Additional file 1: Figure S1. of Fucosyllactose and L-fucose utilization of infant Bifidobacterium longum and Bifidobacterium kashiwanohense

Phylogenetic tree of partial (772 nt) 16S rRNA genes of strains used in this study Partial 16S rRNA gene sequences used to calculate phylogenetic tree. (DOC 2554 kb

Relative 16S rRNA gene abundances of the four major phyla detected in neonatal feces (NF) using pyrosequencing.

<p>Values are expressed as means ± SD at each of the three sampling points, i.e. days 4–6, 9–14 and 25–30 postnatal.</p

Gene copy numbers of the major gut-associated bacterial populations detected in neonatal feces (NF) using qPCR.

<p>Values are expressed as means ± SD at each of the three sampling points, i.e. days 4–6, 9–14 and 25–30 postnatal in neonates harboring high (<b>A</b>, <i>n</i> = 4) and low (<b>B</b>, <i>n</i> = 3) <i>Bacteroides</i> population levels, respectively; and comparison to means obtained from maternal feces (MF) (<i>n = </i>7) over the perinatal period.</p

Relative 16S rRNA gene abundances of the 17 most abundant genera detected in neonatal feces (NF) using pyrosequencing.

<p>Values are expressed as means ± SD at each of the three sampling points, i.e. days 4–6, 9–14 and 25–30 postnatal in neonates harboring high (<b>A</b>, <i>n</i> = 4) and low (<b>B</b>, <i>n</i> = 3) <i>Bacteroides</i> population levels, respectively.</p

Counts of anaerobes and facultative anaerobes (culture) and total bacteria (qPCR) detected in neonatal feces (NF).

<p>Values are expressed as means ± SD at each of the three sampling points, i.e. days 4–6, 9–14 and 25–30 postnatal (<i>n</i> = 7); and compared to means obtained from maternal feces (MF) (<i>n</i> = 7) over the perinatal period.</p

Fecal strain diversity (<i>n</i> = 197), isolated from seven neonates' feces collected at 4–6 d, 9–14 d and 25–30 d postnatal, based on 16S rRNA gene sequence similarities to those deposited in the GenBank database.

1<p>Number of isolates per time point.</p

Data_Sheet_1_Stepwise establishment of functional microbial groups in the infant gut between 6 months and 2 years: A prospective cohort study.DOCX

The early intestinal colonization of functional microbial groups plays an essential role in infant gut health, with most studies targeting the initial colonization period from birth to 6 months of age. In a previous report, we demonstrated the metabolic cross-feeding of lactate and identified keystone species specified for lactate utilization in fecal samples of 40 healthy infants. We present here the extension of our longitudinal study for the period from 6 months to 2 years, with a focus on the colonization of functional groups involved in lactate metabolism and butyrate production. We captured the dynamic changes of the gut microbiota and reported a switch in the predominant lactate-producing and lactate-utilizing bacteria, from Veillonella producing propionate in the first year to Anaerobutyrycum hallii producing butyrate in the second year of life. The significant increase in butyrate producers and fecal butyrate concentration was also pinpointed to the weaning period between 6 and 10 months. Correlation analyses further suggested, for the first time, the metabolic cross-feeding of hydrogen in infants. In conclusion, our longitudinal study of 40 Swiss infants provides important insights into the colonization of functional groups involved in lactate metabolism and butyrate production in the first 2 years of life.</p

Additional file 1: Table S1. of Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium

Salmonella Typhimurium N-15 genes higher expressed in mono-culture. Table S2: Salmonella Typhimurium N-15 genes higher expressed in co-culture with RBL 67. (DOC 2173 kb

Experimental set up for the analysis of cellular cytokines release.

<p>A Caco-2/HT29-MTX co-culture monolayer was grown to confluence on a filter insert of a 24-well plate and freshly collected PBMC were added to the basolateral compartment. <i>Salmonella</i> in DMEM or effluent were applied to the apical compartment and incubated for 24 h before cytokines release was measured in the apical supernatant.</p

PCoA analysis of PolyFermS models based on weighted and unweighted UniFrac analysis.

<p>Each symbol is representing a different reactor. <b>(A)</b> Three last days at the end of the stabilization period of all reactors of model 2 (IR, PC1, DC1, PC2 and DC2) and <b>(B)</b> three last days at the end of the stabilization period of model 3 (IR, CR, TR3 and TR4).</p