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

Abstract

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.

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

“…Each MAG was defined as single operational taxonomic unit (OTU). For MAGs with completeness values of more than 50% and a contamination rate less than 10% (Additional file 4), analysis of the genetic potential was performed using the EMGB [60] annotation system including KEGG pathway mapping and DIAMOND tool [54]. MAGs that meet the criteria mentioned above were subsequently analyzed regarding their transcriptional activities using the EMGB annotation system again.…”

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

“…Moreover, an essential step after sequencing of constructed amplicon libraries is the quality control which ensures increased accuracy and prevents overestimation of community diversity. Pre-processing of amplicon datasets involves several steps (Jünemann et al 2017 ) including removal of chimeric sequences. Subsequently, sequences are subjected to operational taxonomic units (OTUs) clustering, where usually a cutoff of 97% sequence similarity is used, taxonomic classification, and statistical analysis.…”

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

“…Research focus. The BiGi service center offers tools, services and training for microbial genome 11 – 14 , metagenome 15 , and postgenome research 16 that is complemented by a large-scale hardware infrastructure. The focus in Gießen is on genomics (assembly, annotation and comparative analysis and short-read-mapping data evaluation) and read-based metagenomics research.…”