Mutualism between gut microbiota and the host as revealed in a comparative study of breast-fed versus formula-fed infants

Ongoing efforts are directed at understanding the mutualism between the
                gut microbiota and the host in breast-fed versus formula-fed infants. Due to the
                lack of tissue biopsies, no investigators have performed a global transcriptional
                analysis of the developing intestine in healthy infants. As a result, the crosstalk
                between the microbiome and the host transcriptome in the developing
                mucosal-commensal environment has not been determined. In this study, we examined
                the host intestinal mRNA gene expression and microbial DNA profiles in full term 3
                month-old infants exclusively formula fed (FF; n=6) or breast fed (BF; n=6) from
                birth to 3 months. Host mRNA microarray measurements were performed on intact
                sloughed epithelial cells in stool samples collected at 3 months. Microbial
                composition from the same stool samples was assessed by metagenomic pyrosequencing.
                Both host mRNA expression and bacterial microbiome phylogenetic profiles provided
                strong feature sets that classified the two groups of babies (FF and BF). To
                determine the relationship between epithelial cell gene expression and the bacterial
                colony profiles, the host transcriptome and functionally profiled microbiome data
                were analyzed in a multivariate manner. From a functional perspective, analysis of
                the gut microbiota's metagenome revealed that virulence characteristics differed
                between the FF and BF babies. Using canonical correlation analysis, evidence of
                multivariate structure relating eleven host immunity/mucosal defense-related genes
                and microbiome virulence characteristics was observed. These results, for the first
                time, provide insight into the integrated responses of the host and microbiome to
                dietary substrates in the early neonatal period.In this study, we examined the host intestinal mRNA gene expression
                and microbial DNA profiles in full term 3 month-old infants exclusively formula fed
                (FF; n=6) or breast fed (BF; n=6) from birth to 3 months. Host mRNA microarray
                measurements were performed on intact sloughed epithelial cells in stool samples
                collected at 3 months. Microbial composition from the same stool samples was
                assessed by metagenomic pyrosequencing. Both host mRNA expression and bacterial
                microbiome phylogenetic profiles provided strong feature sets that classified the
                two groups of babies (FF and BF). To determine the relationship between epithelial
                cell gene expression and the bacterial colony profiles, the host transcriptome and
                functionally profiled microbiome data were analyzed in a multivariate manner. From a
                functional perspective, analysis of the gut microbiota's metagenome revealed that
                virulence characteristics differed between the FF and BF babies. Using canonical
                correlation analysis, evidence of multivariate structure relating eleven host
                immunity/mucosal defense-related genes and microbiome virulence characteristics was
                observed. These results, for the first time, provide insight into the integrated
                responses of the host and microbiome to dietary substrates in the early neonatal
                period.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal