From Birth to Weaning: Supporting Gut Microbial Stability in Thoroughbred Foals

From Birth to Weaning: Supporting Gut Microbial Stability in Thoroughbred Foals

Alongside a massive increase in human microbiome research, interest in the equine microbiome has accelerated in recent years. What was once a research niche is now increasingly relevant to practical stud management.

A growing body of evidence suggests that early gut microbial development may be associated with long-term health and athletic outcomes in Thoroughbreds. While this research does not justify radical intervention, it does support thoughtful, stability-focused management during the first six to seven months of life.

In this article I outline some evidence-informed considerations for studs seeking to support microbial resilience from birth through weaning.

Early-Life Microbial Diversity and Racing Outcomes

A 2024 longitudinal cohort study by Miller et al., published in Scientific Reports, followed Thoroughbred foals from birth through to three years of age (Miller et al., 2024).

Faecal microbiota samples were collected during early life, including at approximately 28 days of age. The researchers reported that greater bacterial diversity at 28 days was significantly associated with:

• Fewer respiratory disease episodes
• Higher official racing ratings
• Greater prize money earnings
• More race wins

Foals that received antibiotics within the first month of life tended to exhibit lower microbial diversity at 28 days. In this cohort, reduced early diversity was associated with less favourable health and performance outcomes.

The study demonstrates association, not causation. However, it identifies a potentially important early-life window where microbial structure correlates with later respiratory resilience and racing success.

This finding suggests that management practices influencing gut stability during the first months of life warrant consideration.

A 6–7 Month Gut Stability Perspective

Microbial development does not end at 30 days. It progresses through establishment, expansion and stress adaptation phases.

Rather than a rigid protocol, the following sections outline management considerations that may support microbial stability and resilience.

Phase 1: Birth to ~30 Days — Establishment

During the neonatal period, the foal’s microbiome is assembling. Microbes are acquired from:

• The birth canal
• The mare’s skin and milk
• The environment and pasture
• Coprophagy [Eating poo]

Considerations:

• Ensure timely, high-quality colostrum intake for passive immunity. Cattle research suggests that absorption in calves starts to decline very quickly after 6 hours, so it is likely that the earlier the better to get the most benefit.
• Maintain consistent fibre-based nutrition in the mare pre- and post-foaling.
• Avoid abrupt dietary changes around foaling.
• Use testing-led parasite control in mares rather than blanket anthelmintic treatment.
• Avoid unnecessary antibiotic exposure in neonates.

Antibiotic Use and Probiotic Support

When antibiotics are clinically indicated, disruption of the gut microbial ecosystem is very  likely.

Equine studies examining yeast-based probiotics (particularly Saccharomyces cerevisiae strains) have commonly used total daily doses in the range of:

1 × 10⁹ to 1 × 10¹⁰ CFU per day

These levels have been associated with:

• Improved fibre digestibility
• Stabilised hindgut pH
• Enhanced volatile fatty acid production
• Reduced digestive disturbance during disruption

Doses below 10⁸ CFU/day are unlikely to be therapeutically meaningful in large animals during acute disturbance.

If used, probiotic support is typically continued during the antibiotic course and for 7–14 days post-treatment. The objective is stabilisation of fermentation rather than artificial manipulation of diversity.

Phase 2: ~1 to ~4 Months — Substrate Expansion

Between one and four months, dietary exposure broadens. This period plays a significant role in shaping microbial complexity.

A comparative study by Bulmer et al. (2020) in Animal Microbiome examined semi-feral Konik mare–foal pairs and conventionally managed domestic horses.

The semi-feral group demonstrated:

• Significantly greater microbial richness
• Higher overall bacterial diversity
• Greater representation of fibre-degrading microbial pathways
• More stable microbial communities across time

Key differences were management-driven:

• Continuous grazing
• Greater plant species diversity
• Minimal concentrate feeding
• Reduced pharmaceutical intervention

This does not suggest replicating a feral system in commercial studs. It does indicate that:

• Substrate diversity influences microbial diversity.
• Forage-based systems support broader microbial ecosystems.
• High-starch feeding may constrain microbial breadth.

Practical considerations during this phase:

• Prioritise fibre-first creep feeding.
• Introduce concentrates gradually over 2–3 weeks.
• Avoid sudden increases in starch.
• Maintain turnout where feasible.
• Consider multi-species forage inputs where practical.

Substrate diversity appears to be a powerful driver of microbial resilience.

Phase 3: ~4 to ~6 Months — Pre-Weaning Conditioning

Weaning is a predictable stress event involving:

• Social separation
• Dietary change
• Environmental shift

Stress elevates cortisol, which can influence gut permeability and microbial balance. Across species, stress has been shown to reduce microbial diversity and increase inflammatory signalling.

In foals, this period often coincides with:

• Increased gastric ulcer risk
• Appetite fluctuations
• Transient digestive instability

Considerations 3–4 Weeks Prior to Weaning:

• Maintain consistent fibre intake.
• Avoid introducing new high-starch feeds.
• Gradually adjust creep feeding rather than reformulating abruptly.
• Some studs consider introducing yeast-based probiotic support (≥1 × 10⁹ CFU/day) during this conditioning phase.

The intention is buffering stability rather than routine long-term supplementation.

The Weaning Transition (0–3 Weeks Post-Separation)

Weaning is one of the most significant physiological and psychological stress events in a young Thoroughbred’s life - as mentioned above.

It combines:

• Social separation
• Dietary change
• Environmental shift
• Increased management intervention

Stress elevates cortisol, which can influence gut permeability and microbial balance. Across species, stress has been shown to reduce microbial stability and increase inflammatory signalling.

In foals, this period also coincides with:

• Increased incidence of gastric ulceration
• Appetite fluctuation
• Manure instability
• Transient growth dips

A stable gut ecosystem appears to buffer these stress effects.

Considerations During the Weaning Window

• Maintain probiotic support at approximately 1 × 10⁹ CFU/day for 10–14 days post-separation, particularly if feed intake fluctuates.
• Ensure ad libitum access to long-fibre forage to support both gastric buffering and hindgut fermentation.
• Avoid abrupt changes in concentrate formulation immediately post-weaning.
• Use gradual separation protocols where feasible to reduce stress load.

Emerging Nutritional Insights: Amino Acids and Microbial Function

Recent work by Meng et al. (2025) in Microorganisms adds an interesting dimension to the weaning discussion.

In that study, dietary proline supplementation (40 mg/kg bodyweight/day) in weaned foals was associated with:

• Greater bodyweight gains
• Increased circulating growth-related hormones (including IGF-1 and GH)
• Enhanced antioxidant capacity
• Reduced inflammatory markers
• Increased microbial species richness (Chao1 index)
• Enrichment of microbial taxa associated with amino acid metabolism

Importantly, the microbial functional shifts were inferred using predictive pathway analysis rather than direct metabolic flux measurements. The study demonstrates association rather than causation.

However, it suggests that specific amino acid nutrition during the post-weaning period may interact with microbial metabolic pathways, particularly those involved in amino acid metabolism and energy utilisation.

This does not justify routine high-dose amino acid supplementation in all foals.

It does indicate that nutritional composition during weaning — including adequate amino acid provision — may influence both host physiology and microbial ecology during this stress-sensitive period.

A Balanced Interpretation

The current evidence suggests that:

• Stress can destabilise the gut ecosystem.
• Nutritional strategies during weaning influence microbial structure and host metabolic signalling.
• Targeted probiotic support at therapeutic CFU levels may help buffer disruption.
• Fibre continuity remains foundational.

Rather than attempting to manipulate diversity directly, the more defensible goal during weaning is maintaining stability while supporting growth and adaptation.

Given the observed association between early microbial diversity and improved respiratory resilience and racing outcomes, protecting gut stability through the weaning transition appears strategically prudent.

Parasite Management During the First Six Months

Testing-led parasite management using faecal egg counts is increasingly recommended.

Benefits include:

• Reduced unnecessary anthelmintic exposure
• Slower development of drug resistance
• Reduced impact on pasture ecology

For both mares and foals, veterinary-guided treatment based on individual burden supports responsible stewardship and environmental stability.

What We Still Don’t Know

While emerging evidence is compelling, important uncertainties remain:

1. The Miller et al. study demonstrates association, not causation.
2. Optimal microbial diversity thresholds are not defined.
3. Long-term structural microbiome changes from routine probiotic use in healthy foals are not well established.
4. Individual variation remains significant.
5. Mechanisms linking microbial diversity to respiratory resilience and performance require further investigation.

Current evidence supports measured, stability-focused management rather than aggressive manipulation.

Balanced Perspective

From birth through weaning, consider:

• Supporting maternal gut stability
• Prioritising fibre diversity
• Introducing feed changes gradually
• Avoiding unnecessary antimicrobial intervention
• Using testing-led parasite control
• Providing probiotic support at therapeutic CFU levels during disruption
• Buffering the weaning transition thoughtfully

Emerging data linking early microbial diversity with improved respiratory resilience, race wins and prize money suggests that gut stability in the first six months deserves deliberate attention.

Not as a guarantee of performance.

But as part of building a more resilient Thoroughbred.

If you would like to discuss how to build a gut stability strategy tailored to your stud — including appropriate nutritional and probiotic support where indicated — our team is happy to help.

References

Bulmer, L. S., Murray, J. A., Burns, N. M., et al. (2020). The influence of management and environment on the equine gut microbiome: A comparison between semi-feral and domestic horses. Animal Microbiome, 2, 27. https://doi.org/10.1186/s42523-020-00060-6

Miller, G. J., Smith, J. L., Harris, S. D., Brown, A. N., et al. (2024). Early-life gut microbiome diversity is associated with respiratory health and racing performance in Thoroughbred horses. Scientific Reports, 14, Article number 64657. https://doi.org/10.1038/s41598-024-64657-6