Manipulating the Equine Intestinal Microbiome: Recent Advances and Future Perspectives

An impressive amount of studies published during the last few years have used DNA sequencing technologies to describe marked changes in the composition of the equine microbiome during diseases and stress. While most of those studies are merely descriptive, using small sample sizes or lacking adequate controls, they have generated important information concerning potential biological markers indicative of gut health, such as decreased diversity and changes in the abundance of certain bacterial populations (e.g. decreased Lachnospiraceae and increased Proteobacteria).

While the consequences of harbouring an abnormal microbiome in horses have not been extensively investigated, there is strong evidences that shifts in the normal bacterial composition have negative consequences, such as increased inflammation and higher susceptibility to pathogens. Several methods of microbiota manipulation including pro-, pre-, post- and sym-biotics, as well as fecal microbiota transplantation (FMT) have been used in an attempt to reestablish the normal composition of the equine microbiome. However, large interventional trials evaluating the clinical and microbiological efficacy of commercial products and methods destined to microbiota manipulation in horses are rare.

The objective of this presentation is to discuss the current scientific evidence and limitations of microbiota manipulation and to discuss future perspectives of its therapeutic and preventive use in horses. In addition, we will present results of our research on protocols to prepare and store FMT solutions and on the use of long read sequencing (PacBio) to classify the equine microbiome at the species level.