Relationships between rumen volume, body composition and rumen microbial profiles in New Zealand deer.

Context: Methane emissions from ruminant livestock are a significant global greenhouse gas source, with 80% of New Zealand's methane emissions from livestock production. There is increasing pressure to reduce this to meet reduction targets set by the Paris agreement. There are approximately 1 million farmed deer in New Zealand. While breeding for lower methane has proven successful in sheep, direct methane measurements in deer are prohibitively difficult and expensive. Proxies from sheep may enable selection of lower-emitting animals. High and low methane sheep differ in rumen size and microbial profiles. Aims: This study investigated individual variation in deer rumen size and whether size differences were associated with specific microbial profiles. Associations between production phenotypes (eye muscle area, carcass fat and lean proportions estimated by computed tomography (CT) and microbial profiles were also examined. Methods: Ten-month-old animals (n = 126) were CT-scanned to calculate rumen size, eye muscle area, and carcass fat/lean proportions. Rumen samples were processed into operational taxonomic units with 97% homology. Relationships between phenotypes and microbial profiles were estimated using linear mixed models in ASReml 3.0 and R software. Key results: No association was found between deer rumen size and ruminotype profiles linked to low methane in sheep. However, three individual taxonomic groups showed associations with deer rumen size and eye muscle area: Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium , Fibrobacter , and Anoplodinium and Diplodinium. Conclusions: While rumen size in deer does not currently show a clear link to low-methane ruminotypes identified in sheep, microbial composition exhibits notable associations with rumen size and production traits. Importantly, differences in taxonomic groups revealed that Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium – previously thought to be competing species where one clade replaced the other – may not be in direct competition. The relationship between rumen size and methane-related microbial profiles warrants further study. Implications: Understanding microbial associations in deer could inform breeding strategies aimed at reducing methane emissions. Identifying key taxa linked to rumen size and production traits may provide practical proxies for selecting low-emission animals without direct methane measurement. By uncovering specific microbial groups linked to rumen size and carcass traits in deer, this research provides new clues toward identifying practical proxies for methane emissions. The work advances the potential for breeding lower-emitting deer using microbiome-based selection tools. This article belongs to the collection: 11th International Deer Biology Congress. [ABSTRACT FROM AUTHOR]