The MicroScope platform: 20 years of contributing to bacterial genome analyses

MicroScope will unite its users at Genopole on 26 September to celebrate 20 years of activity. Six guest speakers will share their experiences with the platform and the LABGeM team will present the latest in pangenomics methodologies.

MicroScope is a bioinformatics platform unique in France and in Europe. It provides biologists with powerful tools and resources to empower microbial genome research, notably as concerns understanding the metabolism of bacteria and exploring its potential. With its roots to be found in research done by the LABGeM team (Genoscope), MicroScope is one of Genopole’s 24 shared-use technological platforms.

As a laureate of the Atige* program, Claudine Médigue was able to create the Laboratory of Bioinformatics Analyses for Genomics and Metabolism (LABGeM) within the national sequencing center Genoscope in 2001.
In 2002, building upon the sequencing activities at Genoscope and its numerous partnerships with microbiologists seeking to analyze the genomes of their model bacteria, the LABGeM team developed a collaborative platform for the annotation of microbial genomes, originally named MaGe, for “Magnifying Genomes.” The platform would provide its first annotations in 2003, and later change its name to MicroScope in 2007.

MicroScope is a web-based platform for the annotation and exploration of prokaryote genomes. It supplies microbiologists with the tools they need to perform comparative genomics or pangenomics (the study of multi-genome assemblies for a species) analyses and to explore the metabolisms of organisms of interest. The platform itself manages the integration of newly assembled genomes and metagenomes (resulting from DNA sequencing of environmental samples such as sea water or soil). It also furnishes high throughput analysis services for transcriptomics-based gene expression studies and for variants research. MicroScope’s user interface allows collaborative work, benefiting from a wide array of comparative genomics tools, to improve data curation by the scientific community, which in turn eases the exploration of the results stored in the database.

The platform authored its first manuscript in 2006 (Vallenet et al. 2006), and has been regularly enriched since then with new data and functionalities. That evolution has been the subject of five additional publications (more than 1600 citations since 2006) and presented in more than 30 conferences in France and across the globe. The laboratory’s members have moreover contributed to more than 150 published studies, not only in epidemiology and health, focusing on such aspects as human pathogenic bacteria or microbiotas, but also in environmental genomics and biotechnologies. These aspects contribute to the discovery of novel bacterial enzymatic functions that may lead notably to the development of processes for environmental remediation or the biological production of compounds of interest.

Today, the MicroScope platform is headed by David Vallenet and Alexandra Calteau within LABGeM at Genoscope (UMR8030 Génomique Métabolique, CEA/CNRS/Université d’Evry Paris-Saclay).
“MicroScope serves a large, international community of academic microbiologists: more than 6,700 accounts have been created abroad,” underlines Alexandra Calteau. “The platform has contributed to the analysis of more than 25,000 microbial genomess“.

Several private companies call upon MicroScope for the provision of services or collaborative research projects.

MicroScope is one of Genopole’s 24 accredited technological platforms.
It is a member of the French Institute of Bioinformatics and a part of the France Genomics infrastructure. The platform’s activity, mutualized for the biocluster’s actors and the scientific community, is supported by Genopole via regular investments in informatics materials, e.g., €100,000 over the last four years.