Equine mikrobiome and IBD

Written by Silva Uusi-Heikkilä, University lecturer in genetics
Awareness of inflammatory bowel diseases (IBD) in humans and other species living in human-influenced environments has significantly increased over the past decades. In horses, IBD is now recognized as a serious threat to their well-being. It causes not only weight loss, diarrhea, and other gastrointestinal symptoms, but also general symptoms such as reduced performance and pain-related behavior. Diagnosing IBD is expensive and stressful for horses, as it typically requires transport to a clinic, fasting, endoscopy, and biopsy sampling. Due to the horse’s long digestive tract, only a small portion of the intestine can be examined through biopsy, making IBD diagnosis challenging.

Our research group, FINEBIOME, has studied the equine gut microbiome and potential differences in its composition between healthy horses and those with IBD. In humans, cats, and dogs, changes in the gut microbiome have been shown to be a reliable indicator of intestinal inflammation, with detection success rates exceeding 90%. In the future, it would be interesting to explore whether the gut microbiome composition in horse fecal samples could serve as an indicator of intestinal inflammation. However, we are not there yet.

Each horse's gut microbiome is unique. It consists of microorganisms such as bacteria, viruses, and fungi. In our study, we examined the different bacterial species and their abundances in horses participating in the research. We used a specific DNA region of equine gut bacteria—the 16S ribosomal subunit. This DNA region is popular for identifying microbial species because it varies sufficiently between bacterial species. By isolating a DNA fragment approximately 470 base pairs long from the 16S subunit, we were able to detect bacteria in the fecal samples, often down to the species level.

The study included 27 healthy and 49 IBD-affected horses. Some samples were provided by dedicated volunteer horse owners, while others came from the Laukaa equine clinic. Our results showed that certain bacterial groups were increased, while others were decreased in horses with IBD. However, changes in individual species or groups were only indicative—meaning we did not find a single bacterial species or broader taxonomic group whose increase or decrease was strongly associated with IBD. Thus, no individual bacterial species or group could serve as a reliable indicator of IBD. Interestingly, the gut microbiome of horses diagnosed with IBD was not in so-called dysbiosis (a state of complete imbalance), and the diagnosis explained only 5% of the variation in microbial composition.

In many other species, such as mice, dogs, and humans, IBD has been shown to cause dysbiosis of the gut microbiome. The absence of such a finding in our study may partly stem from the diversity of our study material. Horses in the study had been diagnosed with IBD using various methods, including ultrasound, small intestine biopsy, or both. Some horses had already been treated for IBD, and others were no longer in the acute phase of the disease. About 44% of the IBD horses were diagnosed based on a rectal biopsy. It is known that in humans, for example, IBD (Crohn’s disease) often causes inflammation in the rectum (Kelley et al. 2017). However, equine studies exploring the connection between IBD and rectal inflammation show rather variable results (e.g., Lindberg et al. 1996; Boshuizen et al. 2018).

When interpreting the study results, it is also important to consider the effect of fasting on the horse’s gut microbiome composition. Horses undergoing endoscopy for IBD diagnosis are fasted, and in our study, we could not distinguish the effects of fasting from those of the disease. In humans, even short-term fasting is known to alter the gut microbiome composition (Paukkonen et al. 2024). According to a study conducted over a decade ago, a 12-hour fast had little effect on the equine gut microbiome composition (Schoster et al. 2015), but this too warrants further investigation.

References:

Boshuizen B, Ploeg M, Dewulf J, Klooster S, de Bruijn M, Picavet M-T, Palmers K, Plancke L, Cock HD, Theelen M & Delesalle C (2018). Inflammatory bowel disease (IBD) in horses: a retrospective study exploring the value of different diagnostic approaches. BMC Veterinary Research 14: 21.

Lindberg R, Nygren A & Persson SG (1996). Rectal biopsy diagnosis in horses with clinical signs of intestinal disorders: a retrospective study of 116 cases. Equine Veterinary Journal 28: 275–284.

Paukkonen I, Törrönen E-N, Lok J, Schwab U & El-Nezami H (2024). The impact of intermittent fasting on gut microbiota: a systematic review of human studies. Frontiers in Nutrition 11: 1342787.

Schoster A, Mosing M, Jalali M, Staempfli HR & Weese JS (2016). Effects of transport, fasting and anaesthesia on the faecal microbiota of healthy adult horses. Equine Veterinary Journal 48: 595–602.