Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand

SIMPLE SUMMARY: Ten horses were kept on pasture for one year, with hay provided from June to October. Each month we measured how much pasture was present and collected pasture and hay samples to assess their nutrient content, and faecal samples from all horses to investigate the diversity of the bacterial species present using next-generation sequencing technology. The population of faecal bacteria was more diverse during the months when the horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. The diet offered, and the season and the month we sampled the paddock all had a major influence on the diversity of the species of bacteria in the faeces. While there were some differences between the horses, generally the bacterial populations could be grouped together in samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought). More specifically we were able to show an association between specific bacterial species, nutrients (dry matter, protein, and structural carbohydrates), and climatic conditions (rainfall and temperature). Our study showed that the diversity and composition of the bacterial population of horses kept on pasture changes over a 12-month period, and this reflects changes in the nutrient composition of the pasture, which in turn is influenced by climate. The findings of this study may have implications for managing horses on pasture and the use of forages for horses susceptible to digestive problems. ABSTRACT: Seasonal variation in the faecal microbiota of forage-fed horses was investigated over a 12-month period to determine whether the bacterial diversity fluctuated over time. Horses (n = 10) were maintained on pasture for one year, with hay supplemented from June to October. At monthly intervals, data were recorded on pasture availability and climate (collected continuously and averaged on monthly basis), pasture and hay samples were collected for nutrient analysis, and faecal samples were collected from all horses to investigate the diversity of faecal microbiota using next-generation sequencing on the Illumina MiSeq platform. The alpha diversity of bacterial genera was high in all samples (n = 118), with significantly higher Simpson’s (p < 0.001) and Shannon-Wiener (p < 0.001) diversity indices observed during the months when horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. There were significant effects of diet, season, and month (ANOSIM, p < 0.01 for each comparison) on the beta diversity of bacterial genera identified in the faeces. While there was some inter-horse variation, hierarchical clustering of beta diversity indices showed separate clades originating for samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought), with a strong association between bacterial taxa and specific nutrients (dry matter, protein, and structural carbohydrates) and climate variables (rainfall and temperature). Our study supports the hypothesis that the diversity and community structure of the faecal microbiota of horses kept on pasture varied over a 12-month period, and this variation reflects changes in the nutrient composition of the pasture, which in turn is influenced by climatic conditions. The findings of this study may have implications for grazing management and the preparation of conserved forages for those horses susceptible to perturbations of the hindgut microbiota.