Horse species symposium : The microbiome of the horse hindgut: History and current knowledge

International audienceIn the early 1990s, the equine hindgut microbial ecosystem looked like a "black box." Its vital role in hydrolyzing and fermenting fiber, thus providing energy to the host, was recognized. Although there was a critical lack of information on the hindgut microbes, their role in preventing intestinal diseases was suggested. Traditionally, the microbes of the horse hindgut were studied using culture-dependent techniques. More recently, culture-independent methods have been used and provided further insight. This review presents the history and updated knowledge regarding the microbes that live inside the different intestinal ecosystems and which collective genomes compose the hindgut microbiome. In the first section, the quantification and diversity are described for each microbial community as well as the implication of plant fiber degradation and their crucial role for an herbivore host. The microbial communities are presented in chronological order of discovery: due to their large size, protozoa were brought to light as early as 1843 in the horse cecum; in 1897, bacteria were described in the horse intestine; as early as 1910, monoflagellated eukaryotic organisms resembling protozoa were observed in the horse cecum; since then, they have been identified to be zoospores of anaerobic fungi; in 1970, bacteriophage-like particles were recognized in the cecum and colon of pony and horse; and finally, in 1996, archaea were identified in the horse cecum. The second section discusses the variations that can occur between digestive segments or between individuals. The representativeness of the fecal microbiota to the hindgut one is debated, especially as the majority of recent studies conducted on the horse hindgut are in fact focused on the feces, rather than the cecum or colon. Also, the representation of microbiota between individuals is questioned. It has long been suggested in the literature that some ponies or horses that were more susceptible to intestinal diseases may harbor a specific intestinal microbiota. Alternatively, some new studies aim at identifying a core microbiome between all individual equine. A deeper knowledge of the microbiome and its core may allow improvement of nutrition and health, understanding of the onset of digestive diseases, and the development tools for health monitoring and disease prevention