Bioinformatics for NGS-based metagenomics and the application to biogas research

- Introduction into 16S rRNA gene amplicon analysis as well as read- and assembly-based whole genome shotgun metagenomics.
- Presentation of suitable bioinformatic workflows and tools illustrated by applications on the analysis of biogas fermenters.
- EMGB and MGX, two comprehensive bioinformatic platforms for metagenomics provided by de.NBI (BiGi).

Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.