Practical application of microbiome measurements as a phenotype for low methane emission breeding

Methane (CH4) emissions from ruminant livestock contribute significantly to the environmental footprint of agriculture. Methane is mainly produced as an end product from feed fermentation in the rumen. The rumen microbiome (that is, the community of microorganisms that inhabits the rumen) is associated with either high or low methane phenotypes.

“Current commercial breeding schemes of dairy cattle do not take the rumen microbiome into account,” says David Flossdorf, researcher and project leader at ABG. “This is partially because traditional rumen sampling is invasive, costly, and time- and labour intensive. However, we know that a cow’s microbiome has an impact on its methane emission. We also know that individual variation in microbiome exist, and that this variation is partially heritable. On that account, it would be a shame not to use this information in breeding schemes.” 

The overall aim of the research project ‘Practical application of microbiome measurements as a phenotype for low methane emission breeding’ is to create a minimalistic microbiome sampling and phenotyping methodology that is suitable for dairy cows. To do so, the scientists will first have to find out which microbial genes are abundant, heritable, and genetically correlated with methane. Consequently, they will need to develop statistical models for breeding value estimation including this new microbiome data. And that’s not the only challenge they have set for themselves. David: “We also want to investigate whether the rumen microbiome can be represented through easier methods like buccal swabs (a way to collect DNA material from the cells from the cows’ oral cavities), as buccal swabs are less invasive and easier to implement than other sampling techniques.”

Microbiome breeding value 

If the scientists succeed in finding a phenotyping method, the next step would be to conduct a large-scale trial to proof the concept of a microbiome breeding value. “To proof that a microbiome breeding value yields a benefit for a breeding program, a large number of animals needs to be tested,” says Aniek Bouwman, researcher at ABG. “The idea is to set up a trial where we phenotype the microbiome of 2500 cows on farms to demonstrate that it can accelerate the breeding of low methane emission cattle – compared to breeding based only on methane emissions – and show its fitness to be used on farms and by breeding companies.”