A5041918119- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Plant Pathogens and Fungal Diseases
- Mycorrhizal Fungi and Plant Interactions
- Genomics and Phylogenetic Studies
- Vibrio bacteria research studies
- Bacillus and Francisella bacterial research
- Aquaculture disease management and microbiota
- Fungal Biology and Applications
- CRISPR and Genetic Engineering
- Microbial Metabolism and Applications
- Evolution and Genetic Dynamics
- Fungal and yeast genetics research
- Plant Disease Resistance and Genetics
- Gene expression and cancer classification
- Bacterial biofilms and quorum sensing
- Erythrocyte Function and Pathophysiology
- RNA and protein synthesis mechanisms
- Identification and Quantification in Food
- Hemoglobin structure and function
- Fermentation and Sensory Analysis
- Wheat and Barley Genetics and Pathology
- Plant Pathogens and Resistance
- Parasitic Infections and Diagnostics
- Probiotics and Fermented Foods
Université Paris-Saclay
2016-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2021-2025
Mathématiques et Informatique Appliquées du Génome à l'Environnement
2014-2023
Staphylococcus aureus is a major pathogen that colonizes about 20% of the human population. Intriguingly, this Gram-positive bacterium can survive and thrive under wide range different conditions, both inside outside body. Here, we investigated transcriptional adaptation S. HG001, derivative strain NCTC 8325, across experimental conditions ranging from optimal growth in vitro to intracellular host cells. These data establish an extensive repertoire transcription units non-coding RNAs,...
Understanding cellular life requires a comprehensive knowledge of the essential functions, components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains model bacterium, Bacillus subtilis , whose been reduced by ∼36%. These fully viable, growth rates in complex medium comparable those wild type strains. An in-depth multi-omics analysis genome revealed how deletions affect transcription regulatory network cell,...
Bacillus cereus is the 2nd most frequent bacterial agent responsible for food-borne outbreaks in France and 3rd Europe. In addition, local systemic infections have been reported, mainly describing individual cases or single hospital setting. The real incidence of such infection unknown information on genetic phenotypic characteristics incriminated strains generally scarce. We performed an extensive study B. isolated from patients environments nine hospitals during a 5-year study, giving...
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how fungus Magnaporthe oryzae adapts different plants, we sequenced eight M. isolates differing specificity (rice, foxtail millet, wheat, goosegrass), one grisea isolate specific crabgrass. Analysis genomes revealed small variation genome sizes (39–43 Mb) gene content (12,283–14,781 genes) between isolates. The whole set genes comprised 14,966 shared families, 63% which...
The genetic basis of the phenotypic diversity yeast is still poorly understood. Wine strains have specific abilities to grow and ferment under stressful conditions compared with other strains, but underlying these traits unknown. Understanding how sequence variation influences such phenotypes a major challenge address adaptation mechanisms wine yeast. We aimed identify fermentation gain insight into their relationships variations in gene expression among strains. combined trait QTL mapping...
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, the expression individual genes to control development and oncogenesis. prokaryotes, function its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate biological significance Rho-controlled in Gram-positive model bacterium Bacillus subtilis. Rho inactivation...
Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one main pathogens hampering productivity farming worldwide. In this study, genomic diversity F. psychrophilum species analyzed using a set 41 genomes, including 30 newly sequenced isolates. These were selected on basis available MLST data with two-fold objective maximizing coverage allowing focus clonal complex (CC-ST10) infecting farmed...
Abstract Genome-scale engineering enables rational removal of dispensable genes in chassis genomes. Deviating from this approach, we applied greedy accumulation deletions large regions the Bacillus subtilis genome, yielding a library 298 strains with genomes reduced up to 1.48 Mb size. High-throughput physiological phenotyping these confirmed that genome reduction is associated substantial loss cell fitness and synthetic-sick interactions. Transcriptome analysis indicated <15%...
Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. This bacterial species subdominant in healthy physiological state gut microbiota (eubiosis) adults, but can become dominant and cause infections when intestinal homeostasis disrupted (dysbiosis). The relatively high concentrations bile acids deoxycholate (DCA) taurocholate (TCA) hallmark eubiosis dysbiosis, respectively. study aimed to better understand how E. adapts DCA TCA. We showed that impairs growth...
Bacterial pathogens have a critical impact on aquaculture, sector that accounts for half of the human fish consumption. Flavobacterium psychrophilum (phylum Bacteroidetes) is responsible bacterial cold-water disease in salmonids worldwide. The molecular factors involved host invasion, colonization and haemorrhagic septicaemia are mostly unknown. In this study, we identified two new TonB-dependent receptors, HfpR BfpR, required adaptation to iron conditions encountered during infection...
Abstract Polymerase errors during DNA replication are a major source of point mutations in genomes. The spontaneous mutation rate also depends on the counteracting activity repair mechanisms, with mutator phenotypes appearing constantly and allowing for periods rapid evolution nature laboratory. Here, we use Gram-positive model bacterium Bacillus subtilis to disentangle contributions polymerase initial nucleotide selectivity, proofreading, mismatch (MMR) rate. To achieve this, constructed...
As for many opportunistic pathogens, the virulence potential of Listeria monocytogenes is highly heterogeneous between isolates and correlated, to some extent, with phylogeny gene repertoires. In sharp contrast copious data on intraspecies genome diversity, little known about transcriptome diversity despite role complex genetic regulation in pathogenicity. The current study implemented RNA sequencing characterize profiles 33 under optimal vitro growth conditions. Transcript levels conserved...
Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis , de-repression pervasive transcription by inactivation rho revealed regulation post-exponential differentiation programs. To identify other aspects regulatory during adaptation to starvation, we have constructed a B . strain (Rho + ) that expresses at relatively stable high level order compensate decrease...
The family Flavobacteriaceae (phylum Bacteroidetes) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum pathogen that infects salmonid fish worldwide, with critical environmental economic impact. Here, we report an extensive transcriptome analysis established the genome map transcription start sites transcribed regions, predicted alternative sigma factor regulons regulatory RNAs, documented gene expression profiles across...
B. subtilis adapts to changing environments by reprogramming its genetic expression through a variety of transcriptional regulators from the global transition state that allow complete resetting cell expression, stress specific controlling only limited number key genes required for optimal adaptation. Among them, MarR-type are known respond stresses including antibiotics or oxidative stress, and control catabolic virulence gene expression. Here we report characterization ydcFGH operon...
Bacterial response to nitric oxide (NO) is of major importance for bacterial survival. NO stress a main actor the eukaryotic immune and several pathogenic bacteria have developed means detoxification repair damages caused by NO. However, mechanisms resistance Gram-positive are poorly described. In opportunistic foodborne pathogen Bacillus cereus, genome sequence analyses did not identify homologs known reductases transcriptional regulators, such as NsrR, which orchestrate other or...
Abstract The bacterial cell wall (CW) is an essential protective barrier and the frontline of cellular interactions with environment also a target for numerous antimicrobial agents. Accordingly, its integrity homeostasis are closely monitored rapid adaptive responses by transcriptional reprogramming induce appropriate counter-measures against perturbations. Here, we report comprehensive comparative profiling primary envelope stress (CESR), based on combining RNAseq high-resolution tiling...
Genoscapist is a tool to design web interfaces generating high-quality images for interactive visualization of hundreds quantitative profiles along reference genome together with various annotations. Relevance demonstrated by deployment two websites dedicated large condition-dependent transcriptome datasets available Bacillus subtilis and Staphylococcus aureus.Websites source code freely accessible at https://genoscapist.migale.inrae.fr.
Bacillus subtilis mutants lacking the SMC-ScpAB complex are severely impaired for chromosome condensation and partitioning, DNA repair, cells not viable under standard laboratory conditions. We isolated suppressor mutations that restored capacity of a smc deletion mutant (Δsmc) to grow These reduced segregation defects abrogated hypersensitivity gyrase inhibitors Δsmc. Three were mapped in genes involved tRNA aminoacylation maturation pathways. A transcriptomic survey pointed potential link...