A5016671567- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- RNA and protein synthesis mechanisms
- Microbial metabolism and enzyme function
- Amino Acid Enzymes and Metabolism
- Enzyme Structure and Function
- Entomopathogenic Microorganisms in Pest Control
- Plant and animal studies
- Insect symbiosis and bacterial influences
- Biofuel production and bioconversion
- Insect and Arachnid Ecology and Behavior
- Vibrio bacteria research studies
- Mycobacterium research and diagnosis
- Nematode management and characterization studies
- Bioinformatics and Genomic Networks
- Polyamine Metabolism and Applications
- Insect and Pesticide Research
- Wastewater Treatment and Nitrogen Removal
- Microbial Community Ecology and Physiology
- Actinomycetales infections and treatment
- Metal Extraction and Bioleaching
Genoscope
2015-2025
Université Paul-Valéry Montpellier
2024
Institut Universitaire de France
2024
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2013-2023
Centre National de la Recherche Scientifique
2014-2023
CEA Paris-Saclay
2018-2023
Université Paris-Saclay
2018-2023
Génomique Métabolique du Genoscope
2009-2022
Université d'Évry Val-d'Essonne
2018-2019
Institut de Génomique Fonctionnelle
2015
MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and comparative analysis. The resource provides data from completed ongoing projects (automatic expert annotations), together with sources post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users perfect improve understanding gene functions. (http://www.genoscope.cns.fr/agc/microscope) combines tools graphical interfaces analyse genomes perform manual...
The initial outcome of genome sequencing is the creation long text strings written in a four letter alphabet. role silico sequence analysis to assist biologists act associating biological knowledge with these sequences, allowing investigators make inferences and predictions that can be tested experimentally. A wide variety software available scientific community, used identify genomic objects, before predicting their functions. However, only limited number biologically interesting features...
Roland Brosch and colleagues report whole-genome sequencing of tubercle bacilli with smooth colony morphology, also known as Mycobacterium canetti and/or prototuberculosis, obtained from humans tuberculosis geographically diverse regions. Their comparative genomic analysis other M. complex members identifies extensive recombination provides insights into the evolution mycobacteria. The authors that morphology show reduced persistence virulence compared to strains in infection experiments...
Abstract Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount new information that completely transforms our understanding thousands microbial species. However, despite development powerful bioinformatics approaches, full interpretation content these genomes remains difficult task. Launched in 2005, MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous provides analysis for prokaryotic...
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency accuracy in genome is a challenging problem because millions protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can extracted metabolic models. Launched 2005, MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) an integrative resource supports systematic efficient revision microbial annotation, data...
Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes two pink-pigmented facultative methylotrophic bacteria Alpha-proteobacterial genus Methylobacterium, reference species Methylobacterium extorquens strain AM1 and dichloromethane-degrading DM4, were compared. Methodology/Principal Findings 6.88 Mb genome comprises a 5.51 chromosome, 1.26 megaplasmid three plasmids, while 6.12 DM4 features 5.94 chromosome...
Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome one these strains, sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive grow its highly toxic environment. In order explore genomic diversity well genetic evolution spp., a comparative hybridization (CGH) approach used on eight different strains genus, including five same species. Our results suggest...
Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within heterogeneous taxonomically disputed species complex. Some include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, cold-tolerant potato brown rot (also known R3bv2) recently emerged Not Pathogenic to Banana (NPB) strains. These ecotypes offer robust...
ABSTRACT P1 bacteriophages lysogenize bacteria as independent plasmid-like elements. We describe here a P1-like bacteriophage, RCS47, carrying bla SHV-2 gene, isolated from clinical strain of Escherichia coli phylogroup B1, and we report the prevalence prophages in natural E. isolates. found that 70% sequence 115-kb circular molecule, was common to reference bacteriophage under GenBank accession no. AF234172.1 , with shared sequences being 99% identical. RCS47 had acquired two main foreign...
Deinococcus deserti is a desiccation-and radiation-tolerant desert bacterium.Differential RNA sequencing (RNA-seq) was performed to explore the specificities of its transcriptome.Strikingly, for 1,174 (60%) mRNAs, transcription start site found exactly at (916 cases, 47%) or very close translation initiation codon AUG GUG.Such proportion leaderless which may resemble ancestral unprecedented bacterial species.Proteomics showed that mRNAs are efficiently translated in D. deserti.Interestingly,...
The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance thousands stored in public databanks. MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is integrative resource supports systematic and efficient revision microbial annotation, data management comparative analysis. Starting from results our syntactic, functional relational pipelines, provides integrated...
Recent studies revealed that several vibrio species have evolved the capacity to survive inside host cells. However, it is still often ignored if intracellular stages are required for pathogenicity. Virulence of Vibrio tasmaniensis LGP32, a strain pathogenic Crassostrea gigas oysters, depends on entry into hemocytes, oyster immune We investigated here mechanisms LGP32 survival and their consequences host-pathogen interaction. Entry hemocytes were LGP32-driven cytolysis both in vivo vitro....
Abstract The extreme radiation resistance of Deinococcus bacteria requires the radiation‐stimulated cleavage protein DdrO by a specific metalloprotease called IrrE. is repressor predicted radiation/desiccation response ( RDR ) regulon, composed radiation‐induced genes having conserved DNA motif RDRM in their promoter regions. Here, we showed that addition zinc ions to purified apo‐IrrE, and short exposure cells ions, resulted vitro vivo, respectively. Binding IrrE ‐containing or interaction...
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis 116 whole plasmid sequences human or animal origin isolated over period spanning before and after use third-generation cephalosporins (3GCs) using gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable 9 non-transferable 3 P-like bacteriophages. ESBL-encoding were found on 64 6 mobilizable, 2 P1-like...
Despite a fitness cost imposed on bacterial hosts, large conjugative plasmids play key role in the diffusion of resistance determinants, such as CTX-M extended-spectrum β-lactamases. Among plasmids, IncF are most predominant group, and an F2:A1:B- IncF-type plasmid encoding CTX-M-15 variant was recently described being strongly associated with emerging worldwide Escherichia coli sequence type 131 (ST131)-O25b:H4 H30Rx/C2 sublineage. In this context, we investigated narrow-range F-type...
Abstract Background Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder , we investigated units in genomes, by exhaustive description the RGPs two Photorhabdus Xenorhabdus strains, belonging to Enterobacteriaceae interacting with invertebrates (insects nematodes). Results account for about 60% genome each four studied. We classified islands (GIs),...
In this study, an ertapenem-nonsusceptible Escherichia coli isolate was investigated to determine the genetic basis for its carbapenem resistance phenotype. This clinical strain recovered from a patient that received, 1 year previously, ertapenem treat cholangitis due carbapenem-susceptible extended-spectrum-β-lactamase (ESBL)-producing E. isolate. Whole-genome sequencing of these strains performed using Illumina and single-molecule real-time technologies. It revealed they belonged ST131...
In Gram-negative bacteria, resistance-nodulation-division-type efflux pumps, particularly AcrAB-TolC, play a critical role in mediating resistance to antimicrobial agents and toxic metabolites, contributing multidrug resistance. Photorhabdus laumondii is an entomopathogenic bacterium that has garnered significant interest due its production of bioactive specialized metabolites with anti-inflammatory, antimicrobial, scavenger deterrents properties. previous work, we demonstrated AcrAB confers...
Brochothrix thermosphacta is one of the main spoilers in food, responsible for meat and seafood spoilage through production malodorous volatile organic compounds. The molecules produced by this bacterium depend on substrate (meat or seafood) storage conditions such as gas mixtures used packaging. It seems also that potential strain dependent diacetyl acetoin, two spoilage, varies with strains. Therefore, suggests involvement different metabolic functions depending both food capacities. In...
Abstract Background Nocardia cyriacigeorgica is recognized as one of the most prevalent etiological agents human nocardiosis. Human exposure to these Actinobacteria stems from direct contact with contaminated environmental matrices. The full genome sequence N. strain GUH-2 was studied infer major trends in its evolution, including acquisition novel genetic elements that could explain ability thrive multiple habitats. Results size 6.19 Mb-long, 82.7% CDS have homologs at least another...
Abstract Some of the bacterial cells in isogenic populations behave differently from others. We describe here how a new type phenotypic heterogeneity relating to resistance cationic antimicrobial peptides (CAMPs) is determinant for pathogenic infection process entomopathogenic bacterium Photorhabdus luminescens . demonstrate that resistant subpopulation, which accounts only 0.5% wild-type population, causes septicemia insects. Bacterial driven by PhoPQ two-component regulatory system and...
Metformin is one of the most prescribed antidiabetic agents worldwide and also considered for other therapeutic applications including cancer endocrine disorders. It largely unmetabolized by human enzymes its presence in environment has raised concern, with reported toxic effects on aquatic life potentially humans. We report isolation characterisation strain MD1, an aerobic methylotrophic bacterium growing metformin as sole carbon, nitrogen energy source. Strain MD1 degrades into...
The bio-economy relies on microbial strains optimized for efficient large scale production of chemicals and fuels from inexpensive renewable feedstocks under industrial conditions. reduced one carbon compound methanol, whose does not involve carbohydrates needed the feed food sector, can be used as sole energy source by methylotrophic bacteria like Methylobacterium extorquens AM1. This strain has already been engineered to produce various commodity high value methanol. toxic effect methanol...
In May 2010, a cluster of three cases Legionnaires' disease was identified in France. The results the epidemiological, environmental and microbiological investigations allowed rapid identification public whirlpool spa as most probable source contamination implementation appropriate control measures. This investigation has stressed need for good cooperation between partners importance molecular analysis Legionella strains.