Low-abundance taxa are associated with a refined rumen microbiome–resistome interplay in high-yielding dairy cows: an absolute abundance-based metagenomic perspective

Background The rumen microbiota undergoes dynamic shifts in response to fluctuations in physiological stages and host-related factors, and has been associated with productive traits including milk yield, feed efficiency, and methane emissions. However, the ecological mechanisms underlying the relationship between microbial relative abundance, absolute abundance, and shifts in microbiota structure, and their connection to host production performance, remain incompletely understood. This study aimed to characterize the rumen microecological features across cows with divergent lactation performance, with particular emphasis on linking microbial absolute abundance, mobile genetic elements, and antibiotic resistance genes to productivity in high-yielding cows. In this study, rumen fluid was collected from 8 high-yielding cows and 8 low-yielding cows selected from 90 mid-lactation Holstein cows. Shotgun metagenomics with spike-in-based absolute quantification and untargeted metabolomics were employed to investigate the characteristics and potential associations and transmission patterns of rumen microbial communities and ARGs in cows with different milk yields. Results We observed that high-yielding cows exhibited stronger carbohydrate metabolism capacity, higher Chao1 and ACE indices, and lower total microbial absolute abundance. Moreover, high-yielding cows displayed reduced absolute abundances of bacteria and viruses, increased relative abundances of archaea and eukaryotes, and a more intricate microbial network architecture. These shifts were accompanied by a reduction in ARGs prevalence, particularly within peptide, elfamycin, and fluoroquinolone antibiotic categories, and were accompanied by a streamlined ARGs interaction network. Furthermore, the attenuation of ARGs was associated with reduced levels of MGEs, especially those linked to replication, phage activity, genetic transfer, and defense functions. These findings suggest potential associations among microbial structure, MGEs, and ARGs in the rumen ecosystem. Conclusion These findings indicate that complex microbial networks involving low-abundance taxa, together with a streamlined ARGs ecosystem, are associated with high milk yield in dairy cows. This perspective offers valuable implications for mitigating antibiotic resistance risks in intensive livestock systems and advancing efficient, healthy dairy production.