Gut Microbiota Profiling as a Promising Tool to Detect Equine Inflammatory Bowel Disease (IBD)

Simple Summary Inflammatory bowel disease (IBD) has become more common among humans and awareness of its prevalence in animals, including horses, has also increased during the past few decades. Equine IBD is problematic as it decreases the performance of horses and causes diarrhea, weight loss, and pain-related behaviors. Apart from high levels of uncertainty in diagnosing IBD, it is stressful for the horse and expensive for the owner as it typically requires transportation to the horse hospital, fasting, endoscopy, and biopsy assessment. Therefore, there is a need for a non-invasive and affordable method to screen for IBD. Fecal microbiota composition has been shown to change in humans and other animals with IBD; therefore, we used fecal samples to study whether equine IBD is also reflected by changes in the composition of gut microbiota. We show that gut microbiota composition was different and that the abundances of certain bacterial groups were significantly increased or decreased in horses with IBD compared to healthy horses. We further used a machine learning model to predict IBD based on the microbiota composition of the fecal samples. The model produced correct predictions with 100% accuracy in our dataset. We conclude that, in the future, studying the microbiota composition of fecal samples could become an accurate, cheap, and non-invasive method in screening for equine IBD.Abstract Gastrointestinal disorders are common and debilitating in horses, but their diagnosis is often difficult and invasive. Fecal samples offer a non-invasive alternative to assessing the gastrointestinal health of horses by providing information about the gut microbiota and inflammation. In this study, we used 16S sequencing to compare the fecal bacterial diversity and composition of 27 healthy horses and 49 horses diagnosed with inflammatory bowel disease (IBD). We also measured fecal calprotectin concentration, a marker of intestinal inflammation, in healthy horses and horses with IBD. We found that microbiota composition differed between healthy horses and horses with IBD, although less than five percent of the variation in microbiota composition was explained by individual health status and age. Several differentially abundant bacterial taxa associated with IBD, age, or body condition were depleted from the most dominant Firmicutes phylum and enriched with the Bacteroidota phylum. An artificial neural network model predicted the probability of IBD among the test samples with 100% accuracy. Our study is the first to demonstrate the association between gut microbiota composition and chronic forms of IBD in horses and highlights the potential of using fecal samples as a non-invasive source of biomarkers for equine IBD.