A comparison of the microbiome and the metabolome of different regions of the equine hindgut
Authors: Dougal Kirsty, Harris Patricia A., Edwards Arwyn, Pachebat Justin A., Blackmore Tina M., Worgan Hilary J., Newbold C. Jamie
Journal: FEMS Microbiology Ecology
Summary
# Editorial Summary The equine hindgut is not a homogeneous fermentation vessel—different regions harbour distinct microbial communities with markedly different metabolic outputs, as demonstrated by Dougal and colleagues who directly compared microbial populations and their metabolic byproducts across the caecum, right dorsal colon, and faeces. Using 16S rRNA gene analysis and quantitative PCR, the researchers found that caecal microbiota clustered separately from both colonic and faecal samples, with notably lower microbial diversity; protozoal and archaeal populations were significantly more abundant in the colon, whilst volatile fatty acid and ammonia concentrations varied substantially between regions. Crucially, faecal samples—the most practical sampling method in clinical practice—reflected the microbial composition of the right dorsal colon reasonably well but proved a poor proxy for caecal microbiota, suggesting that current diagnostic protocols may be missing important region-specific changes in hindgut health. For practitioners investigating digestive dysfunction or formulating targeted nutritional interventions, these findings underscore that a single faecal analysis provides an incomplete picture of hindgut function and that region-specific pathology (particularly caecal dysbiosis) may not be reliably detected through routine faecal sampling alone.
Read the full abstract on PubMed
Practical Takeaways
- •Faecal sampling is unreliable for assessing caecal microbiota; direct caecal sampling is needed if caecal-specific information is required for diagnosis or research
- •Microbial diversity and metabolic function differ substantially across hindgut regions, so treatment or supplementation targeting specific regions may require region-specific approaches
- •When comparing horses with digestive or metabolic issues, consider which hindgut region is most relevant to the condition before selecting sampling method
Key Findings
- •Caecal microbiome clustered separately from right dorsal colon and faecal samples by 16S rRNA gene analysis, indicating distinct microbial populations by region
- •Protozoal and archaeal concentrations were significantly higher in the colon than caecum or faeces
- •Right dorsal colon and faecal samples showed higher microbial diversity than caecum using Simpson and Shannon-Wiener indices
- •Faecal samples represent the right dorsal colon microbiome but not the caecal microbiome, limiting their use for studying caecal microbiology