Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets

SIMPLE SUMMARY: Abrupt changes in the dietary management of horses are a risk factor for gastrointestinal disturbances, potentially due to the negative effects observed on the population of gut microbiota. In this study, the faecal microbiota of horses was investigated to determine how quickly the bacterial communities respond and stabilise following sudden diet change. Six Thoroughbred mares were stabled for six weeks, consuming freshly cut pasture (on weeks 1, 3 and 5), before being abruptly fed three conserved forage-based diets (weeks 2, 4 and 6). The conserved forage-based diets were a chopped ensiled forage fed exclusively or with whole oats, and perennial ryegrass hay fed with whole oats. Faecal samples were collected at regular intervals from each horse following each diet change. High throughput 16S rRNA gene sequencing was used to evaluate the faecal microbiota. There were significant differences in the diversity of the microbiota (p < 0.001), with clustering of samples observed by diet group. A stable faecal microbiota profile was observed in the samples from 96 h after consumption of the treatment diets containing ensiled chopped forage. The present study confirmed that the diversity and community structure of the faecal bacteria in horses is diet-specific and resilient following dietary transition and emphasised the need for modern horse feeding management to incorporate large proportions of forage into diets. ABSTRACT: The management of competition horses in New Zealand often involves rotations of short periods of stall confinement and concentrate feeding, with periods of time at pasture. Under these systems, horses may undergo abrupt dietary changes, with the incorporation of grains or concentrate feeds to the diet to meet performance needs, or sudden changes in the type of forage fed in response to a lack of fresh or conserved forage. Abrupt changes in dietary management are a risk factor for gastrointestinal (GI) disturbances, potentially due to the negative effects observed on the population of GI microbiota. In the present study, the faecal microbiota of horses was investigated to determine how quickly the bacterial communities; (1) responded to dietary change, and (2) stabilised following abrupt dietary transition. Six Thoroughbred mares were stabled for six weeks, consuming freshly cut pasture (weeks 1, 3 and 5), before being abruptly transitioned to conserved forage-based diets, both offered ad libitum. Intestinal markers were administered to measure digesta transit time immediately before each diet change. The conserved forage-based diets were fed according to a 3 × 3 Latin square design (weeks 2, 4 and 6), and comprised a chopped ensiled forage fed exclusively (Diet FE) or with whole oats (Diet FE + O), and perennial ryegrass hay fed with whole oats (Diet H + O). Faecal samples were collected at regular intervals from each horse following the diet changes. High throughput 16S rRNA gene sequencing was used to evaluate the faecal microbiota. There were significant differences in alpha diversity across diets (p < 0.001), and a significant effect of diet on the beta diversity (ANOSIM, p = 0.001), with clustering of samples observed by diet group. There were differences in the bacterial phyla across diets (p < 0.003), with the highest relative abundances observed for Firmicutes (62–64%) in the two diets containing chopped ensiled forage, Bacteroidetes (32–38%) in the pasture diets, and Spirochaetes (17%) in the diet containing hay. Major changes in relative abundances of faecal bacteria appeared to correspond with the cumulative percentage of intestinal markers retrieved in the faeces as the increasing amounts of digesta from each new diet transited the animals. A stable faecal microbiota profile was observed in the samples from 96 h after abrupt transition to the treatment diets containing ensiled chopped forage. The present study confirmed that the diversity and community structure of the faecal bacteria in horses is diet-specific and resilient following dietary transition and emphasised the need to have modern horse feeding management that reflects the ecological niche, particularly by incorporating large proportions of forage into equine diets.