The effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or Salmonella infection on the fecal microbiome of horses.
Authors: 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
Journal: Journal of veterinary internal medicine
Summary
# Editorial Summary This 2021 investigation examined how signalment, management factors, and gastrointestinal disease shape the equine faecal microbiome by comparing 80 healthy horses sampled across multiple US geographic locations with 14 cases of antimicrobial-associated diarrhoea (AAD) and 12 Salmonella-infected horses, using 16S rRNA gene sequencing to characterise microbial populations. Dietary grain content demonstrated measurable effects on microbial community structure in healthy animals, with high-grain diets clustering distinctly from low-grain feeding; however, colitis—whether secondary to antimicrobial use or Salmonella infection—produced substantially greater microbial dysbiosis than any dietary variable. AAD cases exhibited the most severe microbiota disruption, characterised by significantly reduced richness and evenness alongside marked increases in Bacteroidetes and Proteobacteria with concurrent loss of beneficial Verrucomicrobia, whilst Salmonella-infected horses showed primarily depleted Firmicutes populations despite similar reductions in microbial diversity. These findings carry important clinical implications: they quantify that disease-induced dysbiosis far outweighs dietary composition as a driver of microbiota disruption, suggest that AAD may warrant more aggressive therapeutic intervention than previously considered based on its severity of dysbiosis, and highlight that microbial signatures differ between enteropathogens—meaning standardised probiotic or dietary interventions may require pathogen-specific tailoring to effectively restore microbiota balance during recovery from colitis.
Read the full abstract on PubMed
Practical Takeaways
- •Dietary grain content moderately influences equine fecal microbiota, but disease state (particularly antimicrobial-associated colitis) has substantially greater impact on microbial composition and diversity
- •Horses treated with antimicrobials causing diarrhea develop more severe dysbiosis than those with Salmonella infection, suggesting different therapeutic or management approaches may be warranted
- •Microbiome analysis could help differentiate between antimicrobial-associated diarrhea and infectious causes like Salmonella, potentially guiding treatment decisions
Key Findings
- •Horses fed higher grain amounts showed distinct microbiome clustering (ANOSIM R=0.356-0.385, Q=0.002) compared to lower grain diets
- •AAD and Salmonella-infected horses had significantly decreased microbial richness and evenness compared to healthy horses (P<0.05)
- •AAD horses showed increased Bacteroidetes and Proteobacteria with decreased Verrucomicrobia; Salmonella horses showed decreased Firmicutes relative to healthy controls
- •Colitis had a significantly larger influence on fecal microbiome composition than dietary grain amount, with AAD causing more severe dysbiosis than Salmonella infection