Do the Microbiomes of Horses Process Nutrients Differently Based on Keeper Status?

Abstract This study reports the differential response of the equine gut microbiome to protein and/or carbohydrate based on keeper status (easy keeper (EK), medium keeper (MK), hard keeper (HK)). Anaerobic equine fecal samples (n = 12 total, n = 3 / EK, MK, HK of four breeds) inoculated microcosms with three dietary conditions (C = Carb (cornmeal), P = Protein (soybean meal), and M = mix (50% C, 50% P)). Over 48 hours, fermentation products were measured using colorimetric assays and high-performance liquid chromatography. Microbial populations were surveyed using 16S rRNA gene sequencing analyzed by QIIME2. Linear mixed models were fit with fixed effects of Treatment and Keeper status and their interactions, with random effects of HorseID. Differences in fermentation products by keeper status included: MK had higher pH and greater gas production, EK produced higher hydrogen sulfide, and HK had greater total protein. Total SCFA was not different between keeper status (P = 0.89) but the acetate: propionate ratio was highest for HK (2.45mM) and lowest for EK (1.85mM) (P = 0.05). Isobutyrate production was highest in HK (2.34mM) compared to MK (0.85mM) and EK (0.17mM). Treatment had significant effects across all measurements; M and C treatment values were similar reflecting microbial preferences for carbohydrates before protein. P treated trials had increased fermentation outputs due to lower acidity effects. Keeper status had no effect on α-diversity (P > 0.05) however HK horses were least affected by treatments. P treated samples were more diverse than C and M (P < 0.001). Spearman correlation of Keeper x Treatment identified Oligosphaeria spp. in EK (r = 0.49) and Fusobacteria spp. in HK whole fecal samples (r = 0.37). These data suggest that while the compositions of the gut microbiomes of keeper groups were similar, they were functionally different in processing key nutrients.