Host-microbial co-regulation mediates rumen volatile fatty acid production and utilization in dairy cows

Volatile fatty acids (VFAs) provide more than 70% of the energy source for the ruminants. Understanding the host-microbiota regulation of VFAs production and utilization is highly important for optimizing the feed energy utilization efficiency of ruminants. Here, we conducted whole-genome resequencing, rumen transcriptome sequencing, 16S rRNA gene amplicon sequencing, and VFA concentration determination in 530 Holstein bulls. We treated VFA concentrations as complex traits to perform multi-omics association analyses. The host genetics, rumen microbiota, and rumen expressed genes, on average, explained 23%, 58%, and 61% of the variations in VFAs with the same diet, respectively. We found that the rumen microbial composition and community structure differed significantly between the high and low VFA individuals. We further identified 11 microbes with potential causal relationships with rumen VFAs via the Mendelian randomization method, among which Bacteroidales_RF16_group, Prevotella, Clostridia_UCG-014, and [Eubacterium]_ventriosum_group were positively correlated with acetic acid, propionic acid, and butyric acid. Conversely, rumen epithelial genes involved in fatty acid β-oxidation (e.g., HSD17B4, ACADVL, ACADL, CPT1A, and ANGPTL4) were negatively correlated with the main VFAs and VFA-producing bacteria. These candidate microbes and genes suggest that the host-microbe coregulating mechanism facilitates the efficient production and utilization of rumen VFAs in ruminants. Our study provides a comprehensive perspective on the complex dynamic regulatory patterns of rumen VFAs, highlighting the crucial role of host-microbe interactions in optimizing the feed utilization of ruminants.