The microbiome plays a central role in dairy cattle nutrient utilization, health, and environmental impact. Recent advances in sequencing technologies and quantitative genetics have shown that microbial communities, particularly in the rumen, are not only shaped by management and diet but are also partially under host genetic control, opening new opportunities for microbiome-based breeding strategies. This chapter reviews current knowledge on the microbiome of dairy cattle across anatomical sites, with emphasis on the rumen ecosystem and its links to production, feed efficiency, and methane emissions. Practical considerations for microbiome phenotyping are discussed, including sampling strategies, sequencing approaches, and statistical treatment of compositional data. The chapter then evaluates methods for integrating microbiome information into genetic evaluations, ranging from proxy-based prediction to mixed models, GO-BLUP, and emerging neural network approaches. Finally, key challenges, limitations, and future perspectives for implementing microbiome-driven strategies in dairy cattle breeding programs are outlined.