Gut Microbial Gene Expression in Mother-Fed and Formula-Fed Piglets

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.

Alterations in the Porcine Colon Microbiota Induced by the Gastrointestinal Nematode Trichuris suis

“…The 10 most abundant genera accounted for ϳ90% of all 16S sequences that were positively assigned to any genus in control pigs. Prevotella was the most abundant; this agrees with recently published reports (25,34), accounting for 62.3% and 68.2% of 16S sequences assigned in control and infected pigs, respectively. The secondmost-abundant genus was Oscillibacter (7.8% in control pigs), followed by Treponema (7.5%), Succinivibrio (3.6%), Anaerovibrio (2.2%), and Roseburia (1.9%).…”

Sequence-Based Analysis of the Intestinal Microbiota of Sows and Their Offspring Fed Genetically Modified Maize Expressing a Truncated Form of Bacillus thuringiensis Cry1Ab Protein (Bt Maize)

“…The fecal microbiota of sows and their offspring and the offspring cecal microbiota were dominated for the most part by Firmicutes and Bacteroidetes, similar to previous findings for the cecal and fecal microbiota of weanling and finisher pigs (13,14,51,52) and in agreement with data from humans (47,53). Some similarities are evident between the fecal microbiota of sows and their offspring, providing support for the assumption that maternal flora influences the microbiota of progeny (19).…”

Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

“…The SEED is organised into three hierarchical levels for metabolism and six levels for taxonomy [37][38][39]. Matches with a E-value of <0.05 were considered significant with a minimum alignment of 50 bp [31,[39][40][41][42][43][44][45][46]. All data was normalised to sequencing effort by dividing by the total number of hits.…”