Animal Health Research Reviews

Review Article

The equine intestinal microbiome

Marcio C. Costaa1 and J. Scott Weesea1a2 c1

a1 Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G2W1, Canada

a2 Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G2W1, Canada


The equine intestinal tract contains a complex microbial population (microbiota) that plays an important role in health and disease. Despite the undeniable importance of a ‘normal’ microbiota, understanding of the composition and function of this population is currently limited. As methods to characterize the microbiota and its genetic makeup (the microbiome) have evolved, the composition and complexity of this population are starting to be revealed. As is befitting a hindgut fermenter, members of the Firmicutes phylum appear to predominate, yet there are significant populations of numerous other phyla. The microbiome appears to be profoundly altered in certain disease states, and better understanding of these alterations may offer hope for novel preventive and therapeutic measures. The development and increasing availability of next generation sequencing and bioinformatics methods offer a revolution in microbiome evaluation and it is likely that significant advances will be made in the near future. Yet, proper use of these methods requires further study of basic aspects such as optimal testing protocols, the relationship of the fecal microbiome to more proximal locations where disease occurs, normal intra- and inter-horse variation, seasonal variation, and similar factors.

(Received March 13 2012)

(Accepted April 24 2012)

(Online publication May 25 2012)


c1 Corresponding author. E-mail: