The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Luc Cornet; Benoit Durieu; Frederik Baert; Elizabet D'hooge; David Colignon; Loic Meunier; Valérian Lupo; Ilse Cleenwerck; Heide-Marie Daniel; Leen Rigouts; Damien Sirjacobs; Stéphane Declerck; Peter Vandamme; Annick Wilmotte; Denis Baurain; Pierre Becker

doi:10.1093/gigascience/giad022

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Gigascience. 2022 Dec 28:12:giad022. doi: 10.1093/gigascience/giad022.

Authors

Luc Cornet¹, Benoit Durieu², Frederik Baert¹, Elizabet D'hooge¹, David Colignon³, Loic Meunier⁴, Valérian Lupo⁴, Ilse Cleenwerck⁵, Heide-Marie Daniel⁶, Leen Rigouts⁷, Damien Sirjacobs⁴, Stéphane Declerck⁶, Peter Vandamme⁵, Annick Wilmotte², Denis Baurain⁴, Pierre Becker¹

Affiliations

¹ BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050, Brussels, Belgium.
² InBioS, Physiology and Bacterial Genetics, University of Liège, 4000, Liège, Belgium.
³ Applied and Computational Electromagnetics (ACE), University of Liège, 4000, Liège, Belgium.
⁴ InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, 4000, Liège, Belgium.
⁵ BCCM/LMG and Laboratory of Microbiology, Faculty of Sciences, Ghent University, 9000, Ghent, Belgium.
⁶ BCCM/MUCL and Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, ELIM 1348, Louvain-la-Neuve, Belgium.
⁷ BCCM/ITM, Mycobacteriology Unit, Institute of Tropical Medicine, 2000, Antwerp, Belgium.

Abstract

Background: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts).

Findings: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling.

Technical details: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility.

Testing: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria.

Conclusion: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.

Keywords: Gloeobacterales; Cyanobacteria; Singularity containers; culture collections; genomics; metagenomics; nextflow; phylogenomics; phylogeny; workflow.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology* / methods
Genome, Microbial
Genomics* / methods
Phylogeny
Reproducibility of Results
Workflow