compared with the old females with a t-test to determine the effect of a loss of female sex hormones (human menopause).</p