The microbiome of the digestive tract of ponies: Analysis based on 16S rRNA sequencing

Abstract

The study of the intestinal microbiome of ponies using 16S rRNA sequencing provided a deep insight into its structural organization, richness and ecological diversity. It was found that bacterial communities are characterized by high alpha diversity, a significant number of rare taxa, and the absence of dominance of individual species. The microbiome was dominated by four phyla — Pseudomonadota, Bacillota, Bacteroidota, and Actinomycetota, which accounted for over 90% of all reads. The presence of the genera Escherichia and Bacteroides may indicate transient changes or metabolic adaptation to environmental conditions. Analysis of β-diversity using the PCoA method revealed distinct individual differences caused by both internal (genetic) and external (ecological) factors. The similarity of microbiomes in animals with common housing conditions indicates a significant influence of diet, social structure, local microenvironment, and daily behavioural contacts. The predominance of rare taxa (according to Fisher's alpha and Rarity indices) emphasizes the ecological complexity, flexibility and stability of the microbial environment. Communities formed under natural grazing conditions proved to be more stable and adaptive. The results demonstrate the potential of microbiome monitoring for health diagnosis, feed optimization, probiotic strategy development, and prevention of intestinal dysfunction in ponies. Considering the microbiome as a complete ecosystem opens up new perspectives in veterinary medicine, particularly in the direction of personalised approaches to animal health maintenance. Further research considering the dynamics of the microbiota over time and the influence of seasonality may deepen our understanding of the relationship between the microbial profile, stress factors, and the physiological state of the animal.