The diversity of the microbial ecosystem in the equine digestive tract

Abstract

The equine large intestine (cecum and colon) hosts numerous and various microbiota, which play an essential role in degrading and fermenting cell-walls into products directly used by the host. This microbiota is made of five major microbial communities (protozoa, bacteria, fungi, Archaea and virus) among which the most investigated are bacteria. These communities are equine specific. Protozoal diversities like fungal and viral ones have been described in terms of taxonomy but there is little knowledge about their implication in the digestive processes. Few studies have been conducted on the diversity of Archeae despite the potential contribution of equine livestock to greenhouse gas production. The bacterial community is diverse, belonging predominantly to the Firmicutes and Bacteroides Phyla, and including bacteria with a wide range of functions (cellulolytics, amylolytics, glycolytics, lactate-utilizers and proteolytics) that are implicated in the ingested feed digestion, mainly plant fiber. This bacterial community differs between the cecal and colonic content and the fecal content. Factors specific to the host (genotype, individual variability) and/or environmental (diet, season, exercise) may alter the microbial communities’ diversity of the equine large intestine. This can induce large changes leading to imbalances and sometimes to pathologies (colics, laminitis).