Inter‐breed diversity and temporal dynamics of the faecal microbiota in healthy horses

Abstract

Understanding gut microbiota similarities and differences across breeds in horses has the potential to advance approaches aimed at personalized microbial modifications, particularly those involved in improving sport athletic performance. Here, we explore whether faecal microbiota composition based on faecal 16S ribosomal RNA gene sequencing varies across six different sport breeds at two time points 8 months apart within a cohort of 189 healthy horses cared for under similar conditions. Lusitano horses presented the smallest and Hanoverians the greatest bacterial diversity. We found subtle but significant differences in β‐diversity between Lusitano, Anglo Arabian and the central European breeds, and we reproduced these results across the two time points. Repeat sampling of subjects showed community to be temporally more stable in Lusitano and Anglo Arabian breeds. Additionally, we found that 27 genera significantly varied in abundance across breeds. Overall, 33% of these taxa overlapped with previously identified taxa that were associated with genetic variation in humans or other species. However, a non‐significant correlation was observed between microbial composition and the host pedigree‐based kinship. Despite a notable variation in the diversity and composition of the faecal microbiota, breed exerted limited effects on the equine faecal microbiota.

Priming for welfare: gut microbiota is associated with equitation conditions and behavior in horse athletes

“…In spite of this drift, 29 genera (mostly known commensals) remained sufficiently stable, which allowed us to identify a core microbiota. The observed core microbiota was nearly identical to the one described by Massacci et al 30 . Since a total of 180 individuals (out of the 185 used here) were shared by both studies, similarities in the core microbiota between both studies were expected.…”

“…Cohort characteristics. From the same cohort reported by Massacci et al 30 , we selected 185 healthy sport horses cared for under similar conditions (Fig. 1a).…”

“…Our previous work on the association between breeds and fecal microbiota in the same cohort of individuals demonstrated that breed exerted limited effects on fecal microbiota composition 30 . Until this current study, our prior work had been limited to describe the effect of one single variable (breed) on gut microbiota composition (Massacci et al 30 ), therefore neglecting the global interactions that occur across multiple environmental and host variables across time. Here, instead, we decided to explore the temporal dynamics of the fecal microbiota by simultaneously combining environmental variables together with host factors.…”

“…Strong evidence exists that diet is the major environmental factor contributing to gut microbial variation in horses 11,13,[19][20][21][22][23][24] . Furthermore, the abundance of different species has been reported to vary dramatically based on host-specific factors like co-colonization with enteric parasites 14,25 , pathobionts 7,[26][27][28][29] and host genetics 30 . Yet, in addition to biotic stressors, equine gut microbiota dynamics have been associated to abiotic stressors such as exercise 13,31,32 .…”

“…We have previously reported that breed exerted limited effect on fecal microbiota composition in a large cohort of healthy sport horses, from the same riding school, which we monitored for over an eight-month period 30 . However, the influence of multiple environmental and host-related variables (other than breed) were not assessed in this large-scale cohort study.…”