title: 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 mucosa-associated 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.
authors: Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
authors: Torey
authors: T
authors: Looft
authors: Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
authors: Heather K
authors: HK
authors: Allen
authors: Baylor Institute for Immunology Research, Baylor Healthcare system, Dallas, TX, USA.
authors: Brandi L
authors: BL
authors: Cantarel
authors: Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
authors: Uri Y
authors: UY
authors: Levine
authors: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA.
authors: Darrell O
authors: DO
authors: Bayles
authors: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA.
authors: David P
authors: DP
authors: Alt
authors: 1] Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, 163 Avenue de Luminy, Marseille, France [2] Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
authors: Bernard
authors: B
authors: Henrissat
authors: Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
authors: Thaddeus B
authors: TB
authors: Stanton
mesh_terms: D000821:Animal Feed; D000818:Animals; D000900:Anti-Bacterial Agents / Q000008:administration & dosage / Q000494:pharmacology*; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001435:Bacteriophages / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D007420:Intestine, Large / Q000382:microbiology; D007421:Intestine, Small / Q000382:microbiology; D007422:Intestines / Q000382:microbiology*; D008297:Male; D064307:Microbiota / Q000187:drug effects*; D013552:Swine / Q000382:microbiology*
chemical_list: D000900:Anti-Bacterial Agents