Study offers insights into gut bacteria in horses

Canadian researchers have cast light on potential causes of lower bowel inflammation.
Canadian researchers have cast light on potential causes of lower bowel inflammation.

Inflammation of the lower bowel in horses may result from microbial imbalances in the gut and not the overgrowth of an individual pathogen, Canadian research suggests.

Researchers from the University of Guelph, in Ontario, set out to characterize the totality of microbes, known as the microbiome, in the faeces of healthy horses and compare it to the fecal microbiome of horses with lower bowel inflammation, known as colitis.

The intestinal tract  is home to one of the richest and most complex microbial populations on the planet and plays a critical role in health and a wide range of diseases, the authors noted, adding that limited studies using new DNA sequencing technologies in horses were available.

A total of 195,748 sequences obtained from six healthy horses and 10 horses affected by typical cases of colitis were analyzed.

Firmicutes predominated (68%) among healthy horses, followed by Bacteroidetes (14%) and Proteobacteria (10%).

In contrast, Bacteroidetes (40%) was the most abundant phylum among horses with colitis, followed by Firmicutes (30%) and Proteobacteria (18%).

“Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes, while horses with colitis had significantly more Fusobacteria,” the researchers wrote in the open-access journal, PLoS ONE.

Members of the Clostridia class were more abundant in healthy horses, they found, while members of the Lachnospiraceae family were the most frequently shared among healthy individuals.

“The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The abundance of Fusobacteria in horses with colitis deserves special attention and further investigation, as the role of this phylum in equine colitis is currently unknown.”

The researchers noted that no Escherichia coli sequences were present in feces of any of the healthy horses; however, the organism was found in eight of the ten horses with colitis.

“The species richness reported here indicates the complexity of the equine intestinal microbiome and this study provides the most comprehensive indication of this important and complex microbiome to date,” they said.

“The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis [microbial imbalance], rather than one that occurs simply through overgrowth of an individual pathogen.”

The large intestine of the horse is an anaerobic fermentative chamber where fibrolytic bacteria produce short chain fatty acids that account for most of the horse’s energy requirements, the authors noted.

Overall percentages of bacterial populations at the phylum level (Fig. A) and intra-phylum variation (Fig. B) present in feces of healthy horses and horses affected by colitis.
Overall percentages of bacterial populations at the phylum level (Fig. A) and intra-phylum variation (Fig. B) present in feces of healthy horses and horses affected by colitis.Overall percentages of bacterial populations at the phylum level (Fig. A) and intra-phylum variation (Fig. B) present in feces of healthy horses and horses affected by colitis. © PLoS ONE

A properly functioning intestinal tract and microbiome was critical for maintenance of normal health, they said.

The balance in the equine gut bacteria is sensitive to factors such as gastrointestinal disease and dietary change, which may lead to catastrophic consequences, even culminating in death.

In fact, diseases affecting the gastro-intestinal system are the main cause of mortality in horses.

“Yet, despite the clear importance of the intestinal microbiome, our understanding of what constitutes ‘normal’ and ‘abnormal’ is to date very limited,” they said.

Colitis in horses can be associated with a variety of infectious agents such as Clostridium difficile, Salmonella spp, Clostridium perfringens and Neorickettsia risticii.

In most cases, the pathogen responsible remained undetermined. However, disruption of the normal microbiome was likely a key factor in most cases of colitis.

Characterizing the equine intestinal microbiome was therefore critical, they said, since a good understanding of the “normal” intestinal microbiome is needed for interpretation of “abnormal”.

In explaining their methods, the researchers said most investigations of the equine microbiome had typically involved bacterial culture of feces or intestinal contents.

“However, culture-based methods only allow for superficial assessment of the components of the microbiome, which is a significant limitation, as a large component of the microbiome is thought to consist of unknown or unculturable micro-organisms.”

Molecular approaches were therefore required in order to analyze bacterial diversity in fecal samples, they said.

Alteration of the intestinal microbiome in colitis was not unexpected. “However, these results indicate a rather profound alteration, given the numerous phylum-level differences in relative abundance.”

Significant changes at the phylum level have also been shown in people with chronic inflammatory conditions, obesity and in dogs with diarrhea, they noted.

Identifying organisms disproportionately present in horses with colitis could lead to investigation of their potential role as causative agents, they said.

“Fusobacteria were rare in healthy horses but significantly more abundant in horses with colitis. While cause versus effect cannot be discerned, this raises some interesting questions given increasing information about the role of Fusobacterium spp in various gastrointestinal diseases of humans, including Crohn’s disease, colorectal cancer, and appendicitis.”

The researchers noted that the use of probiotics had been suggested as a prophylactic and therapeutic adjuvant in cases of chronic diarrhea in humans.

“To date, the development of probiotics for the equine species has not been successful. There are many potential reasons for this, but it may relate in part to our previously poor understanding of the equine intestinal microbiome.

“Specifically, probiotic approaches in horses have focused on lactic acid bacteria, which comprise only a small component of the microbiome of healthy horses and which were not decreased in disease.

“It is possible that probiotic therapy should target other, more common, components of the microbiome, particularly clostridia and other abundant members of the Firmicutes phylum.

“Surprisingly, equine colitis was not associated with loss of diversity and richness, but further studies using more uniform groups of horses with specific [causes] are required.

“Microbiota transplantation might potentially be an effective treatment to restore this complex environment towards what is considered more ‘normal’.”

The authors said the digestive tract of a horse was large and it remained uncertain if bacteria in feces directly reflected the bacterial population in the large colon. They said further studies comparing the bacterial population from different compartments of the equine intestinal tract were ultimately required.

The study was carried out by Marcio Costa, Luis Arroyo, Emma Allen-Vercoe, Henry Stämpfli, Peter Kim, Amy Sturgeon and Scott Weese.

Their work was supported by Equine Guelph, a division of the University of Guelph.


Costa MC, Arroyo LG, Allen-Vercoe E, Stämpfli HR, Kim PT, et al. (2012) Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene. PLoS ONE 7(7): e41484. doi:10.1371/journal.pone.0041484

The full study can be read at

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