A5009660232- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Viral gastroenteritis research and epidemiology
- Probiotics and Fermented Foods
- Microbial infections and disease research
- DNA Repair Mechanisms
- RNA and protein synthesis mechanisms
- Respiratory viral infections research
- Escherichia coli research studies
- Agriculture and Rural Development Research
- Agricultural Economics and Policy
- Plant Virus Research Studies
- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Hepatitis B Virus Studies
- Political Economy and Marxism
- CRISPR and Genetic Engineering
- Antibiotic Resistance in Bacteria
- Vibrio bacteria research studies
- DNA and Nucleic Acid Chemistry
- Genomics and Chromatin Dynamics
- Heat shock proteins research
- Microbial Community Ecology and Physiology
- Enzyme Structure and Function
Microbiologie de l’alimentation au service de la santé
2016-2025
Université Paris-Saclay
2016-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
1985-2025
AgroParisTech
2011-2024
Centre Île-de-France - Jouy-en-Josas - Antony
2024
Fondation HEC
2022
Interdisciplinarité en Santé Publique Interventions et Instruments de mesure complexes – Région Est
2010-2015
Institut National de la Recherche Agronomique
1988-2015
Département Génétique Animale
1990-2012
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2010
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety commensal and pathogenic strains that diversify by high rates genetic change. We uniformly (re-) annotated genomes 20 E. strain fergusonii (the closest related species), including seven we sequenced to completion. Within approximately 18,000 families orthologous genes, found 2,000 common all strains. Although recombination are much higher than mutation rates, show, both...
This paper presents standards and best practices for reporting genome sequences of uncultivated viruses. We present an extension the Minimum Information about any (x) Sequence (MIxS) standard virus genomes. Uncultivated Virus Genome (MIUViG) were developed within Genomic Standards Consortium framework include origin, quality, annotation, taxonomic classification, biogeographic distribution in silico host prediction. Community-wide adoption MIUViG standards, which complement a Single...
Abstract Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number different protein families encountered sequence heterogeneity each family. The recent increase sequenced viral genomes constitutes a great opportunity to gain new insights into this consequently urges development annotation resources help functional comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), library generated using...
The genetic diversity observed among bacteriophages remains a major obstacle for the identification of homologs and comparison their functional modules. In structural module, although several classes homologous proteins contributing to head tail structure can be detected, head-to-tail connection (or neck) are generally more divergent. Yet, molecular analyses few tailed phages belonging different morphological suggested that only limited number solutions used in order produce virion. To...
Abstract The gut microbiome is shaped through infancy and impacts the maturation of immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis lysogeny, with latter being especially prominent infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes standardized detection methods. Here we systematically resolved diversity faecal...
The fundamental unit of biological diversity is the species. However, a remarkable extent intraspecies in bacteria was discovered by genome sequencing, and it reveals need to develop clear criteria group strains within Two main types analyses used quantify variation at level are average nucleotide identity (ANI), which detects DNA conservation core genome, content, calculates proportion shared two genomes. Both estimates based on BLAST alignments for definition sequences common pair....
Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral is limited by the lack knowledge phages infecting major gut commensal bacteria, such as Faecalibacterium prausnitzii, bacterial symbiont repeatedly found depleted inflammatory bowel disease (IBD) patients. In particular, no complete genomes F. prausnitzii are present databases. We identified 18 prophages 15 used comparative...
Homologous recombination is a key in contributing to bacteriophages genome repair, circularization and replication. No less than six kinds of recombinase genes have been reported so far bacteriophage genomes, two (UvsX Gp2.5) from virulent, four (Sak, Red beta, Erf Sak4) temperate phages. Using profile-profile comparisons, structure-based modelling gene-context analyses, we provide new views on the global landscape recombinases 465 bacteriophages. We show that Sak, beta belong common large...
Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level horizontal gene transfer among temperate phages, favoring high evolution rate. Molecular mechanisms this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases key players these transfers, thanks to their efficiency low fidelity. Here, we associate two complementary vivo assays bioinformatics...
Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples 1-year-old children and obtain coliphages directly viral fraction same samples. We find that 63% hosted phages, while 24% viromes contain targeting coli. 150 these half recovered strain supernatants, virome (73% 27% virulent) were tested for host range 75 cohort....
Abstract CRISPR–Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria archaea. In Escherichia coli, it is generally accepted inactive in laboratory conditions due to a transcriptional repressor. natural isolates, has been shown CRISPR arrays remain stable over the years most spacer targets (protospacers) unknown. Here, we re-examine E. coli isolates investigate viral bacterial genomes for using bioinformatics approach coupled unique biological...
The only DNA helicase essential for Escherichia coli viability is DnaB, the chromosome replication fork helicase. In contrast, in Bacillus subtilis , addition to DnaB counterpart called DnaC, we have found a second helicase, PcrA. It 40% identical Rep and UvrD helicases of E. 61% PcrA Staphylococcus aureus . This gene located at 55° on belongs putative operon together with ligase ( lig ) two unknown genes named pcrB yerH As was cell viability, conditional mutants were constructed. such...
Abstract Excessive recombination between repeated, interspersed, and diverged DNA sequences is a potential source of genomic instability. We have investigated the possibility that mechanism exists to suppress genetic exchange these quasi-homologous (homeologous) sequences. examined role general mismatch repair system Escherichia coli because previous work has shown pathway functions as barrier interspecies E. Salmonella typhimurium. The formation large duplications by homeologous in was...
Temperate phages, the bacterial viruses able to enter in a dormant prophage state genomes, are present majority of strains for which genome sequence is available. Although these prophages generally considered increase their hosts' fitness by bringing beneficial genes, studies demonstrating such effects ecologically relevant environments relatively limited few species. Here, we investigated impact carriage gastrointestinal tract monoxenic mice. Combined with mathematical modelling,...
ABSTRACT The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development different groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that viral community, mainly composed bacteriophages, also represents common substantial part cheese microbiome. However, composition this its temporal variations, associations between bacteriophages their hosts remain poorly characterized. Here, we studied French...
The Gerber method is used worldwide as a simple and rapid for determining fat in raw processed milks. However, the volume of test portion has not been internationally agreed upon. A collaborative study was conducted to evaluate performance using either weighed (11.13 g) or by 10.77 mL delivered pipet. For each method, laboratories received 10 samples: 5 pasteurized homogenized milks, 2 which were blind duplicate pairs. Eleven participated evaluation aliquot addition weight pipet,...