A Microbiological Map of the Healthy Equine Gastrointestinal Tract

Abstract

Horses are exquisitely sensitive to non-specific gastrointestinal disturbances as well as systemic and extraintestinal conditions related to gut health, yet minimal data are available regarding the composition of the microbiota present in the equine stomach, small intestine, and cecum and their relation to fecal microbiota. Moreover, there is minimal information regarding the concordance of the luminal and mucosal microbial communities throughout the equine gut. Illumina-based 16S rRNA gene amplicon sequencing of the luminal and mucosal microbiota present in seven regions of the gastrointestinal tract of nine healthy adult horses revealed a distinct compositional divide between the small and large intestines. This disparity in composition was more pronounced within the luminal contents, but was also detected within mucosal populations. Moreover, the uniformity of the gut microbiota was much higher in the cecum and colon relative to that in the stomach, jejunum and ileum, despite a significantly higher number of unique sequences detected in the colon. Collectively, the current data suggest that while colonic samples (a proxy for feces) may provide a reasonable profile of the luminal contents of the healthy equine large intestine, they are not informative with regard to the contents of the stomach or small intestine. In contrast to the distinct difference between the highly variable upper gastrointestinal tract microbiota and relatively uniform large bowel microbiota present within the lumen, these data also demonstrate a regional continuity present in mucosal microbial communities throughout the length of the equine gut.

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals

“…First, we explored the perinatal bacterial colonisation events of the foal gut and the phylogenetic structure of the microbial ecosystems from meconium, amniotic fluid and mare faeces were characterised and compared. In agreement with previous studies [11,12,29], the core community of the mare gut showed the characteristic compositional layout of a fibrolytic and short-chain fatty acid-producing mutualistic microbiome, being enriched in Clostridiales, Lachnospiraceae and Ruminococcaceae. Conversely, the phylogenetic layout of the microbial communities from meconium and amniotic fluid shared a peculiar ecological structure, including OTUs from ubiquitous microorganisms and components from mare microbiomes at subdominant, but still relevant percentages.…”

Differences in the equine faecal microbiota between horses presenting to a tertiary referral hospital for colic compared with an elective surgical procedure

“…However, in the current study, Firmicutes (44%) and Bacteroidetes (38%) together comprised more than 90% of total bacterial abundance. The ratio of Firmicutes to Bacteroidetes ranged from 1:1 to greater than 4:1 in the gut microbiota of healthy horses. Some of these discrepancies in the relative abundance of bacterial populations are associated with the variation in the unclassified sequences reported in literature, for example Shepherd et al .…”

Mapping the bacterial ecology on the phyllosphere of grass hay and the potential hazards of soaking fodder for horse gut health

“…Although highly variable between horses, Ericsson et al [25] reported an abundance of α- Proteobacteria in the upper gastrointestinal tract of 9 healthy horses. No information is available on what the horses were fed pre-euthanasia, but it is conceivable that like the forages in this study, Proteobacteria was present in significant numbers.…”

“…The highly individualistic nature of the gut microbiome noted by both 25. Ericsson et al [25] and Dougal et al, [22,23], and the multiple small OTU core suggests that the gastric profile may lack robustness and be easily influenced by external factors. Understanding how the gastric microbiome responds to the epiphytic challenge from fodder may provide additional insight into gastric pathologies such as ulceration.…”

“…Furthermore, the core community has been reported to be smaller than found in ruminants and humans and to be composed of many OTUs of low abundance. Ericsson et al [25] found much variation between individuals in foregut bacterial profiles but that hind gut profiles were more uniform. Thus, it would seem that individual horses have a phylogenetic community specific to themselves and their diet and that profile could make them more or less susceptible to dysbiosis when dietary changes are made.…”