Investigating mechanisms of divergent feed efficiency in dairy cows

The objective was to investigate associations between residual DMI (RFI; calculated as the difference between observed minus predicted DMI) and the rumen microbiome, digestion, behavior, and metabolism that might explain the differences in RFI in lactating cows. A total of 150 genotyped Holstein cows were used in this cohort study, in which exposure was RFI. Rumen microbiota from 114 cows were sequenced, and a subset of 30 cows was used for hepatic mitochondrial respiration analysis. Cows were ranked by RFI and grouped into quartiles (Q1 = most efficient to Q4 = least efficient) according to phenotypic (pQ) or genomic (gQ) quartiles of RFI for data presentation. Statistical models fitted the linear and quadratic RFI as continuous explanatory variables. Increasing efficiency (i.e., from larger to smaller RFI values) whether phenotypic or genomic, was associated with reduced DMI, a 3.0 kg/d difference between Q4 and Q1 according to phenotypic RFI (pRFI), and a 1.9 kg/d difference according to genomic RFI (gRFI), without compromising ECM or body tissue reserves. These differences between Q4 and Q1 of pRFI and gRFI resulted in increased feed conversion ratio by an additional 200 and 100 g of ECM/kg DMI, respectively. Both pRFI and gRFI were associated with fatty acid (FA) profiles in milk fat, with decreasing proportions of de novo and mixed FA and increasing proportions of preformed FA, particularly MUFA, as efficiency improved. Additionally, pRFI and gRFI were moderately correlated (r = 0.48), and ranking of cows was consistent across the 2 grouping methods (ρ = 0.44). Reducing RFI was associated with less total rumination time but greater rumination time per kilogram of DMI by 2.0 and 1.7 min/kg between the extreme quartiles of pRFI and gRFI, respectively. Phenotypically and genomically more efficient cows were associated with less microbial α-diversity based on the inverse Simpson index. A total of 57 amplicon sequence variant groups were differentially abundant between Q1 and Q4 classified based on pRFI and gRFI, with Prevotella and Succinivibrionaceae shared between phenotypic and genomic RFI classifications. Increasing phenotypic and genomic efficiency was associated with an increased concentration of ruminal NH3-N. Genomically more efficient cows tended to have reduced ruminal pH (gQ1 to gQ4; 6.42 vs. 6.47 vs. 6.43 vs. 6.53) despite eating less. Decreasing pRFI was associated with reduced microbial N yield, whereas it tended to increase microbial N yield relative to the amount of N intake. Collectively, phenotypic and genomic RFI have a moderate degree of agreement matching the estimated heritability of the trait, and mechanisms underlying improved feed efficiency were linked with differences in ruminal microbiota and fermentation, and with increased rumination per kilogram of DM rather than total-tract digestibility or hepatic mitochondrial respiration.