title: Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses.
abstract: The advance of new sequencing technologies has allowed more comprehensive characterization of complex microbial communities, including the ones inhabiting the intestinal tract. The presence of extreme environmental filters, such as low pH, digestive enzymes and anaerobic conditions along the tract, acts on the selection of unique bacteria in each compartment. The intestinal microbiota has an enormous impact on the maintenance of health. However, data about the bacteria present in the different intestinal compartments of horses are sparse. In this study, high throughput sequencing was used to characterize and compare bacterial profiles from different intestinal compartments of 11 horses scheduled for euthanasia for reasons other than gastrointestinal problems. Marked differences among compartments even at high taxonomic levels were found, with Firmicutes comprising the main bacterial phylum in all compartments. Lactobacillus spp. and Sarcina spp. predominated in the stomach and a marked increase of Streptococcus spp. occurred in the duodenum. Actinobacillus and Clostridium sensu stricto were the most abundant genera in the ileum and '5 genus incertae sedis', a genus from the Subdivision 5 class of the Verrucomicrobia, was the most abundant from the large colon through feces. There was a significant increase in diversity towards the distal gut with similar profiles observed from the cecum through feces at the class level. The bacterial population comprising the equine intestinal tract varies greatly among compartments and fecal samples may be useful as representative of changes occurring in the distal compartments.
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1. Electronic address: costamc@gmail.com.
authors.forename: M C
authors.initials: MC
authors.lastname: Costa
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1.
authors.forename: G
authors.initials: G
authors.lastname: Silva
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1.
authors.forename: R V
authors.initials: RV
authors.lastname: Ramos
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1.
authors.forename: H R
authors.initials: HR
authors.lastname: Staempfli
authors.affiliation: Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1.
authors.forename: L G
authors.initials: LG
authors.lastname: Arroyo
authors.affiliation: Department of Mathematics and Statistics, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1.
authors.forename: P
authors.initials: P
authors.lastname: Kim
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, ON, Canada N1G 2W1.
authors.forename: J S
authors.initials: JS
authors.lastname: Weese
mesh_terms: D000818:Animals; D004269:DNA, Bacterial; D005260:Female; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006736:Horses / Q000382:microbiology*; D008297:Male; D064307:Microbiota / Q000235:genetics; D012336:RNA, Ribosomal, 16S; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA; Equine; Intestinal microbiota; Microbiome; Next generation sequencing