Meta-analysis with batch-effect adjustment reveals breed-specific ruminal microbiome variation of beef cattle and its implications for meat quality and productivity.
- 1Department of Animal Science and Technology, Chung-Ang University, Anseong, Korea.
- 2Cargill Animal Nutrition, Seongnam, Korea.
Abstract
Various beef cattle breeds are raised in different countries. Hanwoo and Wagyu breeds are primarily raised in 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 the application of an 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 selected adjustment tool (ConQuR). Subsequent analyses were conducted using batch-effect adjusted microbiome data to investigate the breed-specific differences. Cellulolytic bacteria such as Bacteroides, Fibrobacter, Lacrimispora, and Ruminococcus were dominant in Angus, whereas saccharolytic bacteria such as Selenomonas, Olsenella, Sporomusa, Streptococcus, and Bifidobacterium 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, Prevotella and Dialister were the keystone genera in Angus, Mogibacterium in Wagyu, and Streptococcus 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.
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BibTeX
@article{kang2026metaanalysis,
title = {{Meta-analysis with batch-effect adjustment reveals breed-specific ruminal microbiome variation of beef cattle and its implications for meat quality and productivity.}},
author = {Ryukseok Kang and Chaemin Yu and Yeonsue Gwon and Sangmin Lee and Joohyuk Yang and Jongsik Jeong and Geonwoo Kim and Woohyung Lee and Wanho Jo and Myeong-Gwan Oh and Changbeen Jang and Mekonnen Tilahun and Joonpyo Oh and Tansol Park},
journal = {Journal of animal science and technology},
year = {2026},
month = sep,
doi = {10.5187/jast.2500254},
url = {https://europepmc.org/article/MED/42898857},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Meta-analysis with batch-effect adjustment reveals breed-specific ruminal microbiome variation of beef cattle and its implications for meat quality and productivity.
AU - Ryukseok Kang
AU - Chaemin Yu
AU - Yeonsue Gwon
AU - Sangmin Lee
AU - Joohyuk Yang
AU - Jongsik Jeong
AU - Geonwoo Kim
AU - Woohyung Lee
AU - Wanho Jo
AU - Myeong-Gwan Oh
AU - Changbeen Jang
AU - Mekonnen Tilahun
AU - Joonpyo Oh
AU - Tansol Park
PY - 2026
DA - 2026/09/30
JO - Journal of animal science and technology
DO - 10.5187/jast.2500254
UR - https://europepmc.org/article/MED/42898857
AB - Various beef cattle breeds are raised in different countries. Hanwoo and Wagyu breeds are primarily raised in 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 the application of an 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 selected adjustment tool (ConQuR). Subsequent analyses were conducted using batch-effect adjusted microbiome data to investigate the breed-specific differences. Cellulolytic bacteria such as Bacteroides, Fibrobacter, Lacrimispora, and Ruminococcus were dominant in Angus, whereas saccharolytic bacteria such as Selenomonas, Olsenella, Sporomusa, Streptococcus, and Bifidobacterium 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, Prevotella and Dialister were the keystone genera in Angus, Mogibacterium in Wagyu, and Streptococcus 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.
SN - 2055-0391
ER -