The hidden molecules that keep your horse’s gut healthy — and what peer-reviewed science says about them

If you've ever wondered what's actually going on in your horse's hindgut — beyond the broad idea that "gut health matters" — a newly published paper offers one of the clearest explanations we've seen. "The Role of Short-Chain Fatty Acids (SCFAs) in Colic and Anti-Inflammatory Pathways in Horses," published in the journal Animals in December 2025 by Schank and colleagues at Lincoln Memorial University, sets out in careful detail how the health of your horse's gut microbiome connects directly to one of the most serious and common conditions in equine medicine: colic.

Colic remains the leading cause of emergency veterinary intervention in horses, and its origins are often microbial. When the balance of bacteria in the hindgut shifts — triggered by dietary starch, fructan-rich grass, stress, or sudden feed changes — the consequences can escalate quickly from discomfort to something far more serious. The Schank paper explains the molecular mechanism at the heart of this: a group of compounds called short-chain fatty acids, or SCFAs. Produced deep in the hindgut when beneficial bacteria ferment dietary fibre, these molecules are not glamorous, but they may be among the most important substances in your horse's body. And when we read the paper, we found it aligned almost precisely with research we'd already conducted and published ourselves.

What are SCFAs and why do they matter?

The three main SCFAs — acetate, propionate, and butyrate — do an extraordinary amount of work. Butyrate is the primary fuel for the cells lining the gut wall, keeping that barrier strong and intact. Propionate plays a key role in immune regulation. Acetate feeds the wider microbial community. Together they help control inflammation, regulate gut movement, and even cross the blood-brain barrier to influence mood and nervous system function.

"When horses eat too much starch or too little fibre, SCFA levels can drop, leading to gut imbalance, leaky intestines, and inflammation."

The Schank paper explains that when starch or fructans — the sugars in lush spring and autumn grass — overflow into the hindgut, the balance of bacteria shifts. Fibre-fermenting species, the ones that produce SCFAs, get crowded out. Hindgut pH drops, the gut wall becomes more permeable, and the whole system moves in the wrong direction. This is particularly relevant for leisure horses on pasture, where grass fructan levels can swing dramatically — hour to hour, day to day, season to season — creating unpredictable surges of fermentable carbohydrate.

What does this have to do with EquiNectar?

EquiNectar works by supplying digestive enzymes in the foregut — breaking down starches and fructans before they reach the hindgut. If less fermentable material reaches the hindgut undigested, there's less disruption to the microbial community, and the bacteria that produce SCFAs can get on with their job.

In 2022, we carried out a study with ten leisure horses on standard diets, supplementing with EquiNectar for eight weeks. Faecal samples were analysed before and after supplementation using SIFT-MS metabolomics and 16S microbiome sequencing. The results were published in 2024 in the Journal of Modern Agriculture and Biotechnology (Waring, Dagi & Hunter, 2024).

The published findings: SCFAs across all ten horses

Across the full cohort, total short-chain fatty acids increased substantially after supplementation. All three key SCFAs moved in the right direction:

Total mean SCFAs across all ten horses rose from 1,376 ppb before supplementation to 2,077 ppb after — an increase of 51%. At the same time, levels of ethanol and dimethyl disulphide fell, both markers of gut toxicity.

Going deeper: individual responses

In a more detailed analysis of individual horses from the same research programme, we looked specifically at butyrate — the SCFA that the Schank paper identifies as most critical for gut wall integrity and anti-inflammatory function. The responses we recorded were striking:

Every horse showed a meaningful increase, averaging +120% across the three. Tory's near-fourfold increase from a very low baseline suggests her gut wall cells were significantly under-fuelled before supplementation began.

The bacteria behind the numbers

The microbiome data helps explain the mechanism. The published Waring et al. paper reports that after supplementation, horses generally had lower levels of Spirochaetes — a marker of dysbiosis — alongside increases in Fibrobacter, Ruminococcaceae, Blautia, and Oscillospira, all associated with fibre degradation and butyrate production. Paraprevotella, a propionate producer, also increased.

In the individual horse analysis, a genus called Selenomonas — which converts lactate into propionate and other SCFAs — increased with complete consistency across all horses measured. This matters because lactate accumulation is one of the primary ways hindgut pH falls and dysbiosis takes hold. Selenomonas act as a natural pH buffer, clearing lactate before it can cause damage.

What the numbers mean together

The picture that emerges is a coherent chain: EquiNectar's enzymes reduce the amount of undigested starch and fructans reaching the hindgut, which reduces the substrate available to lactate-producing bacteria, which allows lactate-clearing species to expand, which in turn supports the bacteria that produce butyrate, propionate, and acetate.

This is precisely the mechanism that Schank et al. describe — and our data, now with peer-reviewed publication behind it, shows it happening.

"In both species, the use of additional digestive enzymes in a maltodextrin matrix supports an improved microbiome." — Waring, Dagi & Hunter, 2024

Both papers are freely available to read. Links are in the references below.