Genome-resolved metagenomics reveals the taxonomic and functional landscape of the rumen microbiome in Japanese Black × Holstein cattle and its associations with carcass traits

The rumen microbiome plays a central role in degrading dietary fiber and producing volatile fatty acids, thereby contributing to carcass traits in cattle. Although breed-associated differences in rumen microbial composition have been reported, the microbial characteristics of Japanese Black × Holstein crossbred (F1) cattle, an economically important beef breed in Japan, remain poorly understood. Here, the rumen microbiome of F1 cattle ( n = 51) was characterized at both the taxonomic and functional levels using metagenomics and compared it with a previously published Japanese Black (JB) cattle metagenomic dataset to identify microbial features associated with cattle breed and carcass traits. Rumen microbial community structure and functional profiles based on KEGG orthologs and CAZyme families differed significantly between JB and F1 cattle. Comparison of metagenome-assembled genomes (MAGs) abundances between JB and F1 cattle identified a total of 116 MAGs showing significant differences in abundance between the two breeds. F1 cattle were enriched in MAGs affiliated with Ruminococcoides and Prevotella , along with glycoside hydrolase families related to starch metabolism, suggesting a fermentation profile oriented toward readily fermentable carbohydrates. In contrast, JB cattle exhibited enrichment of Ruminococcus - and Verrucomicrobiota-affiliated MAGs harboring glycoside hydrolase families associated with lignocellulose degradation. Functional pathway analysis identified 38 KEGG pathways that differed significantly between JB and F1 cattle, with several amino acid metabolism pathways enriched in F1 cattle. Several MAGs, which harbor diverse glycoside hydrolase families, were significantly correlated with carcass weight and ribeye area in F1 cattle and were positively associated with ruminal acetate proportion, indicating that an acetate-oriented fermentation pattern may contribute to enhanced carcass deposition. These findings reveal distinct taxonomic and functional characteristics of the rumen microbiome in JB and F1 cattle and provide insights into how variation in microbial carbohydrate-processing capacity may be associated with carcass traits such as carcass weight and ribeye area. Together, these results highlight the potential importance of rumen microbial metabolic functions in shaping productivity-related traits in beef cattle.