Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Abstract

Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosaassociated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.

In Situ Prebiotics for Weaning Piglets: In Vitro Production and Fermentation of Potato Galacto-Rhamnogalacturonan

“…Another study from Looft and colleagues reported ϳ20 to 30% Firmicutes and 50 to 60% Bacteroidetes in animals weaned at 12 days and tested at 8 weeks (58). One explanation for the dominance of the Firmicutes in our study is the use of terminal small ileum samples rather than fecal samples, and that explanation is supported by a recent study examining the composition of the microbiota in several segments of the porcine GI tract: here, the ileal microbiota was ϳ95% Firmicutes, whereas the cecal, colonic, and fecal flora was ϳ50% Bacteroidetes (30).…”

“…In light of this, it was hypothesized that feeding of enzymes and substrate should allow the enzymatic degradation of highly complex molecules into prebiotic fibers in situ, thereby decreasing the issues of industrial fiber production, such as purification and transport. Release of these fibers from potato pulp by the gut microbiota is not possible, as the bacteria in the pig ileum do not possess genes for pectinolytic enzymes (30).…”

0991 Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens

“…Similar results were suggested by several previous researchers (Looft et al 2014;Kamada et al 2013;Sekelja et al 2012;Videnska et al 2013); for example, Looft et al reported that ileum, cecum, mid-colon and feces have different microbial communities in swine at the phylum and genus level (Looft et al 2014). Sekelja et al also reported that a clear separation of microbial composition was seen between the upper gut (crop and gizzard), ileum and lower gut (cecum and colon) in broiler chickens (Sekelja et al 2012).…”

Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative

“…In pigs, the ileal mucosa harbors greater bacterial diversity than the lumen and has a makeup similar to that of the mucosa of the large intestine, suggesting that mucosal microbes of the ileum serve as an inoculum for the large intestine (12). High-dose BLS mix treatment increases the abundance of members of the phylum Proteobacteria during F4 ϩ ETEC infection, raising the possibility that excessive BLS mix treatment increases the risk for enteritis.…”

“…Moreover, culture or targeted molecular biology-based analyses provide an incomplete profile of the microbiota. Next-generation high-throughput sequencing of PCR amplicons from the 16S rRNA genes has been used for high-resolution surveys of microbiota communities, and this technological development has facilitated detailed analysis of the microbiota structure (12). The microbial ecosystem of the swine gut changes across growth stages, and these variations in the gut microbiota are driven by a variety of factors, including exogenous bacteria (13).…”