A5015379548- Probiotics and Fermented Foods
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Microbial Metabolism and Applications
- Bacteriophages and microbial interactions
- Fermentation and Sensory Analysis
- Microbial Metabolites in Food Biotechnology
- Oral microbiology and periodontitis research
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Microbial infections and disease research
- Plant Pathogens and Fungal Diseases
- Enzyme Production and Characterization
- Advanced Proteomics Techniques and Applications
- Aquaculture disease management and microbiota
- Identification and Quantification in Food
- Milk Quality and Mastitis in Dairy Cows
- RNA and protein synthesis mechanisms
- Clostridium difficile and Clostridium perfringens research
- Streptococcal Infections and Treatments
- Gene expression and cancer classification
- Antimicrobial Resistance in Staphylococcus
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
Mathématiques et Informatique Appliquées du Génome à l'Environnement
2015-2024
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2019-2024
Université Paris-Saclay
2016-2024
AgroParisTech
2023
Institut National de la Recherche Agronomique
2005-2018
Département Génétique Animale
2014
Institut Pasteur
2013
Institut National de la Recherche Agronomique du Niger
2013
Mathématiques et Informatique Appliquées
2009
Lactobacillus delbrueckii ssp. bulgaricus ( L. ) is a representative of the group lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence this bacterium has been determined and shows signs ongoing specialization, with substantial number pseudogenes incomplete metabolic pathways relatively few regulatory functions. Several unique features support hypothesis that phase rapid evolution. i Exceptionally high numbers rRNA tRNA genes...
Lactobacillus sakei is a psychotrophic lactic acid bacterium found naturally on fresh meat and fish. This microorganism widely used in the manufacture of fermented meats has biotechnological potential biopreservation food safety. We have explored 1,884,661-base-pair (bp) circular chromosome strain 23K encoding 1,883 predicted genes. Genome sequencing revealed specialized metabolic repertoire, including purine nucleoside scavenging that may contribute to an ability successfully compete raw...
We report here the complete genome sequence of virulent strain JIP02/86 (ATCC 49511) Flavobacterium psychrophilum, a widely distributed pathogen wild and cultured salmonid fish. The consists 2,861,988–base pair (bp) circular chromosome with 2,432 predicted protein-coding genes. Among these proteins, stress response mediators, gliding motility adhesins many putative secreted proteases are probably involved in colonization, invasion destruction host tissues. provides basis for explaining...
Background Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and also considered for its probiotic use [1]. This species exhibits slow growth, low nutritional requirements, hardiness many habitats. It belongs to the taxonomic group of dairy propionibacteria, contrast cutaneous P. acnes. The genome type strain, subsp. shermanii CIRM-BIA1 (CIP 103027T), was sequenced with an 11-fold coverage. Methodology/Principal Findings circular chromosome 2.7 Mb...
The entire genome of Lactobacillus casei BL23, a strain with probiotic properties, has been sequenced. genomes BL23 and the industrially used Shirota YIT 9029 (Yakult) seem to be very similar.
Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but large strains with different metabolic potential. To decipher the intraspecies such microbiota, traditional metagenetic analysis using 16S rRNA gene inadequate. We therefore assessed potential benefit an alternative genetic marker, gyrB, which encodes subunit B DNA gyrase, type II topoisomerase. A comparison between rDNA-based (V3-V4) amplicon sequencing...
The in silico prediction of bacterial surface exposed proteins is growing interest for the rational development vaccines and study bacteria-host relationships, whether pathogenic or host beneficial. This driven by increase use DNA sequencing as a major tool early characterization bacteria and, more recently, even complex ecosystems at host-environment interface metagenomics approaches. Current protein localization protocols are not suited to this task they ignore potential exposition many...
Mapping short reads against a reference genome is classically the first step of many next-generation sequencing data analyses, and it should be as accurate possible. Because large number to handle, numerous sophisticated algorithms have been developped in last 3 years tackle this problem. In article, we review underlying used most existing mapping tools, then compare performance nine these tools on well controled benchmark built for purpose. We set that exist single or multiple copies which...
<h3>Objective</h3> No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role the gut microbial community in CD. Here we explore feasibility extracting bacterial protein signals relevant CD, by interrogating myriads intestinal proteomes from small number patients healthy controls. <h3>Design</h3> We first developed validated workflow—including extraction communities, two-dimensional difference gel electrophoresis (2D-DIGE),...
Lactobacillus delbrueckii ssp. lactis and bulgaricus are lactic acid producing bacteria that largely used in dairy industries, notably cheese-making yogurt production. An earlier in-depth study of the first completely sequenced genome revealed characteristics a an active phase rapid evolution, what appears to be adaptation milk environment. Here we examine for time if same conclusions apply lactis, discuss intra- inter-subspecies genomic diversity context evolutionary adaptation. Both L....
Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety functional role in cheese making these microbial still not well understood. Metagenomic analysis by high throughput shotgun sequencing is a promising approach to characterize their genomic profiles. Such analyses, however, critically depend on the availability appropriate reference genome databases against which reads can be aligned. We built catalog suitable for short read...
In this study, we searched for integrative conjugative elements (ICEs) in chromosomes of 124 strains Streptococci. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed that were grouped 7 distinct families. Comparison the conjugation modules belonging to each family allowed identification conserved proteins. The phylogenetic analysis also exchanges or acquisition recombination are frequent. Integration these streptococcal is catalyzed either by site-specific tyrosine...
Arthrobacter arilaitensis is one of the major bacterial species found at surface cheeses, especially in smear-ripened where it contributes to typical colour, flavour and texture properties final product. The A. Re117 genome composed a 3,859,257 bp chromosome two plasmids 50,407 8,528 bp. shares large regions synteny with chromosomes three environmental strains for which sequences are available: aurescens TC1, chlorophenolicus A6 sp. FB24. In contrast however, 4.92% ISs elements, portion that...
Members of the genus Flavobacterium occur in a variety ecological niches and represent an interesting diversity lifestyles. branchiophilum is main causative agent bacterial gill disease, severe condition affecting various cultured freshwater fish species worldwide, particular salmonids Canada Japan. We report here complete genome sequence strain FL-15 isolated from diseased sheatfish (Silurus glanis) Hungary. The analysis F. revealed putative mechanisms pathogenicity strikingly different...
Leuconostoc citreum NRRL B-1299 has long been known to produce α-glucans containing both α-(1→6) and α-(1→2) linkages, which are synthesized by α-transglucosylases of the GH70 family. We sequenced genome identify full inventory enzymes in this strain. Three new genes (brsA, dsrM dsrDP) putatively encoding were identified. The corresponding recombinant characterized. Branching sucrase A (BRS-A) grafts linear dextran with α-(1→2)-linked glucosyl units, is probably involved branching L....
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...
Propionibacterium freudenreichii, a dairy starter, can reach population of almost 109 propionibacteria per gram in Swiss-type cheese at the time consumption. Also consumed as probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 leukocytes. We selected 23 strains with varied potentials order to identify protein(s) involved. After comparative genomic analysis, 12 these were further analysed proteomics, eight them being submitted...
Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number locomotor disorders and septicemia, particularly in fast-growing broilers.
Milk oligosaccharides are bioactive components that regulate the composition of neonatal microbiota and exert immunomodulatory functions. Their beneficial effects depend on their structure. Numerous studies have shown intra- inter-species variation in structural concentration these compounds mammalian milk, yet biological significance such remains poorly understood. Automated natural language processing methods promising tools for extracting gathering structured data from unstructured texts...
"Candidatus Arthromitus" sp. strain SFB-mouse-NL (SFB, segmented filamentous bacteria) is a commensal bacterium necessary for inducing the postnatal maturation of homeostatic innate and adaptive immune responses in mouse gut. Here, we report genome sequence this bacterium, which sets it apart from earlier sequenced SFB isolates.