Host Genome–Metagenome Analyses Using Combinatorial Network Methods Reveal Key Metagenomic and Host Genetic Features for Methane Emission and Feed Efficiency in Cattle

Cattle production is one of the key contributors to global warming due to methane emission, which is a by-product of converting feed stuff into milk and meat for human consumption. Rumen hosts numerous microbial communities that are involved in the digestive process, leading to notable amounts of methane emission.

The key factors underlying differences in methane emission between individual animals are due to, among other factors, both specific enrichments of certain microbial communities and host genetic factors that influence the microbial abundances. The detection of such factors involves various biostatistical and bioinformatics methods.

In this study, our main objective was to reanalyze a publicly available data set using our proprietary Synomics Insights platform that is based on novel combinatorial network and machine learning methods to detect key metagenomic and host genetic features for methane emission and residual feed intake (RFI) in dairy cattle.

The other objective was to compare the results with publicly available standard tools, such as those found in the microbiome bioinformatics platform QIIME2 and classic GWAS analysis. The data set used was publicly available and comprised 1,016 dairy cows with 16S short read sequencing data from two dairy cow breeds: Holstein and Nordic Reds.

Host genomic data consisted of both 50 k and 150 k SNP arrays. Although several traits were analyzed by the original authors, here, we considered only methane emission as key phenotype for associating microbial communities and host genetic factors. The Synomics Insights platform is based on combinatorial methods that can identify taxa that are differentially abundant between animals showing high or low methane emission or RFI.

Focusing exclusively on enriched taxa, for methane emission, the study identified 26 order-level taxa that combinatorial networks reported as significantly enriched either in high or low emitters. Additionally, a Z-test on proportions found 21/26 (81%) of these taxa were differentially enriched between high and low emitters (p value 90% of these core heritable taxonomies.

Finally, we have characterized a small set (