Discovery linking microbes to methane emissions could make agriculture more sustainable

Common dairy cows share the same core group of genetically inherited gut microbes, which influence factors such as how much methane the animals release during digestion and how efficiently they produce milk, according to a new study. By identifying these microbes, the research may help enable scientists to manipulate the rumen (a cow’s first stomach, where microbes break down ingested food), facilitating a transition towards more eco-friendly and productive agriculture. Scientists have long wondered about the connection between a cow’s genetics, its productivity, and the composition of its microbiome. To begin to uncover answers, Robert John Wallace and his team used common nucleotide variations between genes to study the genotypes of an unprecedented 1000 Holstein and Nordic Red dairy cows from the UK, Italy, Sweden, and Finland–the most popular and productive milking cow breeds in developed countries. They identified a core microbiome: a selection of closely related microbes present in at least 50% of all the cattle. The researchers then used two machine learning algorithms to determine that they could accurately predict rumen metabolism, diet, and traits including milk output and methane emissions based on this core microbiome’s composition. A Canonical Correlation Analysis (CCA) showed that the core microbiome was correlated with genetics, suggesting that inherited genes give rise to microbes responsible for methane emissions and other cattle traits. The finding that these influential microbes are linked to heritable genes could enable programs in which breeders select for cattle with microbiomes that produce the least methane.

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