Host and rumen microbiome contributions to feed efficiency traits in Holstein cows

It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h²) and microbiability (m²), respectively. However, if the genome and microbiome are included in the model, then the h² reflects only the contribution of the direct genetic effects quantified as direct heritability (h_d²), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho²). The objectives of this study were to estimate h², h_d²,m², and ho² for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The h_d² estimates were always 10% to 15% lower than h² estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m² estimates were moderate for all traits, and up to 26% for milk energy. The ho² was greater than the sum of h_d² and m², suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.