Multi-omics analysis reveals microbial and metabolic signatures associated with neutral detergent fiber digestibility in dairy cattle

Background The rumen microbiome is central to fiber degradation in dairy cows, yet the precise functional and metabolic networks driving variations in neutral detergent fiber (NDF) digestibility remain poorly understood. Elucidating these microbiome-host interactions is critical for improving forage utilization and advancing sustainable dairy production. Results Employing an integrative metagenomics-metabolomics approach, we characterized the rumen microecology of lactating dairy cows exhibiting high and low NDF digestibility phenotypes ( n = 10/group). Metagenomic profiling revealed a significant enrichment of fibrolytic taxa ( Prevotella sp., Lachnospiraceae bacterium) and carbohydrate-active enzymes in the high-NDF group (HI). In addition, species-level differential abundance testing showed that Methanobrevibacter spp. was more abundant in the low-NDF group (LO) than in the HI group, whereas no archaeal differences were detected at the phylum or genus levels. Functional and metabolomic analyses indicated broader enrichment of amino acid degradation functions and higher concentrations of major volatile fatty acids (VFAs) in HI cows, consistent with stronger overall ruminal fermentation activity. Furthermore, VFAs and microbial composition explained 54.3% and 43.0% of the variation in NDF digestibility, respectively. An exploratory machine learning model based on selected annotated metabolite features showed moderate discriminatory performance, with an out-of-bag accuracy of 77.19%. Conclusions Our findings suggest that coordinated shifts in rumen microbial composition, amino acid metabolism, and VFA production are associated with variation in NDF digestibility in dairy cattle. These results provide a basis for future studies aimed at improving fiber utilization through microbiome-informed nutritional or breeding strategies.