THE EQUINE FECAL MICROBIOME - EFFECTS OF DIET, ANTIMICROBIALS, AND COLITIS

The microbiome of the equine gastrointestinal tract (GIT) form a symbiotic relationship with the horse, and play a critical role in nutrition, metabolism, and immunity. This work utilized 16S rRNA sequencing and metabolomics to characterize the fecal microbiome of healthy horses and to measure the dysbiosis caused by antimicrobial use and colitis. The fecal microbiome of healthy horses was comprised of the following phyla: Firmicutes (45%), Bacteroidetes (31.5%), Verrucomicrobia (9%), Spirochaetes (6%), Tenericutes (1.8%) with the remainder (6.7%) unclassified. Amongst healthy horses, diet had more influence on the fecal microbiome than other variables, such as age, breed, sex, geographic location, or season. Feeding concentrate at > 1-2% BW in kg/day altered the community composition but not diversity. The presence of colitis had a marked effect on the fecal microbiome. Horses with acute colitis caused by antimicrobial use (AAD) or infection with Salmonella showed a decreased richness and evenness compared to healthy horses. Horses with colitis showed an increased abundance of Bacteroidetes (q=0.002) and Proteobacteria (q=0.001), while horses with Salmonella infection showed a decrease in Firmicutes (q=0.001) and AAD horses showed a decreased abundance of Verrucomicrobia (q=0.001). Metronidazole administration decreased species richness and evenness and altered the bacterial community composition (ANOSIM, p=0.008). The most abundant phyla were Bacteroidetes and Firmicutes, but significant changes in Actinobacteria, Spirochaetes, Lentisphaerae, and Verrucomicrobia occurred during metronidazole administration and coincided with clinical signs of GIT disease. Metronidazole altered the metabolism of amino acids, carbohydrates, lipids, nucleic acids and cofactors, and vitamins. Antimicrobial agents induced a severe dysbiosis, regardless of whether horses developed diarrhea. Antibiotics markedly reduced diversity measures compared to control horses. All horses on antibiotics, including diarrhea and non-diarrhea controls, had changes in phyla compared to non-antibiotic-treated control horses. The phylum Verrucomicrobia distinguished horses with antibiotic induced colitis from antibiotic-treated and non-antibiotic-treated control horses. In summary, diet can affect the fecal microbiome of healthy horses by feeding high amounts of concentrate. The effects of antibiotic administration in itself, antibiotic-induced colitis, or Salmonella infection, all dramatically reduced diversity and altered bacterial community composition. The effects of antibiotics and disease are larger than those of diet