The crosstalk between host and rumen microbiome in cattle: insights from multi-omics approaches and genome-wide association studies.

The rumen microbiome plays a pivotal role in cattle health, productivity, and environmental sustainability by driving key processes such as nutrient metabolism, feed efficiency, and methane emissions. The intricate interactions among host genome, microbiome composition, and dietary factors shape a dynamic ecosystem that underpins animal performance and sustainability outcomes. Leveraging recent advancements in sequencing technologies and multi-omics approaches, this review synthesizes emerging insights into the genetic and functional profile of the rumen microbiome. Meanwhile, association studies with microbiome and genome-wide markers have identified key microbial and genetic markers linked to methane emissions, paving the way for microbiome-driven breeding programs aimed at reducing environmental impacts. This review also addresses challenges in integrating microbiome datasets, bioinformatics workflows, and reference databases, offering strategies to overcome these obstacles through multi-omics and advanced computational tools. By highlighting actionable pathways for microbiome-informed breeding and management strategies, this work provides a novel framework for improving livestock productivity and mitigating environmental footprints.