Cattle microbiome plays a vital role in cattle growth and performance and affects many economically important traits such as feed efficiency, milk/meat yield and quality, methane emission, immunity and health. To date, most cattle microbiome research has focused on metataxonomic and metagenomic characterization to reveal who are there and what they may do, preventing the determination of the active functional dynamics in vivo and their causal relationships with the traits. Therefore, there is an urgent need to combine other advanced omics approaches to improve microbiome analysis to determine their mode of actions and host–microbiome interactions in vivo. This review will critically discuss the current multi-omics microbiome research in beef and dairy cattle, aiming to provide insights on how the information generated can be applied to future strategies to improve production efficiency, health and welfare, and environment-friendliness in cattle production through microbiome manipulations.

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