Since 1980, Sciensano houses the BCCM/IHEM culture collection, a member of the BCCM consortium. The latter collects, preserves and distributes thousands of living microorganisms. It is a key activity to support science, research and applications in microbiology. Recent technological advances have greatly facilitated the sequencing of the entire genome of microbial strains. This is a source of new information which opens exiting areas of applied and fundamental research. However, handling genomic (big) data also requires specific skills. To answer this challenge, the BCCM GEN-ERA project aimed at implementing expertise in genomics within the BCCM collections.
The Belgian Coordinated Collections of Microorganisms (BCCM) is a biological resource centre (BRC) that preserves and provides microbial and genetic resources to support life sciences and the biotechnology sector in the field of fundamental and applied research.
The study, valorisation and documentation of the BCCM microbial patrimony need to stay up to date with the current developments in modern technologies. Nowadays, microbial research is greatly facilitated by new approaches in genomics including whole genome sequencing. The latter provides the entire genetic information of an organism and is increasingly requested in many disciplines. Acquiring know-how in genomics is thus crucial for BCCM to remain a major BRC, for future national and international collaborations and to answer upcoming research questions.
The first objective of the BCCM GEN-ERA project was to implement expertise in genomics in the BCCM collections for which the real challenge was the handling and analysis of genomic big data. This required the installation of specific bioinformatics structures (hardware) and software for which the BCCM scientists had to be trained to ensure a long-term implementation. The focus was primarily on whole genome sequencing because the determination of the entire gene repertoire of microorganisms supports the leading expertise of the collections in the field of taxonomy and phylogeny while allowing potential functional analyses. Moreover, offering strains having their whole genome sequenced is necessary to meet the needs of BRCs users and is thus an added value for the visibility and attractiveness of BCCM.
The BCCM GEN-ERA project also aimed at answering specific research questions covering the microbial diversity of the BCCM collections (i.e., bacteria, mycobacteria, cyanobacteria, yeasts and moulds) and more specifically on selected microorganisms having a societal impact (i.e., associated with pollinating insects, causing pathologies or producing bioactive compounds).
The objectives were achieved by developing a Nextflow infrastructure covering the common genomics needs for microbial taxonomy and metabolic modelling of microbial collections like BCCM, in a FAIR manner. It can be used on prokaryotes and small eukaryotes in a completely reproducible manner. This “GEN-ERA toolbox” was made freely available from the GitHub repository which also includes a large documentation for the users.