A metagenomic analysis of the effect of antibiotic feed additives on the ovine rumen metabolism

Abstract

Antibiotics are used as feed additives for domesticated ruminants as they can improve feed efficiency and simultaneously reduce disease. However, the effects of such antibiotic usage on the symbiotic relationship between those animals and their ruminal microorganisms is not well understood. We used shotgun metagenomics to compare the microbial communities from 16 sheep fed an antibiotic-supplemented diet to those of 16 sheep fed an unsupplemented diet. Metagenomic reads from each sheep were mapped to a microbial metabolic network which was linked to the host metabolic network by sets of metabolites that are assumed to be absorbed by that host. Several differences in the global structure of this network were evident between the two groups of animals. There were 546 microbial enzymes that were significantly different in their relative abundance between the two groups. On a broader scale, the animals fed antibiotics showed a set of microbial enzymes that were closer in network space to the host metabolism than were the enzymes of the microbes of animals not fed antibiotics. There were also differences in the microbial taxa present in the two groups of animals, with members of the genus Prevotella representing approximately 68 % of microbial individuals in sheep not fed antibiotics, but only 46 % in antibiotic-fed sheep. We found greater microbial taxonomic diversity in sheep fed antibiotics. The addition of antibiotics to ruminant feed alters both the taxonomic and functional structure of their ruminal microbial communities, even if the overall effects of these changes are not fully understood.