Open AccessThe effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or Salmonella infection on the fecal microbiome of horses
Author(s) -
Arnold Carolyn E.,
Pilla Rachel,
Chaffin M. Keith,
Leatherwood Jessica L.,
Wickersham Tryon A.,
Callaway Todd R.,
Lawhon Sara D.,
Lidbury Jonathan A.,
Steiner Joerg M.,
Suchodolski Jan S.
Publication year - 2021
Publication title -
journal of veterinary internal medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.356
H-Index - 103
eISSN - 1939-1676
pISSN - 0891-6640
DOI - 10.1111/jvim.16206
Subject(s) - firmicutes , feces , microbiome , salmonella , bacteroidetes , diarrhea , medicine , veterinary medicine , colitis , breed , biology , microbiology and biotechnology , zoology , bacteria , 16s ribosomal rna , bioinformatics , genetics
Abstract Background The fecal microbiome of healthy horses may be influenced by signalment, diet, environmental factors, and disease. Objectives To assess the effects of age, breed, sex, geographic location, season, diet, and colitis caused by antibiotic use (antimicrobial‐associated diarrhea [AAD]) and Salmonella infection on fecal microbiota. Animals Healthy horses ( n = 80) were sampled from nonhospital environments across multiple geographical locations in the United States. Horses with AAD ( n = 14) were defined as those that developed diarrhea secondary to antimicrobial use. Horses with Salmonella infection ( n = 12) were presented with spontaneous onset of colitis and subsequently tested positive on Salmonella quantitative polymerase chain reaction. All horses were >1 year of age and stratified by a dietary scale that included forages (pasture and hay) and concentrates grouped by percentage of fiber and amount. Methods Illumina sequencing of 16S rRNA genes was performed on fecal DNA. Results Healthy horses fed higher amounts of grain clustered separately from those fed lower amounts of grain (analysis of similarities [ANOSIM], R = 0.356‐0.385, Q = 0.002). Horses with AAD and Salmonella had decreased richness and evenness compared to healthy horses ( P < .05). Univariable analysis of the 3 groups identified increases in Bacteroidetes ( Q = 0.002) and Protebacteria ( Q = 0.001) and decreases in Verrucomicrobia ( Q = 0.001) in AAD horses whereas Salmonella horses had less Firmicutes ( Q = 0.001) when compared to healthy horses. Conclusions and Clinical Importance Although the amount of grain in the diet had some impact on the fecal microbiome, colitis had a significantly larger influence. Horses with ADD have a more severe dysbiosis than do horses with Salmonella .