MGkit: Metagenomic Framework For The Study Of Microbial Communities

<p><strong>Introduction</strong></p> <p>While metagenomics has been used extensively to study microbial communities from a taxonomic and functional perspective, little has been done to address how the species in a microbiome are adapted to and maintain specific roles in dynamic environments like the rumen.</p> <p><strong>Rationale</strong></p> <p>To address this issue we have developed a framework for the robust analysis of metagenomic data that includes fully automated analysis from next-generation sequencing (NGS) reads to assembly, gene predicition and taxonomic identification. Furthermore we imple- ment approaches to estimate SNP diversity in metagenomic samples and carry out statistical tests to identify genes where sequence diver- sity exists.</p

Metagenomic analysis of the Rumen microbiome reveals functional isoforms drive niche differentiation for nutrient acquisition and use

<p>Metagenomics has provided insights into the species composi- tion and function of the rumen microbial community and revealed that many species seem to share the same genes for acquiring and utilising nutrients. This questions whether niche specialisation between rumen microbes exists and if so, how it is maintained.</p> <p>One possibility is that niche specialisation is not driven by gene presence or absence, but by the diversity of functional isoforms, where we would expect to see isoform diversity to be related to niche specialisation.</p