Does the Microbiome Matter? Microbiome Profiling in the Horse and Other Livestock Species

With advancements in next generation sequencing technologies, molecular identification of microbial species has become less expensive and more routine. The tools exist to determine the presence and abundance of microbial species in a given sample (16S rRNA amplicon sequencing) as well as the functions they are performing (metagenomics/metatranscriptomics). This is enabling the study of the importance and contributions microbial populations make to host defense and maintenance. Indeed in humans, microbiota dysbiosis has been implicated in a variety of diseases including inflammatory bowel disease, diabetes and obesity, thus offering the opportunity to investigate potential microbiota modulating interventions to treat and prevent disease. By comparison, microbiota studies in the horse and livestock species are still in their infancy. An overview of the techniques and concepts in microbiome research will be given along with specific examples of microbiota profiling in various species including pigs, goats, cows and a study in horses examining the gut microbiota of foals from birth to weaning.