Preventing Gut Dysbiosis: The Long-Term Impact of Antibiotics and High-Starch Diets on the Equine Microbiome
In equine medicine, the hindgut is often described as the “engine room” of the horse. Yet, many of our routine clinical interventions – from prescribing a course of antibiotics to hospitalizing a case for monitoring – can stall that engine.
Recent longitudinal research from 2023 and 2024 has shed new light on the “recovery curve” of the equine microbiome, revealing that the damage caused by dysbiosis lasts far longer than previously thought.
1. The “TMS Effect”: A 6-Month Recovery Window
Trimethoprim-sulfadiazine (TMS) is a staple in ambulatory practice, but its impact on the microbial “resistome” is profound. A landmark 2023 study by Theelen et al. followed horses after a standard 5-day course of oral TMS.
The findings were a wake-up call for antimicrobial stewardship: while the microbiome composition appeared to stabilize two weeks post-treatment, it remained significantly altered six months later.
Specifically, populations of Spirochaetes and Verrucomicrobia – essential for fiber fermentation – remained depleted, while resistance genes like sul2 stayed elevated by 15-fold.
2. Starch Overload: Mapping the Pathogenic Shift
We know high-starch diets are linked to laminitis, but we now have a species-level map of why 2024 research by Raspa et al. characterized the microbiota across the entire digestive tract of horses fed high-starch (HS) vs. high-fiber (HF) diets.
The HS diet didn’t just lower diversity; it actively promoted “pro-inflammatory” bacteria:
- Small Intestine: Increased Enterobacteriaceae.
- Caecum: A surge in Streptococcus, the primary driver of lactic acid production.
- Sternal Flexure: An overgrowth of Fusobacterium, a genus frequently associated with inflammatory diseases.
3. Hospitalization: Environment vs. Intervention
Does the hospital environment itself cause dysbiosis? Interestingly, research suggests that hospitalization without medication does not significantly shift the microbiome.
The primary drivers of dysbiosis in the clinic are the underlying disease (such as inflammatory colic) and the administration of drugs, rather than the change in stall or transport stress alone.
Bridge the Gap to Hands-On Mastery
Protecting the microbiome requires a shift from “reactive” to “proactive” clinical reasoning. The Practitioner’s Program provides the evidence-based frameworks to help you choose the right antimicrobial and manage complex gastrointestinal cases safely.
Member Call to Action: Log in now to watch these critical CE training videos:
- Antimicrobial Selection in Equine Practice: Balancing clinical efficacy with stewardship.
- Clinical Approach to Chronic Diarrhoea in the Adult Horse: Diagnostic steps for the dysbiotic patient recorded by Nathan Slovis DVM, Dipl. ACVIM, CHT
- Practical Management of Infectious Disease Outbreaks: Protecting the herd and the individual.
References:
- Theelen MJP, et al. (2023). Longitudinal study of the short- and long-term effects of hospitalisation and oral TMS on the equine faecal microbiome. Microbiome.
- Raspa F, et al. (2024). Microbiota characterization throughout the digestive tract of horses fed a high-fiber vs. a high-starch diet. Front Vet Sci.
- Menzies-Gow NJ, et al. (2025). Equine Colic: Longitudinal Changes in Fecal Microbiota During Hospitalization.
- Practitioner’s Program 2026 Annual. The Equine Practice Company.
