Abstract
BackgroundEffects of diet on the structure and function of gut microbial communities in newborn infants are poorly understood. High-resolution molecular studies are needed to definitively ascertain whether gut microbial communities are distinct in milk-fed and formula-fed infants.Methodology/Principal FindingsPyrosequencing-based whole transcriptome shotgun sequencing (RNA-seq) was used to evaluate community wide gut microbial gene expression in 21 day old neonatal piglets fed either with sow's milk (mother fed, MF; n = 4) or with artificial formula (formula fed, FF; n = 4). Microbial DNA and RNA were harvested from cecal contents for each animal. cDNA libraries and 16S rDNA amplicons were sequenced on the Roche 454 GS-FLX Titanium system. Communities were similar at the level of phylum but were dissimilar at the level of genus; Prevotella was the dominant genus within MF samples and Bacteroides was most abundant within FF samples. Screened cDNA sequences were assigned functional annotations by the MG-RAST annotation pipeline and based upon best-BLASTX-hits to the NCBI COG database. Patterns of gene expression were very similar in MF and FF animals. All samples were enriched with transcripts encoding enzymes for carbohydrate and protein metabolism, as well as proteins involved in stress response, binding to host epithelium, and lipopolysaccharide metabolism. Carbohydrate utilization transcripts were generally similar in both groups. The abundance of enzymes involved in several pathways related to amino acid metabolism (e.g., arginine metabolism) and oxidative stress response differed in MF and FF animals.Conclusions/SignificanceAbundant transcripts identified in this study likely contribute to a core microbial metatranscriptome in the distal intestine. Although microbial community gene expression was generally similar in the cecal contents of MF and FF neonatal piglets, several differentially abundant gene clusters were identified. Further investigations of gut microbial gene expression will contribute to a better understanding of normal and abnormal enteric microbiology in animals and humans.
Highlights
The principles that govern early microbial colonization in the mammalian intestine are poorly understood
Bold advances have been made in understanding the metabolic potential of intestinal microbes based upon a massive amount of DNA sequencing of bacterial isolates and in metagenomic studies [9,11], few functional studies have been performed characterizing community wide gene and protein expression in the gut
This study represents the largest number of independent samples (8 subjects) used to date for analysis of community wide gene expression in the gut
Summary
The principles that govern early microbial colonization in the mammalian intestine are poorly understood. Culture-based studies of enteric microbiology supported the notion that the benefits of breast milk derive partly from the growth of beneficial probiotic bacteria in milk fed infants [1,2]. This idea has been called into question by studies that used cultureindependent methodologies [3,4,5,6]. It is well accepted that some microbe-mediated diseases including neonatal necrotizing enterocolitis (NEC) are less common in mother-fed (MF) infants than in formula-fed (FF) infants [7,8] For this reason, highresolution studies are needed to better characterize both the finescale structure and function of gut microbial communities in MF and FF neonates. High-resolution molecular studies are needed to definitively ascertain whether gut microbial communities are distinct in milk-fed and formula-fed infants
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