Adresse postale
2, rue Gaston Crémieux, CP 5706 91057 Evry
Structure(s) :
Unité :
LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay
Responsable(s) scientifique
Responsable(s) opérationnel
  • France-Génomique
  • ISO 9001
  • Label IBiSA
  • NF X50-900
Visites annuelles :
55 000 an
Visites uniques :
11 000 an
Citations :
Téléchargements :
Non renseigné



Located at Genoscope (CEA sequencing center for environmental genomics), the LABGeM bioinformatics team has developed MicroScope, a web-based platform for prokaryotic genome analysis and expert functional annotation.

MicroScope combines tools and graphical interfaces to analyze genomes and to perform manual curation of gene function in a comparative and metabolic context.

This platform provides data from completed and ongoing genome projects together with post-genomic experiments (i.e. transcriptomics, re-sequencing of evolved strains) allowing users to improve the understanding of gene functions. Expert annotations are continuously gathered in the MicroScope database contributing to the improvement of the quality of microbial genome annotations, and thus to the predicted metabolic networks.

MicroScope can be used as a community resource for comparative analysis and annotation of publicly available genomes but also as a private resource with restricted access rights on genomic data. In addition, we regularly hold professional trainings sessions on the use of MicroScope platform.

Conditions d'accès
  • Free for academics.
  • Sales quote available on demand for non-academics 

Service features:

  • Microbial genome annotation (complete, WGS or metagenome-assembled genomes)
  • Comparative genomics and pangenomics
  • Function and biological process predictions
  • Metabolic network reconstruction 
  • Analysis of transcriptomics data
  • Variant calling of evolved strains
  • Technical support
  • Trainings on prokaryotic genome annotation  and on the curation of metabolic networks 

More details here.

Domaines d'activité
  • Biomédical
  • Agro-alimentaire
  • Environnement
  • Biotechnologie
Description des expertises
  • Tools and databases for bacterial genome annotation and comparative genomics
  • Metabolic network reconstruction
  • Curation of metabolic data
  • Discovery of new enzymatic activities
  • Quantitative transcriptomics via RNA-seq
  • Variant analysis
  • Pangenomics and (meta)genomics analyses
Mots clés:
  • Analyse de données de séquençage NGS
  • Méthodologie
  • Alignements de lectures sur des génomes
  • Génomique (DNA-seq)
  • Analyse de génomes
  • Transcriptomique (RNA-seq)
  • Analyse différentielle de l’expression des gènes
  • Analyses de transcrits et transcrits variants
  • Analyse de variants
  • Génomes complets
  • Métagénomique, métatranscriptomique
  • Algorithmique des séquences
  • Alignement (multiple) de séquences
  • Annotation de séquences
  • Recherche de motifs
  • Prédiction d'homologie/orthologie
  • Apprentissage automatique
  • Extraction de connaissances
  • Intégration de données hétérogènes
  • Représentation des connaissances
  • Biologie des systèmes
  • Modélisation des réseaux métaboliques
  • Modélisation des systèmes
  • Curation de collections de données
  • Développements technologiques de l‘Information et de la Communication
  • Outils
  • Intégration d'outils
  • Interopérabilité
  • Interfaces, portails web
  • Développement de workflows
  • Intégration de données
  • Gestion et transfert de données
  • Bases de données et systèmes d’informations
  • Génomique comparative
  • Comparaison des génomes
  • Comparaison des voies fonctionnelles et régulatrices

Formation professionnelle

Personnes formées :
30 personnes / an
Temps de formation :
10 jour(s) / an
Pas de nouvelle session prévue

Formations à la plate-forme Microscope


The LABGeM team at Genoscope regularly organizes training courses dedicated to the analysis of bacterial genomes via the use of the MicroScope platform at the University of Évry.
The course "Annotation and analysis of prokaryotic genomes using the MicroScope platform" lasting 4.5 days is aimed at:

  • acquiring theoretical and practical knowledge of genome annotation tools (structural and functional annotation, metabolic networks annotation)
  • knowing how to interpret the results of functional annotation tools
  • knowing how to carry out various comparative analyzes: analyzes of conserved syntenia, pan-genomes, phylogenetic and metabolic profiles
  • learning to interpret the results of metabolic network prediction tools and search for candidate genes for enzymatic activities
  • applying those tools to the analysis of genomes of interest to the participants 

Each session is made up of half theory and half practical work. During the training, participants have the opportunity to work on their own data during practical work.
This training is aimed at doctoral students, engineers, researchers, experienced biological or medical laboratory technicians. It concerns both people who already have an annotation project on the MicroScope platform and wishing to deepen its use, as well as those wishing to learn microbial genomics.
In addition, if you are a user of the MicroScope platform and you have already followed the training "Annotation and analysis of prokaryotic genomes using the MicroScope platform" a few years ago we have implemented a new training , the "MicroScope Platform - Advanced Course" training in order to update your knowledge on the latest evolutions of the platform and to deepen some of its major functionalities.
This training, lasting 2 days, will consolidate your use of the platform but also go further:

  • Presentation of the evolutions of the MicroScope platform
  • Presentation of the new flagship features of the MicroScope platform
  • Presentation of tools for RNA-seq analyzes
  • Deepening of the functionalities allowing the exploration of the bacterial metabolism
Conditions d'accès

For more information and registration : https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/.

Formation universitaire

Personnes formées :
50 personnes / an
Temps de formation :
Non renseigné
Pas de nouvelle session prévue

Formation universitaire


LABGeM's researchers are involved in different training programs in collaboration with :

  • the University of Paris Saclay: master GENIOMHE, master MSSB, master NRBCe
  • the University Denis Diderot: master M2BI
  • the University Paris Descartes: master IMVI
  • the Institut Pasteur: Training ‘Analyse des génomes’
Conditions d'accès
Non renseigné
Publications internes

Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., Le Fevre, F., Longin, C., Mornico, D., Roche, D., Rouy, Z., Salvignol, G., Scarpelli, C., Thil Smith, A. A., Weiman, M. & Médigue, C. (2013).
"MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data." Nucleic Acids Res 41(Database issue): D636-647.

Belda, E., Sekowska, A., Le Fevre, F., Morgat, A., Mornico, D., Ouzounis, C., Vallenet, D., Médigue, C. & Danchin, A. (2013). "An updated metabolic view of the Bacillus subtilis 168 genome." Microbiology 159(Pt 4): 757-770.

Sorokina M., Stam M., Médigue C., Lespinet O. and Vallenet D. (2014). "Profiling the orphan enzymes." Biol Direct 9: 10.

Calteau A, Fewer DP, Latifi A, Coursin T, Laurent T, Jokela J, Kerfeld CA, Sivonen K, Piel J, Gugger M. (2014). "Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria." BMC Genomics 15: 977.
Publications externes
Goudenege, D., Labreuche, Y., Krin, E., Ansquer, D., Mangenot, S., Calteau, A., Médigue, C., Mazel, D., Polz, M. F. & Le Roux, F. (2013). "Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits." ISME J 7(10): 1985-1996.

Guan, S. H., Gris, C., Cruveiller, S., Pouzet, C., Tasse, L., Leru, A., Maillard, A., Médigue, C., Batut, J., Masson-Boivin, C. & Capela, D. (2013). "Experimental evolution of nodule intracellular infection in legume symbionts." ISME J 7(7): 1367-1377.

Humbert, J. F., Barbe, V., Latifi, A., Gugger, M., Calteau, A., Coursin, T., Lajus, A., Castelli, V., Oztas, S., Samson, G., Longin, C., Médigue, C. & de Marsac, N. T. (2013). "A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa." PLoS One 8(8): e70747.

Kristiansen, R., Nguyen, H. T., Saunders, A. M., Nielsen, J. L., Wimmer, R., Le, V. Q., McIlroy, S. J., Petrovski, S., Seviour, R. J., Calteau, A., Nielsen, K. L. & Nielsen, P. H. (2013). "A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal." ISME J 7(3): 543-554.

Leikoski, N., Liu, L., Jokela, J., Wahlsten, M., Gugger, M., Calteau, A., Permi, P., Kerfeld, C. A., Sivonen, K. & Fewer, D. P. (2013). "Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides." Chem Biol 20(8): 1033-1043.

Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN. (2013). "Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26." Genome Biol Evol 5(5): 934-953.

Le Gac M, Cooper TF, Cruveiller S, Médigue C, Schneider D. (2013). "Evolutionary history and genetic parallelism affect correlated responses to evolution." Mol Ecol 22(12): 3292-3303.

Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R., Herdman, M., Sivonen, K., Coursin, T., Laurent, T., Goodwin, L., Nolan, M., Davenport, K. W., Han, C. S., Rubin, E. M., Eisen, J. A., Woyke, T., Gugger, M. & Kerfeld, C. A. (2013). "Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing." Proc Natl Acad Sci U S A 110(3): 1053-1058.

Supply, P., Marceau, M., Mangenot, S., Roche, D., Rouanet, C., Khanna, V., Majlessi, L., Criscuolo, A., Tap, J., Pawlik, A., Fiette, L., Orgeur, M., Fabre, M., Parmentier, C., Frigui, W., Simeone, R., Boritsch, E. C., Debrie, A. S., Willery, E., Walker, D., Quail, M. A., Ma, L., Bouchier, C., Salvignol, G., Sayes, F., Cascioferro, A., Seemann, T., Barbe, V., Locht, C., Gutierrez, M. C., Leclerc, C., Bentley, S. D., Stinear, T. P., Brisse, S., Médigue, C., Parkhill, J., Cruveiller, S. & Brosch, R. (2013). "Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis." Nat Genet 45(2): 172-179.

Sugawara, M., Epstein, B., Badgley, B., Unno, T., Xu, L., Reese, J., Gyaneshwar, P., Denny, R., Mudge, J., Bharti, A. K., Farmer, A. D., May, G. D., Woodward, J. E., Médigue, C., Vallenet, D., Lajus, A., Rouy, Z., Martinez-Vaz, B., Tiffin, P., Young, N. D. & Sadowsky, M. J. (2013). "Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies." Genome Biol 14(2): R17.

Wielgoss, S., Barrick, J. E., Tenaillon, O., Wiser, M. J., Dittmar, W. J., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E. & Schneider, D. (2013). "Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load." Proc Natl Acad Sci U S A 110(1): 222-227.

Zoropogui, A., Pujic, P., Normand, P., Barbe, V., Belli, P., Graindorge, A., Roche, D., Vallenet, D., Mangenot, S., Boiron, P., Rodriguez-Nava, V., Ribun, S., Richard, Y., Cournoyer, B. & Blaha, D. (2013). "The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle." BMC Genomics 14: 286.

Ji, B., Zhang, S. D., Arnoux, P., Rouy, Z., Alberto, F., Philippe, N., Murat, D., Zhang, W. J., Rioux, J. B., Ginet, N., Sabaty, M., Mangenot, S., Pradel, N., Tian, J., Yang, J., Zhang, L., Zhang, W., Pan, H., Henrissat, B., Coutinho, P. M., Li, Y., Xiao, T., Médigue, C., Barbe, V., Pignol, D., Talla, E. & Wu, L. F. (2014). "Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain." Environ Microbiol 16(2): 525-544.

Plucain J, Hindré T, Le Gac M, Tenaillon O, Cruveiller S, Médigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE, Schneider D. (2014). "Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli." Science 343(6177): 1366-1369.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D. (2014). "Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli." MBio 5(5): e01377-01314.

Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EP, Masson-Boivin C. (2014). "Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer." PLoS Biol 12(9): e1001942.

Billard-Pomares T, Fouteau S, Jacquet ME, Roche D, Barbe V, Castellanos M, Bouet JY, Cruveiller S, Médigue C, Blanco J, Clermont O, Denamur E, Branger C. (2014). "Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum beta-lactamase from an Escherichia coli strain." Antimicrob Agents Chemother 58(11): 6550-6557.

de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L. (2014). "RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti." Genome Biol Evol 6(4): 932-948.

Ramos PI, Picão RC, Almeida LG, Lima NC, Girardello R, Vivan AC, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Médigue C, Vasconcelos AT, Gales AC, Nicolás MF. (2014). "Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms." BMC Genomics 15: 54.

Ogier JC, Pagès S, Bisch G, Chiapello H, Médigue C, Rouy Z, Teyssier C, Vincent S, Tailliez P, Givaudan A, Gaudriault S. (2014). "Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii." Genome Biol Evol 6(6): 1495-1513.

Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J. 2014 Dec 9. doi: 10.1038/ismej.2014.233. [Epub ahead of print].

Goudenège D, Travers M, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A, Le Roux F. (2014). "A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters." Environ Microbiol.

Gomez-Valero L, Rusniok C, Rolando M, Neou M, Dervins-Ravault D, Demirtas J, Rouy Z, Moore RJ, Chen H, Petty NK, Jarraud S, Etienne J, Steinert M, Heuner K, Gribaldo S, Médigue C, Glöckner G, Hartland EL, Buchrieser C. (2014). "Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease." Genome Biol 15(11): 505.

Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P. (2014). "genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?" PLoS One 9(9): e108522.

Moulin, L., Mornico, D., Melkonian, R. & Klonowska, A. (2013). "Draft Genome Sequence of Rhizobium mesoamericanum STM3625, a Nitrogen-Fixing Symbiont of Mimosa pudica Isolated in French Guiana (South America)." Genome Announc 1(1).

Lanois, A., Ogier J. C., Gouzy, J., Laroui, C., Rouy, Z., Givaudan, A. & Gaudriault, S. (2013). "Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1." Genome Announc 1(3).

Kits, K. D., Kalyuzhnaya, M. G., Klotz, M. G., Jetten, M. S., Op den Camp, H. J., Vuilleumier, S., Bringel, F., Dispirito, A. A., Murrell, J. C., Bruce, D., Cheng, J. F., Copeland, A., Goodwin, L., Hauser, L., Lajus, A., Land, M. L., Lapidus, A., Lucas, S., Médigue, C., Pitluck, S., Woyke, T., Zeytun, A. & Stein, L. Y. (2013). "Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8." Genome Announc 1(2): e0017013.

Ji, B., Gimenez, G., Barbe, V., Vacherie, B., Rouy, Z., Amrani, A., Fardeau, M. L., Bertin, P., Alazard, D., Leroy, S., Talla, E., Ollivier, B., Dolla, A. & Pradel, N. (2013). "Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.)." Genome Announc 1(1).

Amin, O., Fardeau, M. L., Valette, O., Hirschler-Rea, A., Barbe, V., Médigue, C., Vacherie, B., Ollivier, B., Bertin, P. N. & Dolla, A. (2013). "Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T)." Genome Announc 1(1).

Zhang SD, Barbe V, Garel M, Zhang WJ, Chen H, Santini CL, Murat D, Jing H, Zhao Y, Lajus A, Martini S, Pradel N, Tamburini C, Wu LF. (2014). "Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200." Genome Announc 2(2).
Publications avec le laboratoire d'hébergement
Bastard K, Smith AA, Vergne-Vaxelaire C, Perret A, Zaparucha A, De Melo-Minardi R, Mariage A, Boutard M, Debard A, Lechaplais C, Pelle C, Pellouin V, Perchat N, Petit JL, Kreimeyer A, Médigue C, Weissenbach J, Artiguenave F, De Berardinis V, Vallenet D, Salanoubat M. (2014). "Revealing the hidden functional diversity of an enzyme family." Nat Chem Biol 10(1): 42-49.

Stuani L, Lechaplais C, Salminen AV, Ségurens B, Durot M, Castelli V, Pinet A, Labadie K, Cruveiller S, Weissenbach J, de Berardinis V, Salanoubat M, Perret A. (2014). "Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach." Metabolomics 10(6): 1223-1238.
Répartition des utilisateurs
60 %
25 %
10 %
Description de la répartition :

From <400 user accounts in 2006, MicroScope counts >4200 personal accounts at present time. The number of registered users has doubled since 2013, and the platform has even widened its international popularity with 64% of accounts outside France.

Many international projects are conducted through the platform involving users from distant geographic areas. Although authentication is not required to navigate in MicroScope, it allows users to annotate genes and save data on their personal session.

On average per month, we count 360 active accounts (i.e. the user logged in at least once in the month). 

Projets propres de la plateforme
  • Tools for bacterial genome annotation and comparative genomics
  • Metabolic network reconstruction
  • Curation of metabolic data
  • Discovery of new enzymatic activities
  • Quantitative transcriptomics via RNA-seq
  • Variant analysis
  • Pangenomics and (meta)genomics analyses
Projets d'ANR

REPLICOLSCOPE (ANR GENOM 2011-2015) ; VIBRIOGEN: (ANR Blanc 2011-2015) ; SHAPE (ANR BioAdapt 2012-2016) ; BugInACell (ANR Blanc 013-2017) ; BLUE ENZYMES (ANR “Sécurité alimentaire et défi démographique” 2014-2018) ; MOPAD  (projet BPI 2014-2017)
France Génomique (FG)  - Développements méthodologiques pour le workpackage 2.7.2 de FG: annotation et analyse de métagénomes (2012-2016)
Institut Français de Bioinformatique (IFB) – Développements méthodologiques pour la thématique “Microbial bioinformatics” de l’IFB (2013-2016)
SYNBIOWATCH (NRBC programme transversal du CEA 2011-2015)

Projets européens et internationaux

MetaCat (EU ERA NET 2015) ; ELIXIR (WS « Data and Resources »)

Projets avec des industriels

Contrat de service avec DANONE RESEARCH (depuis 2010)
MOPAD  (projet BPI en partenariat avec LIMAGRAIN & BIOVITIS Sept. 2014-2017)

Projets de collaboration non financés par un organisme extérieur
Non renseigné
Prestations de service non financés par un organisme extérieur
Non renseigné
Non renseigné
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