It’s no secret that “good” microbes play a vital role in maintaining horses’ proper digestive health—a necessity to keep them happy, healthy, and performing at their best. But less is known about how the medications veterinarians use to treat equine health problems, such as antimicrobials, impact good microbes’ populations. Previous studies on the matter have yielded conflicting results; however, a group of researchers from the University of Guelph, in Ontario, Canada, recently decided to take another look.

“Traditionally, studies investigating microbial communities have used culture-based methods,” explained researcher Marcio Costa, DVM, DVSc, now based at the Universidade Estadual de Londrina, in Brazil. “However, only a minority of species can grow with those methods, as many bacteria require very specific conditions and nutrients to grow. The method we used—DNA sequencing—has been considered a landmark on the characterization of microbial communities, as it detects the bacterial DNA and classifies them by comparison with reference data banks.”

The team randomly assigned 24 healthy mares to one of four groups that received the following treatments:

  • Intramuscular (IM) procaine penicillin;
  • IM ceftiofur sodium;
  • Oral trimethoprim sulfadiazine (TMS); or
  • No treatment to serve as a control.

The horses received treatment for five consecutive days. The team collected fecal samples before treatment on Day 1, at the end of treatment on Day 5, and on Days 14 and 30.

Costa said the team was specifically looking to evaluate two things:

  • Community membership (which takes into account all bacteria species present in that sample, but not the distribution of those species, he said); and
  • Population structure, (which, he said, takes into account the bacteria species constituting that community and how evenly distributed they are in the sample).

Upon reviewing their results, the team found significant changes in both population structure and community membership of microbes after the use of all treatments. But TMS affected fecal microbes the most, they said, drastically reducing the number of bacteria in the Verrucomicrobia phylum (the second-largest standard unit of biological classification). The researchers believe this was probably because TMS was the only oral treatment.

The team said they observed the most profound effects immediately after treatment, starting on Day 5.

“Significant changes were still present nine days after the end of treatment,” they noted. “By Day 30, the microbiota was more similar to baseline.”

The study, "Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs," was published in BMC Veterinary Research.