Benoît Remenant's research while affiliated with Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail and other places

Publications (36)

Article
Poultry meat, the second most consumed meat in France, is commercialized mainly as portions of chicken cuts with various quality labels, stored under various modified atmosphere packaging (MAP), with shelf-life ranging from 9 to 17 days. We used 16S rDNA pyrosequencing to describe microbiota of chicken legs. Ten samples representing a wide diversit...
Article
Full-text available
Lactic Acid Bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis...
Article
Full-text available
In this study, we present the draft genome sequence of Carnobacterium divergens V41. This strain was previously reported as producing divercin V41, a bacteriocin of interest for food biopreservation. Its genome revealed also the presence of a gene cluster putatively involved in polyketide production, which is unique in lactic acid bacteria.
Article
Influenced by production and storage processes and by seasonal changes the diversity of meat products microbiota can be very variable. Because microbiotas influence meat quality and safety, characterizing and understanding their dynamics during processing and storage is important for proposing innovative and efficient storage conditions. Challenge...
Article
Full-text available
The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensiv...
Article
Most food products are highly perishable as they constitute a rich nutrient source for microbial development. Among the microorganisms contaminating food, some present metabolic activities leading to spoilage. In addition to hygienic rules to reduce contamination, various treatments are applied during production and storage to avoid the growth of u...
Conference Paper
Full-text available
L. piscium CNCM I-4031 DNA was obtained using standard salt-extraction method. The whole genome sequencing of L. piscium CNCM I-4031 was carried out using GS FLX+ and GS FLX technologies with shotgun and long paired-end library of 8 kbp (EUROFINS-MWG operon laboratories, Ebersberg, Germany). Automatic annotation was performed and datas were manuall...
Data
Distribution of the genes specific to the six sequences strains. Phylogenetic tree of the R. solanacearum species complex along with the per-strain proportion of genes targeted by probes designed as specific to the GMI1000, CFBP2957, Molk2, IPO1609, CMR15 and PSI07 strains. (TIFF)
Data
CGH microarrays validation on R229 and UW551. Plot of the false-positive (blue), and false-negative (blue) calls from the CGH-microarrays on the UW551 (solid lines) and R229 (dashed lines) genomes depending on the cutoff used to define homology. (B) Pairwise homology of the CDS from the six sequenced genomes targeted by the same probe. (TIFF)
Article
Full-text available
Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool...
Data
Cold-spots and hot-spots of gene movement. Schematic representation of the cold-spots and hot-spots of gene movement along the genomes of the GMI1000, CFBP2957, CMR15 and PSI07 strains. Cold-spots are indicated in blue while hot-spots are indicated in red. Putative IS elements are represented with purple lines. On every genome, two tests (p-value <...
Data
Phylogenetic tree based on the 2,992 blocks of probes. Phylogenetic tree of the R. solanacearum species complex inferred using MrBayes and based on the hybridization results of 2,992 blocks of contiguous probes in the genomes and display the same evolutionary patterns. Strains used for the construction of the microarrays are in bold. Phylotype clas...
Article
Full-text available
Ralstonia solanacearum is a widespread and destructive plant pathogen. We present the genome of the type strain, K60 (phylotype IIA, sequevar 7). Sequevar 7 strains cause ongoing tomato bacterial wilt outbreaks in the southeastern United States. K60 generally resembles R. solanacearum CFBP2957, a Caribbean tomato isolate, but has almost 360 unique...
Article
Full-text available
The ancient soilborne plant vascular pathogen Ralstonia solanacearum has evolved and adapted to cause severe damage in an unusually wide range of plants. In order to better describe and understand these adaptations, strains with very similar lifestyles and host specializations are grouped into ecotypes. We used comparative genomic hybridization (CG...
Data
Overview of genomes in the R. solanacearum species complex. (XLS)
Article
Full-text available
The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease o...
Data
A: percentage of CDS in synteny and average number of CDS per synteny with PSI07 as reference strain. B: PSI07 chromosome and megaplasmid alignment with the complete genome of BDB and R. syzygii. (XLS)
Data
R. solanacearum virulence genes (updated from Remenant et al [3] ). (XLS)
Data
Gene expression patterns of specific functional clusters in GMI1000 and UW551 in planta vs. in rich medium, and their presence in Phylotype IV strains PSI07, BDB, and R. syzygii. (XLS)
Data
List of adhesins and hemagluttinins genes in sequenced strains from the R. solanacearum species complex. (XLS)
Data
Genomics Islands. Genomic Island predicted in CMR15 (sheet 1 and 2), CFBP2957 (sheet 3 and 4) and PSI07 (sheet 5 and 6) genomes.
Article
Full-text available
The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in R. solanacearum and strains with high genetic variation can...
Data
genomes overview. Main features of CMR15, CFBP2957, PSI07, GMI1000, Molk2 and IPO1609 genomes.
Data
strains (microarray). Strains used in CGH microarray experiments.
Data
new CDS GMI1000. New CDS detected in GMI1000 chromosome (sheet 1) and megaplasmide (sheet2).
Data
Metabolic pathways. Sheet A: class of each pathway class according to figure 6. Sheet B: Pathway completion.
Article
Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soil close to basal roots (core clods) and (iii) unpl...
Article
So far, the analysis of microbial populations associated with wheat monocropping-induced decline of take-all disease (Gaeumannomyces graminis var. tritici) has focused mainly on culturable biocontrol pseudomonads. The objective of this study was to develop a taxonomic rrs (16S rRNA gene) microarray to assess the changes in Pseudomonas populations t...
Article
Full-text available
Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize...

Citations

... The number of time series studies using metataxonomic or meta-omic approaches for the study of the dynamics of cheese microbiota is increasing (Choi et al., 2020;De Filippis et al., 2016;De Pasquale et al., 2014), and the lack of quantitative measurements of the target genes and the lack of metadata related to significant environmental variables (temperature, pH, a W , salt in moisture) prevents the use of model-based approaches for the inference of microbial interactions. In principle, using absolute quantification of the total amount of target (16S RNA or RNA gene) is possible, and has been attempted in a few studies (Cauchie et al., 2017;Fougy et al., 2016;Rouger et al., 2018;Zotta et al., 2019). However, only rarely have attempts been made to use these data to study the dynamics of members of the bacterial community . ...
... Both metagenomic analysis and identification of the isolates revealed that, even at the opening of packages, all the products presented high microbial load and a quite rich microbiota, generally dominated by LAB. This result is in agreement with data reported in the literature indicating the genera Leuconostoc, Carnobacterium, and Latilactobacillus as among the main colonizers of MAP and vacuum-packed cooked ham (Vasilopoulos et al., 2010;Iskandar et al., 2017;Raimondi et al., 2019;Candeliere et al., 2021). The 16S rRNA gene profiles were analyzed at the opening of packages and after 8 days of storing before samples became spoiled. ...
... Among other species, some strains displayed activities against Gram-negative bacteria and fungi, although the mechanisms have not been identified yet [28,29]. Moreover, a hybrid NRPS/PKS BGC was predicted in C. divergens V41 strain, but no product or biological activity has been linked to this cluster yet [30]. ...
... Other studies also reported similar findings showing that isolates of phylogroup A were the most prevalent E. coli isolates in animal intestinal tract [34,35]. The occurrence of group A and B1 in the raw chicken meat suggest that fecal contamination which may occur at any stage of processing could be a source of contamination [36]. Such possibilities may expose consumers to contaminated chicken meat and may increase the possibilities of acquiring foodborne illnesses especially if the meat is handled unhygienically and undercooked. ...
... Some strains can exhibit a partial Tagatose-6P pathway as exemplified by C. maltaromaticum 3.18 which lack a lacB homologue. It can be noticed that these lac homologues are dispersed in the genome and are likey involved in other cellular processes than lactose and galactose metabolism (Iskandar et al., 2016). ...
... Phylogenetic analyses of Ralstonia strains that cause wilt diseases revealed great genetic diversity (Genin and Denny 2012;Peeters et al. 2013;Prior et al. 2016). This group of organisms is referred to as the R. solanacearum species complex (RSSC). ...
... Annotated genomic nucleotide sequences are not accessible yet. A major part of its CDS-encoded proteins are classified as proteins of unknown function, 24% as enzymes, 20% represent transporters, regulators and factors, and 16% fall under components of cell processes and miscellaneous categories (March e et al. 2014). ...
... The slaughtering and butchering of food animals provide a wide range of micro-organisms introduced to meat surfaces as it contains abundant nutrients and water. It is argued that only a small portion (10%) of these microorganisms is capable of survival and proliferation during storage, distribution, and retail sales of meats (Remenant et al., 2015). Additionally, an even a smaller portion will eventually predominate and cause spoilage. ...
... tritici, il a été montré qu'une monoculture de blé sur plusieurs années réduit in fine l'impact du pathogène. Cette suppression de la maladie est liée à une modification de la composition microbienne du sol rhizosphérique (Sanguin et al., 2009) au cours du temps, favorisant la présence de certaines bactéries inhibitrices de la maladie telles que des populations du complexe d'espèces Pseudomonas fluorescens (Mazzola, 2002;Sanguin et al., 2008). ...
... Cluster analysis of orthologous genes showed that the clusters with translation, ribosomal structure, and biogenesis activity were the most stable in R. solanacearum, whereas the genes involved in motility, transcription, lipid transport, and metabolism showed high mobilities [91]. Gene clusters associated with pathogenicity and adaptation were highly unstable. ...