Meta-analysis with batch-effect adjustment reveals breed-specific ruminal microbiome variation of beef cattle and its implications for meat quality and productivity

Various beef cattle breeds are raised in different countries. Hanwoo and Wagyu breeds are primarily raised in South Korea and Japan, respectively, whereas Angus breed is one of the most widely bred beef cattle breed worldwide. Although microbiome studies have been conducted for each breed, comparative analyses of the ruminal microbiome and their functions across breeds remain limited. Moreover, the potential links between the ruminal microbiome and animal traits related to meat quality and productivity have not been studied. Based on 13 studies comprising 954 samples (Hanwoo: 384, Angus: 246, Wagyu: 324) with application of optimal batch-effect adjustment tool, this meta-analysis aimed to compare the ruminal microbiome across Hanwoo, Angus, and Wagyu and explore potential associations between breed-specific microbiome profiles and key phenotypic traits, such as meat quality and production performance. The overall microbial composition at the phylum, genus, and Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog levels was effectively adjusted batch effect using the select adjustment tool (ConQuR). Subsequent analyses were conducted using batch-effect adjusted microbiome data to investigate the breed-specific differences. Cellulolytic bacteria such as <italic>Bacteroides</italic>, <italic>Fibrobacter</italic>, <italic>Lacrimispora</italic>, and <italic>Ruminococcus</italic> were dominant in Angus, whereas saccharolytic bacteria such as <italic>Selenomonas</italic>, <italic>Olsenella</italic>, <italic>Sporomusa</italic>, <italic>Streptococcus</italic>, and <italic>Bifidobacterium</italic> were relatively abundant in Wagyu. Predicted KEGG modules revealed that ubiquinone and biotin biosynthesis pathways were enriched in Angus, whereas amino acid biosynthesis was enriched in Wagyu. Hanwoo exhibited intermediate traits at both the phylum and genus taxonomic levels. In the comparative network analysis, <italic>Prevotella</italic> and <italic>Dialister</italic> were the keystone genera in Angus, <italic>Mogibacterium</italic> in Wagyu, and <italic>Streptococcus</italic> in Hanwoo. In archaeal microbiome comparisons, methane metabolism-related KEGG modules were enriched in Angus. KEGG modules and taxa previously known as high average daily gain-related were relatively enriched in Angus, whereas Wagyu was characterized by those related to high intramuscular fat. Hanwoo exhibited intermediate traits in both productivity and meat quality, and the microbiome features were between those of Angus and Wagyu. These findings suggest a potential link between the ruminal microbiome and meat quality- and productivity-related traits in beef cattle.