Integrated Host Genome Rumen Microbiome Metabolome Prediction of Low-Methane, High-Feed-Efficiency Sheep Under Climate Stress

Sheep are well adapted to marginal grazing systems and provide important products such as wool, milk and meat. However, microbial fermentation in the rumen and reticulum generates enteric methane, which contributes to greenhouse gas emissions from livestock production. Both methane emissions and feed efficiency show heritable variation, while host genetics can also shape rumen microbial composition through complex host–microbe interactions. This review explores how host genomics, rumen microbiome profiles, methanogenic archaeal communities, and rumen and blood metabolomics can be combined to identify biomarkers of low methane emissions and improved feed efficiency, particularly under environmental stress. Evidence suggests that methane production is repeatable and genetically influenced, and that rumen microbiome composition is associated with methane emission and feed efficiency, although current evidence does not show that specific microbial taxa directly cause these traits. Integrating host genotype with microbial and metabolic information may therefore improve statistical prediction of methane emissions and residual feed intake, which is not the same as identifying validated biomarkers or showing biological causation. Nevertheless, reliable microbial biomarkers have yet to be established, and validation across breeds, diets, and production environments remains limited. Heat stress adds further complexity by altering rumen fermentation, oxidative status, and microbial community structure, yet integrated omics research under climatic stress remains scarce. Future studies should prioritize longitudinal, multi-breed designs, standardized methane phenotyping, and coordinated multi-omics analyses to develop robust biomarkers for sustainable, low-emission sheep production.