Invited review: Novel methods and perspectives for modulating the rumen microbiome through selective breeding as a means to improve complex traits: Implications for methane emissions in cattle

The rumen microbiome is responsible for methane emission in ruminants. The study of microbes in the rumen has attracted great interest in the last decade. High-throughput sequencing technologies have been key in expanding the knowledge of the microorganisms that populate the rumen through metagenomic studies. There is substantial evidence that the composition of the rumen microbiota is influenced by host genotype. Therefore, modulation of the microbiota poses an important tool for breeding for lower emissions in large and small ruminants. The main challenges of metagenomic studies are addressed and some solutions are proposed when available, including the incorporation of metagenomic information into statistical models regularly used in animal breeding. To incorporate microbiome information into breeding programs, the particularities of the rumen microbiome must be considered, from sampling to inclusion in selection indices. The latest advances in this area are discussed in this review.