Additional file 1: Tables S1–S5. of Prolonged transfer of feces from the lean mice modulates gut microbiota in obese mice

Table S1. Taxonomic Assignments Table. Full taxonomic assignments in SILVA Taxonomy, as classified by Mothur. Taxa are given with bootstrap values for each taxonomic level. Taxa are classified to family, unless there was only one classifiable genus (or lower level) present in the family. Table S2. Serum biochemical parameters at the end of the experiment. Normal diet (ND), high-fat diet (HFD), HFD supplemented with feces of ND-fed mice (HFDS). Table S3. Differential taxa abundances between weeks 0 and 12 and weeks 0 and 28, tested with paired Mann-Whitney U-tests for each experimental group. Taxon = taxon denotation (full taxonomic assignments in SILVA taxonomy are presented in Additional file 1: Table S1); Mann-Whitney U statistic = statistic from paired Mann-Whitney U-tests; pValue = p-value from paired Mann-Whitney U-test; qValue = p-value after FDR correction. Table S4. Results of model comparison for taxa. Taxon = taxon denotation (full taxonomic assignments in SILVA taxonomy are presented in Additional file 1: Table S1); pValue time and pValue diet = p-values for comparisons between null models, models including time and models including time and diet, respectively; qValue time and diet = p-values after FDR correction. Table S5. Differential taxa abundances at 12 and 28 weeks. Taxon = bacteria taxon in SILVA taxonomy, genera (if applicable) are given in parentheses; week = week of experiment; comparison = groups compared; mean 1 group = mean abundance of taxon in first group in comparison field; mean 2 group = mean abundance of taxon in second group; pValue = p-value of Mann-Whitney U-tests; qValue = p-value after FDR correction. Taxa that were differentiated in two groups at both time points are highlighted in bold text. (XLSX 60 kb

Additional file 2: Figure S1. of Prolonged transfer of feces from the lean mice modulates gut microbiota in obese mice

Rarefraction curves from all samples on family level drawn with MEGAN5 software. (PDF 4369 kb

Results of PCA analysis of infant gut microbiome in infants delivered vaginally compared with those of infants delivered by cesarean section.

<p>Only 10 of the most abundant OTUs are shown. PC, principal component; var., variance; 0, day 0; 2w, 2 weeks; and 6w, 6 weeks after probiotic or placebo supplementation.</p

Boxplot of community α diversity, as expressed by the Simpson index, categorized according to the administration of the probiotic <i>Saccharomyces boulardii</i> (<i>S</i>. <i>Boulardii</i>) or placebo at 2 (2w) and 6 (6w) weeks following intervention.

<p>P-values in Mann-Whitney U-test are shown for respective times.</p

Boxplot of community α diversity at day 0 (prior to supplementation) according to the Simpson index and categorized according to gestational age at birth.

<p>Data are shown only for the weeks in which at least five infants were born.</p

PCA analysis of the preterm infant gut microbiome grouped according to the administration of <i>Saccharomyces boulardii</i> or placebo, categorized according to the time points 2 (2w) and 6 (6w) weeks following supplementation.

<p>Only ten of the most abundant OTUs are shown. PC, principal component; var., variation; and <i>S</i>. <i>Boulardii</i>, <i>Saccharomyces boulardii</i>.</p

Effect of <i>Saccharomyces boulardii</i> and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants

<div><p>Background</p><p>Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities.</p><p>Objectives</p><p>To examine the effect of oral administration of <i>Saccharomyces (S</i>.<i>) boulardii</i> and mode of delivery on the intestinal microbial community in preterm infants.</p><p>Study Design</p><p>Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by <i>16S ribosomal RNA</i> (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform.</p><p>Results</p><p>A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, <i>Firmicutes Actinobacteria</i>, <i>Proteobacteria</i>, and <i>Bacteroidetes</i> were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to <i>S</i>. <i>boulardii</i> administration. <i>Firmicutes</i> and <i>Proteobacteria</i> remained stable during the observation period, whereas <i>Actinobacteria</i> and <i>Bacteroidetes</i> increased in abundance, the latter particularly more sharply in vaginally delivered infants.</p><p>Conclusion</p><p>While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on <i>S</i>. <i>boulardii</i> effect on gut microbiome composition in preterm newborns.</p></div

Relative levels of bacterial DNA extracted from fecal samples in preterm infants delivered vaginally (VD) or by cesarean section (CS).

<p>0, day 0; 2w, 2 weeks; and 6w, 6 weeks after supplementation.</p

PCA analysis of the infant gut microbiome, categorized according to time points and mode of delivery.

<p>Only the ten most abundant OTUs are shown. 0, prior to supplementation; 2w and 6w, 2 weeks and 6 weeks following commencement of supplementation; PC, principal component; var., variation; VD, vaginal delivery; and CC, cesarean section.</p

Boxplot of community α diversity expressed by the Simpson index in stool samples collected from preterm infants at day 0 (prior to supplementation), and 2 (2w) and 6 (6w) weeks following probiotic or placebo supplementation.

<p>P-values on the figure are p-values obtained by the pairwise t-test, adjusted for multiple testing by the Benjamini–Hochberg procedure.</p