Analysis of rumen microbial community in cattle through the integration of metagenomic and network-based approaches

A better understanding of the composition of rumen microbial communities and the association between host genetic and microbial activities has important applications and implication in bioscience. Being capable of revealing the full extent of microbial gene diversity, metagenomics-based approaches hold great promises in this endeavor. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions of this study is to develop a random matrix theory-based approach to automatically determine the correlation threshold used to construct the co-abundance network. It has been shown that the network exhibits a highly modular structure with each of the three main modules well separated. The involvement of KEGG pathways in each module was analysed. A close look at the abundance profiles highlights that Module B is strongly associated with methane emissions while Module C is highly enriched with microbial genes associated with feed conversion efficiency.