Research Article: Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

Date Published: October 12, 2018

Publisher: Public Library of Science

Author(s): Gareth Frank Difford, Damian Rafal Plichta, Peter Løvendahl, Jan Lassen, Samantha Joan Noel, Ole Højberg, André-Denis G. Wright, Zhigang Zhu, Lise Kristensen, Henrik Bjørn Nielsen, Bernt Guldbrandtsen, Goutam Sahana, Tosso Leeb

Abstract: Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host’s rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host’s genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.

Partial Text: Methane (CH4) is a potent greenhouse gas (GHG) with a climate change potential ~32 times greater than carbon dioxide (CO2)[1] and an atmospheric half-life of 12 years, which is substantially shorter than CO2 (> 100 years)[2]. Therefore, reducing CH4 emissions from anthropogenic-related sources has been identified as a key area for mitigating climate change with immediate effects[2,3]. Livestock accounts for 14.5% of anthropogenic-related GHG emissions and enteric CH4 emissions from ruminants accounts for 5.8%[3]. Furthermore, CH4 emissions from livestock is predicted to markedly increase due to an expected doubling in the global milk and meat demand by 2050[4].

Methane production by dairy cows is not only influenced by factors such as feed intake and composition among others, but also the cow’s individual genetic composition and rumen microbial composition. Each cow’s additive genetic effects influence a modest amount of variation in the abundance of a small percentage of rumen bacterial and archaeal taxa, and thereby contribute to variation in rumen microbiome composition and function. We detected associations between CH4 emissions and rumen bacteria abundance, which are known to produce methanogenesis substrates, suggesting bacteria driven CH4 production pathways. Although we detected a heritable component to ruminotypes, the association to CH4 production was weak. Concurrently, host additive genetic effects and rumen microbes contributed to inter-animal differences in CH4 production, however negligible interaction was observed between microbiability and heritability. Consequently, cow additive genetic effects on CH4 emissions were largely unmodulated by cow additive genetic effects on rumen bacteria and archaea abundance. Strategies to reduce CH4 emissions in ruminants can be optimized by a multifaceted approach, for instance, selective breeding to unlock host’s genetic potential and strategies which may effect desired changes in the rumen microbiota like rumen transplantation, and probiotics.