Analysing Microbial Communities

Anaerobic digestion, the decomposition of organic matter to biogas and digestate in the absence of oxygen, is carried out by diverse communities of microorganisms. Until recently, 16S rRNA gene amplification has been the main focus towards better understanding of these communities, ultimately for their exploitation in industry and waste management. Metagenomics and shotgun whole genome sequencing now offers a different approach, allowing for the functional analysis of individual members of the community without the need for cell culturing. But metagenomics is not without its own pitfalls. Currently there are limited tools and methods available for use with large and complex datasets from sequencing of anaerobic digestion communities. Here we present the development of a rapid fully automated software pipeline for the large-scale identification and functional analysis of quality genomes extracted from anaerobic digestion metagenomic datasets. The pipeline consists of two new tools for the analysis of metagenomic data; the MCCR tool for reducing contamination in proposed genomes formed from metagenomic data, and the MPP tool for simultaneously predicting metabolic pathways across the large numbers of organisms found in metagenomes. The tools and pipeline were tested on both synthetic and real datasets during their development, and while further development will be needed in the future, this pipeline shows high potential to be both viable and extremely useful in understanding complex metagenomic datasets.