Comparative analysis of ruminal and fecal microbiomes in Holstein, Jersey, and Jeju Black cattle using multiple taxonomic classifiers

The gastrointestinal microbiome is pivotal to nutrient utilization and productivity in dairy cattle. This study compared the ruminal and fecal microbiomes of Holstein, Jersey, and Jeju Black cattle using 16S rRNA gene sequencing and three taxonomic classification databases to identify microbial differences across breeds. A total of 25 samples were analysed to evaluate microbial composition, diversity, functional phenotypes, and interactions. Jeju Black cattle exhibited significantly higher ruminal diversity (<i>p</i> < 0.001), whereas Holstein and Jersey cows had more diverse fecal microbiomes. <i>Prevotella</i>, <i>Ruminococcus</i> and <i>Succinivibrio</i> dominated the rumen of commercial breeds, while <i>Methanobrevibacter</i> and <i>Desulfovibrio</i> were enriched in Jeju Black cattle. Amino acid prototrophs were abundant in Holstein and Jersey feces, while sulfur-metabolizing microbial phenotypes predominated in the Jeju Black rumen, with implications for nitrogen metabolism and methane production. Microbial network analysis revealed <i>Mogibacterium</i> as a high-centrality genus in Holstein and Jersey cows, and <i>Anaerovibrio</i> in Jersey cows, potentially linked to propionate production. Jeju Black cattle displayed distinct microbial interactions involving sulphur-reducing and methanogenic bacteria. These results might be showing breed-related microbiome variability, potentially influencing feed efficiency, fermentation, and emissions. However, future work should standardize diets, feeding conditions, sampling methods, and include performance metrics to clarify breed-specificity of microbiome-function relationships.