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[hal-05229886] Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome
Abstract Recent evidence indicates that the bacterial Rho helicase regulates Bacillus subtilis gene expression in a growth-dependent manner. This regulation, along with extensive in vivo trimming of Rho-dependent transcript 3′-ends, complicates the identification of Rho-dependent transcription terminators using standard transcriptomic approaches. To overcome this challenge, we applied Helicase-SELEX to precisely map Rho utilization (Rut) sites genome-wide. Using B. subtilis Rho (BsRho), we identified 600 putative Rut sites, while the more permissive Escherichia coli Rho (EcRho) revealed 4189 sites, including specimens known to regulate B. subtilis genes. Comparative analysis showed that both enzymes recognize similar pyrimidine-rich sequences, though BsRho favors short unstructured Rut motifs whereas EcRho can act on presumably more structured RNAs without requiring accessory factors. In vivo validation of selected Rut sites confirmed Rho-dependent regulation and extensive PNPase-mediated processing of Rho-terminated transcripts. Collectively, our results reveal a rich and complex Rho-dependent regulatory network in B. subtilis, encompassing the widespread control of antisense transcription and genes/operons of both primary and secondary metabolism. Although nonessential under standard laboratory conditions, Rho thus likely contributes to B. subtilis fitness and survival in more demanding environments. Our comprehensive compendium of Rut sites offers a valuable resource for exploring this adaptive regulatory landscape.
ano.nymous@ccsd.cnrs.fr.invalid (Mildred Delaleau) 29 Aug 2025
https://hal.science/hal-05229886v1
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[hal-02941029] Sulfiredoxin Protects Mice from Lipopolysaccharide-Induced Endotoxic Shock
Peroxiredoxins constitute a major family of cysteine-based peroxide-scavenging enzymes. They carry an intriguing redox switch by undergoing substrate-mediated inactivation via overoxidation of their catalytic cysteine to the sulfinic acid form that is reverted by reduction catalyzed by the sulfinic acid reductase sulfiredoxin (Srx). The biological significance of such inactivation is not understood, nor is the function of Srx1. To address this question, we generated a mouse line with a null deletion of the Srx1-encoding Srxn1 gene. We show here that Srxn1(-/-) mice are perfectly viable and do not suffer from any apparent defects under laboratory conditions, but have an abnormal response to lipopolysaccharide that manifests by increased mortality during endotoxic shock. Microarray-based mRNA profiles show that although the response of Srxn1(-/-) mice to lipopolysaccharide is typical, spanning all spectrum and all pathways of innate immunity, it is delayed by several hours and remains intense when the response of Srxn1(+/+) mice has already dissipated. These data indicate that Srx1 activity protects mice from the lethality of endotoxic shock, adding this enzyme to other host factors, as NRF2 and peroxiredoxin 2, which by regulating cellular reactive oxygen species levels act as important modifiers in the pathogenesis of sepsis.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Gaëlle Planson) 16 Sep 2020
https://hal.inrae.fr/hal-02941029v1
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[anses-03792909] Évaluation des risques en appui des mesures de gestion de produits dans la filière bovine, lors de suspicion et de confirmation de cas de botulisme
Le botulisme est une maladie neurologique humaine et animale provoquée par l’action de neurotoxines bactériennes (toxines botuliques) produites par des bactéries du genre Clostridium et qui se manifeste par des paralysies flasques pouvant aller jusqu’à la paralysie respiratoire et l’arrêt cardiaque. Il existe neuf types connus de toxines botuliques. Le botulisme animal en France concerne essentiellement les oiseaux (sauvages et domestiques) et les bovins. Les cas chez les bovins sont dus aux types mosaïque D/C (majoritaire), C, C/D et rarement au D. Au niveau national, l’incidence observée les 10 dernières années est en moyenne d’une dizaine de foyers par an. Bien qu’il s’agisse d’une maladie animale de première catégorie, il n’y a pas à l’heure actuelle de mesures de police sanitaire établies par la réglementation, lors de la confirmation d’un foyer de botulisme animal, ce qui conduit à une gestion au cas par cas par les directions départementales de la protection des populations (DDPP) et la mission des urgences sanitaires (MUS) de la DGAL. Ces services peuvent s’appuyer sur deux documents émis par l’Afssa : le rapport sur le botulisme animal établi en 2002 et l’avis rendu en janvier 2009 sur un projet d’arrêté fixant des mesures techniques et administratives relatives à la lutte contre le botulisme aviaire. Les rapports et avis cités étant relativement anciens, la DGAL a saisi l’Anses via 4 saisines (saisines 2019-SA-0112 à 2019-SA-0115), dont l’objet est une demande d’actualisation des connaissances et des évaluations de risque pour la santé humaine et/ou animale. L’expertise a été réalisée en deux étapes : 1. Une mise à jour des connaissances sur Clostridium botulinum (types C, D, mosaïques C/D et D/C et E) effectuée par le groupe de travail (GT) « Groupe socle botulisme », portant sur les caractéristiques microbiologiques, les maladies humaine et animale (bovins, oiseaux et poissons), la présence des différentes formes et types dans l’environnement, le danger dans les denrées alimentaires d’origine animale ainsi que l’efficacité des méthodes et procédés d’inactivation. 2. Le traitement des questions d’évaluation des risques par des groupes de travail spécifiques (« Botulisme bovin-aviaire » ; « Décontamination » ; « Faune sauvage et environnement »). La présente saisine porte sur l’évaluation des risques en appui des mesures de gestion de produits dans la filière bovine, lors de suspicion et de confirmation de cas de botulisme dans un troupeau. Les questions posées dans la saisine sont les suivantes : - « Quel est le risque pour l’Homme lié à la consommation de produits carnés ou laitiers provenant d’un bovin en incubation ou atteint de botulisme ? Le risque est-il différent selon les souches bactériennes et la population concernée (nourrissons, enfants, adultes, personnes fragiles) ? Comment l’état de santé des animaux influence-t-il le risque pour le consommateur final (importance relative entre la phase d’incubation et la phase clinique) ? - Quel est le risque potentiel associé aux produits carnés et laitiers issus des autres animaux du troupeau que ceux strictement malades ? Existe-t-il des moyens pour diminuer ce risque de contamination des produits ? - La manipulation de carcasses en abattoir d’un animal issu d’un lot de bovins atteints de botulisme mais dépourvus de signes cliniques présente-t-elle un risque pour les employés de contracter le botulisme ? Comment le maîtriser ? - Quelle est l’efficacité des différents traitements du lait sur les formes végétatives et sporulées (pasteurisation, traitement UHT, bactofugation, filtration membranaire) ? Dans quelle mesure peuvent-ils être considérés comme assainissant ?
ano.nymous@ccsd.cnrs.fr.invalid (Philippe Fravalo) 30 Sep 2022
https://anses.hal.science/anses-03792909v1
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[hal-05322292] High-Throughput Analysis of the Flagella FliK-Dependent Surfaceome and Secretome in Bacillus thuringiensis
Bacillus thuringiensis is a entomopathogenic member of the Bacillus cereus group, known for its resistance to host antimicrobial peptides (AMPs) and high virulence in insect models. While flagella are traditionally associated with motility, they also contribute to virulence through secretion systems. This study identifies FliK, a protein involved in flagellar hook length control, as a critical determinant of AMP resistance and virulence, independent of motility. A ∆fliK mutant exhibited heightened AMP sensitivity and reduced pathogenicity in Drosophila, unlike other flagella-deficient strains. Using LC-MS/MS, we conducted a comparative secretome and surfaceome analysis of the wild-type WT and ∆fliK strains. The ∆fliK mutant showed reduced secretion of virulence factors and an increase in cell wall remodeling proteins, pointing to a broader role for FliK in protein regulation and cell surface composition. These findings highlight FliK as a key regulator in B. thuringiensis pathogenesis and AMP resistance, offering new targets for investigating bacterial immune evasion mechanisms.
ano.nymous@ccsd.cnrs.fr.invalid (Carine Mouawad) 20 Oct 2025
https://hal.science/hal-05322292v1
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[hal-05347161] Intestinal hepcidin overexpression promotes iron deficiency anemia and counteracts iron overload via DMT1 downregulation
Hepcidin is the key hyposideremic hormone produced primarily by the liver. However, recent reports reveal extra-hepatic functional sources of hepcidin, including the intestine, the site of dietary iron absorption. To determine whether intestinal hepcidin may play a role in plasma iron lowering, we generated transgenic mice overexpressing the peptide specifically in this tissue. At one month of age, transgenic mice exhibited severe iron deficiency along with decreased haematological indices and a drastic suppression of liver hepcidin in response to hyposideremia. Mechanistically, we showed that intestinal hepcidin was produced in the intestine lumen, inducing a striking down-regulation of Divalent Metal Transporter 1 (DMT1) protein at the enterocyte. To confirm the capacity of hepcidin to decrease DMT1, we developed food-grade recombinant lactic acid bacteria (recLAB) genetically modified to deliver hepcidin directly into the intestinal lumen. These recLAB induced a rapid decrease of duodenal DMT1 and, most importantly, when daily orally administrated, protected against iron overload in a mouse model of hemochromatosis. Taken together, our data reveal a previously unrecognized role of intestinal hepcidin as a regulator of systemic iron homeostasis, acting on DMT1 on the apical side of enterocytes, with potential therapeutics relevance for haematological or iron disorders.
ano.nymous@ccsd.cnrs.fr.invalid (Marion Falabrègue) 04 Nov 2025
https://hal.inrae.fr/hal-05347161v1
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[hal-04492600] Transient inhibition of cell division in competent pneumococcal cells results from deceleration of the septal peptidoglycan complex
Bacterial cells are known to produce inhibitors of cell division in response to stress responses and developmental programs. Knowledge of the underlying molecular mechanisms remains however largely limited. In this study, we investigated the mechanism of transient cell division inhibition observed during the development of competence for transformation in the human pathogen Streptococcus pneumoniae . In this species, ComM, a membrane protein specifically produced during competence, transiently inhibits cell division to preserve genomic integrity during transformation. We show that ComM reduces specifically the dynamics of the septal peptidoglycan synthetic complex FtsW:PBP2x. We also present evidence that ComM interacts with the peptidoglycan precursor synthetic enzyme MurA, and show that overproduction of MurA suppresses FtsW:PBP2x deceleration along the cell division delay in competent cells. Collectively, our data support a model in which ComM interferes with MurA activity to reduce septal peptidoglycan synthesis during competence in S. pneumoniae .
ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 03 Sep 2025
https://hal.inrae.fr/hal-04492600v1
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[hal-05238621] Transient inhibition of cell division in competent pneumococcal cells results from deceleration of the septal peptidoglycan complex
Membrane protein ComM transiently inhibits cell division during the development of the competence state in the pathogenic bacterium Streptococcus pneumoniae , but the underlying molecular mechanisms remain unclear. Here we show that, in competent cells, ComM moves together with, and reduces the speed of, septal peptidoglycan synthetic complex FtsW:PBP2x. ComM directly interacts with the putative FtsW:PBP2x activator DivIB, and overproduction of DivIB counteracts FtsW:PBP2x deceleration along the cell division delay in competent cells. Our results support a model in which ComM reduces septal peptidoglycan synthesis by interfering with DivIB activity during competence in S. pneumoniae .
ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 03 Sep 2025
https://hal.science/hal-05238621v1
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[hal-02618848] Biopréservation et hautes pressions: des outils pour la maîtrise des dangers microbiologiques dans les aliments.
L'utilisation d’additifs conservateurs est souvent nécessaire pour assurer la sécurité microbiologique des produits carnés réfrigérés faiblement acides. Le projet ANR BLac HP (2014-2019) a étudié une nouvelle stratégie de stabilisation des produits carnés réfrigérés pour assurer le contrôle des flores indésirables à la fois végétatives et sporulées. Grâce à une approche pluridisciplinaire, les travaux ont montré que la combinaison de la biopréservation par des bactéries lactiques et d’un traitement hautes pressions permettait d’assurer la qualité microbiologique de dés de jambon cuits à teneur réduite en nitrite pendant toute leur durée de vie. Le traitement permet de plus une qualité sensorielle optimale sans impact environnemental supplémentaire par rapport au procédé conventionnel. Mots-clés: spores, jambon, nitrites.
ano.nymous@ccsd.cnrs.fr.invalid (Hélène Simonin) 25 May 2020
https://hal.inrae.fr/hal-02618848v1
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[hal-01607686] Diversity and Mechanisms of Genomic Adaptation in Penicillium
Penicillium is a diverse fungal genus with hundreds of species occurring worldwide in various substrates, from soil to food, and with various lifestyles, from necrotrophic pathogenicity to endophytic mutualism. Several species are important for human affairs, being widely used in industry, such as the penicillin-producer P. rubens, the two cheese starters P. camemberti and P. roqueforti, and the mould used for fermenting sausages, P. nalgiovense. Other species are food spoilers that produce harmful mycotoxins or cause damages in fruit crops. Currently, 30 genomes of Penicillium belonging to 18 species are available. In this chapter, we reconstruct a phylogenetic tree based on available Penicillium genomes and outline the main features of the genomes, such as gene and transposable element content. We then review the recent advances that the available genomic and transcriptomic resources in the Penicillium genus have allowed regarding our understanding of the genomic processes of adaptation, including changes in gene content, expression and strikingly frequent and recent horizontal gene transfers. In addition, we summarize recent studies using genetic markers on the level of genetic diversity, mode of reproduction and population structure within Penicillium species. Overall, the Penicillium genus appears a highly suitable model for studying the mechanisms of adaptation.
ano.nymous@ccsd.cnrs.fr.invalid (Jeanne Ropars) 03 Oct 2017
https://hal.science/hal-01607686v1
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[hal-01579131] Domestication of Lambda Phage Genes into a Putative Third Type of Replicative Helicase Matchmaker
At the onset of the initiation of chromosome replication, bacterial replicative helicases are recruited and loaded on the DnaA-oriC nucleoprotein platform, assisted by proteins like DnaC/DnaI or DciA. Two orders of bacteria appear, however, to lack either of these factors, raising the question of the essentiality of these factors in bacteria. Through a phylogenomic approach, we identified a pair of genes that could have substituted for dciA. The two domesticated genes are specific of the dnaC/dnaI-and dciA-lacking organisms and apparently domesticated from lambdoid phage genes. They derive from kO and kP and were renamed dopC and dopE, respectively. DopE is expected to bring the replicative helicase to the bacterial origin of replication, while DopC might assist DopE in this function. The confirmation of the implication of DopCE in the handling of the replicative helicase at the onset of replication in these organisms would generalize to all bacteria and therefore to all living organisms the need for specific factors dedicated to this function.
ano.nymous@ccsd.cnrs.fr.invalid (Pierre Brézellec) 30 Aug 2017
https://hal.sorbonne-universite.fr/hal-01579131v1
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[hal-04296513] Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Laura Di Lodovico) 20 Nov 2023
https://hal.inrae.fr/hal-04296513v1
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[hal-05380993] Correction: Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut – Le Microbiote Français Study
[This corrects the article DOI: 10.2196/64894.].
ano.nymous@ccsd.cnrs.fr.invalid (Chloe Connan) 25 Nov 2025
https://hal.science/hal-05380993v1
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[hal-04770329] Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets
This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal highfiber diets significantly alter the chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed overexpression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by the critical role of maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.
ano.nymous@ccsd.cnrs.fr.invalid (Smahane Chalabi) 07 Feb 2025
https://hal.science/hal-04770329v2
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[hal-03231028] Perturbed Microbiota/Immune Homeostasis in Multiple Sclerosis
Objective: Based on animal models and human studies, there is now strong suspicion that host/microbiota mutualism in the context of gut microbial dysbiosis could influence immunity and multiple sclerosis (MS) evolution. Our goal was to seek evidence of deregulated microbiota-induced systemic immune responses in patients with MS. Methods: We investigated gut and systemic commensal-specific antibody responses in healthy controls (n = 32), patients with relapsing-remitting MS (n = 30), and individuals with clinically isolated syndromes (CISs) (n = 15). Gut microbiota composition and diversity were compared between controls and patients by analysis of 16S ribosomal ribonucleic acid (rRNA) sequencing. Autologous microbiota and cultivable bacterial strains were used in bacterial flow cytometry assays to quantify autologous serum IgG and secretory IgA responses to microbiota. IgG-bound bacteria were sorted by flow cytometry and identified using 16S rRNA sequencing. Results: We show that commensal-specific gut IgA responses are drastically reduced in patients with severe MS, disease severity being correlated with the IgA-coated fecal microbiota fraction (r = -0.647, p < 0.0001). At the same time, IgA-unbound bacteria elicit qualitatively broad and quantitatively increased serum IgG responses in patients with MS and CIS compared with controls (4.1% and 2.5% vs 1.9%, respectively, p < 0.001). Conclusions: Gut and systemic microbiota/immune homeostasis are perturbed in MS. Our results argue that defective IgA responses in MS are linked to a breakdown of systemic tolerance to gut microbiota leading to an enhanced triggering of systemic IgG immunity against gut commensals occurring early in MS.
ano.nymous@ccsd.cnrs.fr.invalid (Delphine Sterlin) 20 May 2021
https://hal.sorbonne-universite.fr/hal-03231028v1
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[hal-04456282] Microalgal biofilms as a source of unexplored bioactive compounds: Anti-adhesive effect against bacterial pathogens
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Julia Mougin) 13 Feb 2024
https://hal.science/hal-04456282v1
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[hal-04412571] Bacterial adhesion inhibition by microalgal EPSs from Cylindrotheca closterium and Tetraselmis suecica biofilms
In the food industry, successful bacterial pathogen colonization and persistence begin with their adhesion to a surface, followed by the spatial development of mature biofilm of public health concerns. Compromising bacterial settlement with natural inhibitors is a promising alternative to conventional anti-fouling treatments typically based on chemical biocides that contribute to the growing burden of antimicrobial resistance. In this study, three extracellular polymeric substance (EPS) fractions extracted from microalgae biofilms of Cylindrotheca closterium (fraction C) and Tetraselmis suecica (fraction Ta rich in insoluble scale structure and fraction Tb rich in soluble EPS) were screened for their anti-adhesive properties, against eight human food-borne pathogens belonging to Escherichia coli, Staphylococcus aureus, Salmonella enterica subsp. enterica, and Listeria monocytogenes species. The results showed that the fraction Ta was the most effective inducing statistically significant reduction for three strains of E. coli, S. aureus, and L. monocytogenes. Overall, EPSs coating on polystyrene surfaces of the different fractions increased the hydrophilic character of the support. Differences in bacterial adhesion on the different coated surfaces could be explained by several dissimilarities in the structural and physicochemical EPS compositions, according to HPLC and ATR-FTIR analysis. Interestingly, while fractions Ta and Tb were extracted from the same microalgal culture, distinct adhesion patterns were observed, highlighting the importance of the extraction process. Overall, the findings showed that EPS extracted from microalgal photosynthetic biofilms can exhibit anti-adhesive effects against food-borne pathogens and could help develop sustainable and non-toxic anti-adhesive surfaces for the food industry. KEY POINTS: •EPSs from a biofilm-based culture of C. closterium/T. suecica were characterized. •Microalgal EPS extracted from T. suecica biofilms showed bacterial anti-adhesive effects. •The anti-adhesive effect is strain-specific and affects both Gram - and Gram + bacteria.
ano.nymous@ccsd.cnrs.fr.invalid (Julia Mougin) 23 Jan 2024
https://hal.inrae.fr/hal-04412571v1
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[hal-05005963] Illuminating microalgal biofilms using advanced photonic imaging techniques
<div xmlns="http://www.tei-c.org/ns/1.0"><p>This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Julia Mougin) 26 Mar 2025
https://hal.inrae.fr/hal-05005963v1
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[hal-04923152] Embedding a ribonuclease in the spore crust couples gene expression to spore development in <i>Bacillus subtilis</i>
Faced with nutritional stress, some bacteria form endospores capable of enduring extreme conditions for long periods of time; yet the function of many proteins expressed during sporulation remains a mystery. We identify one such protein, KapD, as a 3 -e x oribonuclease e xpressed under control of the mother cell-specific transcription factors SigE and SigK in Bacillus subtilis . KapD dynamically assembles o v er the spore surface through a direct interaction with the major crust protein CotY. KapD catalytic activity is essential for normal adhesiveness of spore surface layers. We identify the sigK mRNA as a k e y KapD substrate and and show that the st abilit y of this transcript is regulated by CotY-mediated sequestration of KapD. SigK is tightly controlled through e x cision of a prophage-lik e element, transcriptional regulation and the remo v al of an inhibitory prosequence. Our findings unco v er a f ourth, post-transcriptional la y er of control of sigK e xpression that couples late-stage gene e xpression in the mother cell to spore morphogenesis.
ano.nymous@ccsd.cnrs.fr.invalid (Alexandre d'Halluin) 31 Jan 2025
https://hal.inrae.fr/hal-04923152v1
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[hal-04314199] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les femmes dès la ménopause et les hommes de plus de 65 ans
Les bases scientifiques nécessaires à l’établissement des repères alimentaires du Programme National Nutrition Santé (PNNS) ont été actualisées par l’Anses en 2016 pour la population générale adulte sur la base des nouvelles références nutritionnelles et des données actuelles de consommation et de composition des aliment (Anses 2016c). Ces repères concernant la population générale, hommes et femmes adultes hors populations particulières, le Directeur général de la santé a saisi l’Anses le 12 juillet 2016 afin que des repères soient également énoncés pour les populations spécifiques que constituent les femmes enceintes et allaitantes, les enfants et adolescents, les personnes âgées et les femmes ménopausées. Le présent avis concerne la population spécifique des femmes dès la ménopause et des hommes de plus de 65 ans.
ano.nymous@ccsd.cnrs.fr.invalid (François Mariotti) 21 Dec 2023
https://hal.inrae.fr/hal-04314199v1
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[hal-02790439] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les enfants de 4 à 17 ans
Les bases scientifiques nécessaires à l’établissement des repères alimentaires du Programme National Nutrition Santé (PNNS) ont été actualisées par l’Anses en 2016 pour la population générale adulte sur la base des nouvelles références nutritionnelles et des données actuelles de consommation et de composition des aliment (Anses 2016d). Ces repères concernant la population générale, hommes et femmes adultes hors populations particulières, le Directeur général de la santé a saisi l’Anses le 12 juillet 2016 afin que des repères soient également énoncés pour les populations spécifiques que constituent les femmes enceintes et allaitantes, les enfants et adolescents et les personnes âgées et les femmes ménopausées. Le présent avis concerne la population spécifique des enfants âgés de 4 à 17 ans.
ano.nymous@ccsd.cnrs.fr.invalid (François Mariotti) 16 May 2024
https://hal.inrae.fr/hal-02790439v1
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[hal-04297740] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les enfants de 0 à 3 ans
Les bases scientifiques nécessaires à l’établissement des repères alimentaires du Programme National Nutrition Santé (PNNS) ont été actualisées par l’Anses en 2016 pour les hommes et femmes adultes sur la base des nouvelles références nutritionnelles et des données actuelles de consommation et de composition des aliments (Anses 2016b). Ces repères concernant la population générale, hommes et femmes adultes hors populations particulières, le Directeur général de la santé a saisi l’Anses le 12 juillet 2016 afin que des repères soient également énoncés pour les populations spécifiques que constituent les femmes enceintes et allaitantes, les enfants et adolescents et les personnes âgées et les femmes ménopausées. Le présent avis porte sur les enfants âgés de 0 à 3 ans.
ano.nymous@ccsd.cnrs.fr.invalid (François Mariotti) 21 Dec 2023
https://hal.inrae.fr/hal-04297740v1
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[hal-04314263] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les femmes enceintes ou allaitantes
Les bases scientifiques nécessaires à l’établissement des repères du Programme National Nutrition Santé (PNNS) ont été actualisées par l’Anses en 2016 pour la population générale adulte sur la base des nouvelles références nutritionnelles et des données récentes de consommation et de composition des aliments (Anses 2016b). Par ailleurs, l’activité physique a été traitée dans le rapport « Actualisation des repères du PNNS - Révisions des repères relatifs à l’activité physique et à la sédentarité », saisine n°2012-SA-0155, publié en 2016 (Anses 2016c). L’actualisation des repères alimentaires en vigueur dans le cadre du précédent PNNS 2011-2015 pour la population des femmes enceintes ou allaitantes se fonde sur l’analyse des recommandations existantes dans d’autres pays et sur les relations épidémiologiques entre la consommation de groupes d’aliments et la santé des femmes enceintes ou allaitantes et de leur enfant. Le présent avis porte sur les femmes enceintes et allaitantes dont la grossesse ne présente pas de risque particulier et n’est pas qualifiée de pathologique. Les risques liés à la consommation d’alcool par les femmes enceintes ou allaitantes ne sont pas traités dans le cadre de cet avis car c’est une question spécifique, indépendante des autres facteurs alimentaires, qui a fait l’objet d’évaluation et de procédure de gestion récentes (Santé publique France 2017).
ano.nymous@ccsd.cnrs.fr.invalid (François Mariotti) 21 Dec 2023
https://hal.inrae.fr/hal-04314263v1
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[hal-04649763] MAIT cells monitor intestinal dysbiosis and contribute to host protection during colitis
Intestinal inflammation shifts microbiota composition and metabolism. How the host monitors and responds to such changes remains unclear. Here, we describe a protective mechanism by which mucosal-associated invariant T (MAIT) cells detect microbiota metabolites produced upon intestinal inflammation and promote tissue repair. At steady state, MAIT ligands derived from the riboflavin biosynthesis pathway were produced by aerotolerant bacteria residing in the colonic mucosa. Experimental colitis triggered luminal expansion of riboflavin-producing bacteria, leading to increased production of MAIT ligands. Modulation of intestinal oxygen levels suggested a role for oxygen in inducing MAIT ligand production. MAIT ligands produced in the colon rapidly crossed the intestinal barrier and activated MAIT cells, which expressed tissue-repair genes and produced barrier-promoting mediators during colitis. Mice lacking MAIT cells were more susceptible to colitis and colitis-driven colorectal cancer. Thus, MAIT cells are sensitive to a bacterial metabolic pathway indicative of intestinal inflammation.
ano.nymous@ccsd.cnrs.fr.invalid (Yara El Morr) 10 Oct 2024
https://hal.science/hal-04649763v1
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[hal-01204360] Two unrelated episodes of Bacillus cereus bacteremia in a neonatal intensive care unit
absent
ano.nymous@ccsd.cnrs.fr.invalid (Nalini Rama Rao) 27 May 2020
https://hal.science/hal-01204360v1
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[hal-05237608] Membrane vesicles of the food grade bacteria L. helveticus stimulate autophagy in vitro and in vivo in aged mice
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Agnès Bringer) 03 Sep 2025
https://hal.inrae.fr/hal-05237608v1
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[hal-05237727] Membrane vesicles of the food grade bacteria L. helveticus stimulate autophagy in vitro and in vivo in aged mice
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Agnès Bringer) 03 Sep 2025
https://hal.inrae.fr/hal-05237727v1
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[hal-05237544] Membrane vesicles of the food grade bacteria L. helveticus stimulate autophagy in vitro and in vivo in aged mice
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Agnès Bringer) 03 Sep 2025
https://hal.inrae.fr/hal-05237544v1
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[hal-03364386] Parasites and diet as main drivers of the Malagasy gut microbiome richness and function
Abstract Interactions between the prokaryotic microbiome and eukaryotic parasites in the vertebrate gut may affect overall host health and disease. While intertropical areas exhibit a high rate of parasites carriers, such interactions are understudied in these populations. Our objectives were to (1) describe the gut microbiome of individuals living in Madagascar, (2) identify potential associations between bacterial taxa and parasites colonizing the digestive tract and (3) highlight main determinants of the gut microbiota composition in this developing country. Metadata (socioeconomic, diet, clinical) and fecal samples were collected from 219 volunteers from North-West Madagascar (Mahajanga). Fecal microbiome was assessed through 16S rRNA gene sequencing and metabolomics, and related to dietary habits and parasites carriage. We highlight important Malagasy gut microbiome peculiarities. Out of three detected enterotypes, only one is similar to that observed in Westernized countries ( Ruminococcus -driven). Functions associated with the two others ( Clostridium sensu stricto-driven and Escherichia/Shigella -driven) are mostly directed toward amino acids biosynthesis and degradation, respectively. Diet and protozoan carriage were the main drivers of microbiota composition. High protozoan carriage was associated with higher diversity, richness and microbial functionalities. The gut microbiome of Malagasy strongly differs from that of Westernized countries. Asymptomatic protozoan carriage and dietary habits are the external factors with the deepest impact on gut microbiome. Further studies are needed to understand whether gut microbial richness constitute a predilection niche for protozoans colonization, due to their gazing features, or whether the parasites themselves induce a higher bacterial richness.
ano.nymous@ccsd.cnrs.fr.invalid (Stanislas Mondot) 15 Mar 2024
https://hal.science/hal-03364386v1
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[hal-01003303] Identification of Critical Genes for Growth in Olive Brine by Transposon Mutagenesis of Lactobacillus pentosus C11
Olive brine represents a stressful environment due to the high NaCl concentration, presence of phenolic compounds known as antimicrobials, and low availability of nutrients. Thus, only a few strains of lactic acid bacteria (LAB) are adapted to grow in and ferment table olives. To identify the mechanisms by which these few strains are able to grow in olive brine, Lactobacillus pentosus C11, a particularly resistant strain isolated from naturally fermented table olives, was mutagenized by random transposition using the P-junc-TpaseIS1223 system (H. Licandro-Seraut, S. Brinster, M. van de Guchte, H. Scornec, E. Maguin, P. Sansonetti, J. F. Cavin, and P. Serror, Appl. Environ. Microbiol. 78:5417-5423, 2012). A library of 6,000 mutants was generated and screened for adaptation and subsequent growth in a medium, named BSM (brine screening medium), which presents the stressful conditions encountered in olive brine. Five transposition mutants impaired in growth on BSM were identified. Transposition occurred in two open reading frames and in three transcription terminators affecting stability of transcripts. Thus, several essential genes for adaptation and growth of L. pentosus C11 in olive brine were identified.
ano.nymous@ccsd.cnrs.fr.invalid (G. Perpetuini) 10 Jun 2014
https://hal.science/hal-01003303v1
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[hal-05193520] The microbiologist's guide to metaproteomics
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative ( www.metaproteomics.org ), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state‐of‐the‐art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.
ano.nymous@ccsd.cnrs.fr.invalid (Tim van den Bossche) 30 Jul 2025
https://hal.inrae.fr/hal-05193520v1
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[hal-05237415] Membrane vesicles of the food grade bacteria L. helveticus stimulate autophagy in vitro and in vivo in aged mice
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Agnès Bringer) 03 Sep 2025
https://hal.inrae.fr/hal-05237415v1
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[hal-04223303] A 14-3-3γ dimer-based scaffold bridges CtBP1-S/BARS to PI(4)KIIIβ to regulate post-Golgi carrier formation
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Carmen Valente) 29 Sep 2023
https://hal.inrae.fr/hal-04223303v1
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[hal-04315646] Identification of a Bacillus thuringiensis gene that positively regulates transcription of the phosphatidylinositol-specific phospholipase C gene at the onset of the stationary phase
A transcriptional analysis of the phosphatidylinositol-specific phospholipase C (plcA) gene of Bacillus thuringiensis indicated that its transcription was activated at the onset of the stationary phase in B. thuringiensis but was not activated in B. subtilis. The B. thuringiensis gene encoding a transcriptional activator required for plcA expression was cloned by using a B. subtilis strain carrying a chromosomal plcA'-'lacZ fusion as a heterologous host for selection. This trans activator (designated PlcR) is a protein of a calculated molecular weight of 33,762 which appears to be distantly related to PreL and NprA, regulator proteins enhancing transcription of neutral protease genes during the stationary phase of a Lactobacillus sp. and B. stearothermophilus, respectively. plcR gene transcription was analyzed in B. thuringiensis and in B. subtilis. PlcR positively regulated its own transcription at the onset of the stationary phase. There is a highly conserved DNA sequence (17 bp) 34 nucleotides upstream from the plcR transcriptional start site and 49 nucleotides upstream from the plcA transcriptional start site. As PlcR positively regulates its own transcription and plcA transcription, this conserved DNA sequence may be the specific recognition target for PlcR activation.
ano.nymous@ccsd.cnrs.fr.invalid (Didier Lereclus) 30 Nov 2023
https://hal.inrae.fr/hal-04315646v1
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[hal-04315617] A recombinase-mediated system for elimination of antibiotic resistance gene markers from genetically engineered Bacillus thuringiensis strains
A TnpI-mediated site-specific recombination system to construct genetically modified Bacillus thuringiensis strains was developed. Recombinant B. thuringiensis strains from which antibiotic resistance genes can be selectively eliminated were obtained in vivo with a new vector based on the specific resolution site of transposon Tn4430. For example, a cryIC gene, whose product is active against Spodoptera littoralis, was introduced into B. thuringiensis Kto harboring a cryIA(c) gene active against Ostrinia nubilalis. The resulting strain had a broader activity spectrum than that of the parental strain. It contained only B. thuringiensis DNA and was free of antibiotic resistance genes. This should facilitate regulatory approval for its development as a commercial biopesticide.
ano.nymous@ccsd.cnrs.fr.invalid (V Sanchis) 30 Nov 2023
https://hal.inrae.fr/hal-04315617v1
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[hal-04841808] Méthodes d’évaluation des risques sanitaires et environnementaux et des enjeux socio-économiques associés aux plantes obtenues au moyen de certaines nouvelles techniques génomiques (NTG)
Depuis le 1er janvier 2022, conformément à l’ordonnance n° 2021-1325 du 13 octobre 2021 et au décret n° 2021-1905 du 30 décembre 2021, l’Anses reprend les missions du Haut conseil des biotechnologies (HCB) concernant l’évaluation des risques pour l’environnement de l’ensemble des utilisations de biotechnologies en milieu ouvert, et les impacts socioéconomiques. L’Anses a été saisie dans le cadre de ces nouvelles missions par la Direction générale de la prévention des risques (DGPR) et la Direction générale de l’alimentation (DGAl) sur l’utilisation des nouvelle techniques génomiques (NTG) sur les végétaux. Les autres instances ayant repris les missions du HCB, à savoir le Conseil économique, social et environnemental (CESE) et le Comité consultatif national d’éthique (CCNE), ont également été sollicité sur cette question sur les périmètres correspondant respectivement aux questions sociétales et éthiques. Par ailleurs, il convient de noter que de nombreux acteurs institutionnels publics, organisations professionnelles et syndicales ont également produit des rapports sur les NTG. Le rapport d’expertise collective est réalisé dans le périmètre des missions de l’Anses sur les biotechnologies, incluant l’évaluation des risques sanitaires et environnementaux et les impacts socio-économiques. Il vise à éclairer les demandeurs sur ce périmètre qui couvre seulement une partie des enjeux liés à l’utilisation des NTG dans le domaine de la sélection végétale. Les questions instruites dans ce rapport sont donc limitées à ce périmètre et les conclusions devront être prises en compte uniquement dans ce cadre et mises en perspective avec les avis des autres instances sollicitées. Il convient de noter que cette expertise a été engagée avant la proposition de règlement de la Commission du 5 juillet 20231. Suite à sa publication, l’Anses a décidé de s’autosaisir afin de mener une analyse des critères définissant les plantes NTG de catégorie 1, considérées comme équivalentes aux plantes conventionnelles, exposés dans l’annexe 1 et justifiés par une note technique diffusée par la Commission européenne en octobre (Anses 2023). Cette analyse a été réalisée en parallèle et ses conclusions n’ont donc pas été prises en compte dans le présent travail d’expertise, réalisé dans le cadre du périmètre défini précédemment, qui ne fait pas la distinction entre les plantes NTG de catégorie 1 et 2.
ano.nymous@ccsd.cnrs.fr.invalid (Michel Gautier) 16 Dec 2024
https://cnrs.hal.science/hal-04841808v1
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[hal-05379552] Microbiote néonatal et comportement alimentaire chez l’adulte
In our study published in 2021 (Pocheron et al. 2021), we investigated the influence of the maternal gut microbiota on the programming of offspring feeding behavior, independently of genetic and metabolic factors. The gut microbiota is known to play a key role in the regulation of metabolism and feeding behaviors, particularly in the context of obesity and eating disorders. While correlations between microbiota alterations and behavioral changes are well established, the long-term programming effects of the microbiota remain largely hypothetical. From a theoretical perspective, early-life disruptions of the microbiota — induced by birth mode, diet, medical treatments, or maternal transmission — could have lasting impacts on feeding behavior. Two principal mechanisms have been proposed: either behavior is directly influenced by the metabolic properties of the microbiota, or the microbiota interferes with the neurodevelopment of systems involved in behavioral regulation. Our findings, together with recent evidence, indicate that early microbiota disturbances can leave lasting effects, even if microbial composition returns to baseline in adulthood. This supports the existence of a critical window of vulnerability during early life, in which microbial metabolites may influence neurodevelopment and contribute to long-term behavioral modulation.
ano.nymous@ccsd.cnrs.fr.invalid (Patricia Parnet) 24 Nov 2025
https://hal.science/hal-05379552v1
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[hal-02987130] Intestinal release of biofilm-like microcolonies encased in calcium-pectinate beads increases probiotic properties of Lacticaseibacillus paracasei
In this study, we show that calcium pectinate beads (CPB) allow the formation of 20 µm spherical microcolonies of the probiotic bacteria Lacticaseibacillus paracasei (formerly designated as Lactobacillus paracasei) ATCC334 with a high cell density, reaching more than 10 log (CFU/g). The bacteria within these microcolonies are well structured and adhere to a three-dimensional network made of calcium-pectinate through the synthesis of extracellular polymeric substances (EPS) and thus display a biofilm-like phenotype, an attractive property for their use as probiotics. During bacterial development in the CPB, a coalescence phenomenon arises between neighboring microcolonies accompanied by their peripheral spatialization within the bead. Moreover, the cells of L. paracasei ATCC334 encased in these pectinate beads exhibit increased resistance to acidic stress (pH 1.5), osmotic stress (4.5 M NaCl), the freeze-drying process and combined stresses, simulating the harsh conditions encountered in the gastrointestinal (GI) tract. In vivo, the oral administration of CPB-formulated L. paracasei ATCC334 in mice demonstrated that biofilm-like microcolonies are successfully released from the CPB matrix in the colonic environment. In addition, these CPB-formulated probiotic bacteria display the ability to reduce the severity of a DSS-induced colitis mouse model, with a decrease in colonic mucosal injuries, less inflammation, and reduced weight loss compared to DSS control mice. To conclude, this work paves the way for a new form of probiotic administration in the form of biofilm-like microcolonies with enhanced functionalities.
ano.nymous@ccsd.cnrs.fr.invalid (Arnaud Heumann) 08 Jun 2021
https://institut-agro-dijon.hal.science/hal-02987130v1
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[hal-02789820] Modulation of autophagy by probiotic bacteria: selecting and engineering strains able to stimulate autophagy in intestinal epithelial cells
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Jana Al Azzaz) 05 Jun 2020
https://hal.inrae.fr/hal-02789820v1
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[hal-05237123] The food grade bacterium Lactobacillus helveticus VEL12193 promotes autophagy by releasing membrane vesicles
Autophagy-related processes, including canonical macroautophagy, are crucial for maintaining cellular homeostasis in eukaryotic organisms. Alterations or reduced activity of these processes have been strongly linked to a broad range of human diseases including inflammatory bowel disease (IBD) and age-related diseases such as age-related macular degeneration - a disease that affect the central area of the retina. In contrast, long-term autophagy stimulation appears to be safe and to extend lifespan in model organisms such as mice. Thus, enhancing autophagy represents a promising strategy for promoting healthy aging. Several studies indicate that the gut microbiota can influence host autophagy at the gut mucosa but also in peripheral organs, and some microbial metabolites have been identified as autophagy modulators. In this study, we studied the capacity of bacterial species commonly used in food fermentation (ferments) or health (probiotics) to modulate host autophagy by in vitro and in vivo approaches. In vitro screening of a library of 11 bacterial strains revealed a strain-dependent ability of lactobacilli and bifidobacteria to stimulate autophagy in human epithelial cells. The Lactobacillus helveticus strain VEL12193, isolated from cheese, emerged as the most effective inducer of autophagy. In vivo experiment using mice showed that long-term dietary supplementation with L. helveticus VEL12193 was associated with stimulation of autophagy in the gut mucosa and retina. We identified L. helveticus -derived membrane vesicles (MVs) as a bacterial component involved in bacterial-induced autophagy in epithelial and immune cells. Moreover, in vitro , we demonstrated that L. helveticus VEL12193 possesses immunomodulatory properties in macrophages, as well as in the gut mucosa of a preclinical mouse model of IBD. With this study we provide robust proof of concept that ferments/probiotics can stimulate autophagy at the organism scale and that this phenotype involved MVs. In addition, we identify L. helveticus VEL12193 as a candidate strain of interest for the design of healthy-aging strategies.
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Agnès Bringer) 03 Sep 2025
https://hal.inrae.fr/hal-05237123v1
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[hal-00453479] Listeria monocytogenes EGD-e biofilms: no mushrooms but a network of knitted chains.
Listeria monocytogenes is a food pathogen that can attach on most of the surfaces encountered in the food industry. Biofilms are three-dimensional microbial structures that facilitate the persistence of pathogens on surfaces, their resistance toward antimicrobials, and the final contamination of processed goods. So far, little is known about the structural dynamics of L. monocytogenes biofilm formation and its regulation. The aims of this study were, by combining genetics and time-lapse laser-scanning confocal microscopy (LSCM), (i) to characterize the structural dynamics of L. monocytogenes EGD-e sessile growth in two nutritional environments (with or without a nutrient flow), and (ii) to evaluate the possible role of the L. monocytogenes agr system during biofilm formation by tracking the spatiotemporal fluorescence expression of a green fluorescent protein (GFP) reporter system. In the absence of nutrient flow (static conditions), unstructured biofilms composed of a few layers of cells that covered the substratum were observed. In contrast, when grown under dynamic conditions, L. monocytogenes EGD-e biofilms were highly organized. Indeed, ball-shaped microcolonies were surrounded by a network of knitted chains. The spatiotemporal tracking of fluorescence emitted by the GFP reporter system revealed that agr expression was barely detectable under static conditions, but it progressively increased during 40 h under dynamic conditions. Moreover, spatial analysis revealed that agr was expressed preferentially in cells located outside the microcolonies. Finally, the in-frame deletion of agrA, which encodes a transcriptional regulator, resulted in a decrease in initial adherence without affecting the subsequent biofilm development.
ano.nymous@ccsd.cnrs.fr.invalid (Aurélie Rieu) 04 Feb 2010
https://hal.science/hal-00453479v1
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[hal-02625154] Binding activity to intestinal cells and transient colonization in mice of two <em>Lactobacillus paracasei</em> subsp. <em>paracasei</em> strains with high aggregation potential
Surface properties like hydrophobicity, aggregation ability, adhesion to mucosal surfaces and epithelial cells and transit time are key features for the characterization of probiotic strains. In this study, we used two Lactobacillus paracasei subsp. paracasei strains (BGNJ1-64 and BGSJ2-8) strains which were previously described with very strong aggregation capacity. The aggregation promoting factor (AggLb) expressed in these strains showed high level of binding to collagen and fibronectin, components of extracellular matrix. The working hypothesis was that strains able to aggregate have an advantage to resist in intestinal tract. So, we assessed whether these strains and their derivatives (without aggLb gene) are able to bind or not to intestinal components and we compared the transit time of each strains in mice. In that purpose parental strains (BGNJ1-64 and BGSJ2-8) and their aggregation negative derivatives (BGNJ1-641 and BGSJ2-83) were marked with double antibiotic resistance in order to be tracked in in vivo experiments in mice. Comparative analysis of binding ability of WT and aggregation negative strains to different human intestinal cell lines and mucin revealed no significant difference among them, excluding involvement of AggLb in interaction with surface of intestinal cells and mucin. In vivo experiments showed that surviving and transit time of marked strains in mice did not drastically depend on the presence of the AggLb aggregation factor.
ano.nymous@ccsd.cnrs.fr.invalid (Marija Miljković) 26 May 2020
https://hal.inrae.fr/hal-02625154v1
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[hal-02627688] Point-of-need dna testing for detection of foodborne pathogenic bacteria
Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.
ano.nymous@ccsd.cnrs.fr.invalid (Jasmina Vidic) 26 May 2020
https://hal.inrae.fr/hal-02627688v1
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[hal-01432554] Biofilms of Lactobacillus plantarum and Lactobacillus fermentum: effect on stress responses, antagonistic effects on pathogen growth and immunomodulatory properties
Few studies have extensively investigated probiotic functions associated with biofilms. Here, we show that strains of Lactobacillus plantarum and Lactobacillus fermentum are able to grow as biofilm on abiotic surfaces, but the biomass density differs between strains. We performed microtiter plate biofilm assays under growth conditions mimicking to the gastrointestinal environment. Osmolarity and low concentrations of bile significantly enhanced Lactobacillus spatial organization. Two L. plantarum strains were able to form biofilms under high concentrations of bile and mucus. We used the agar well-diffusion method to show that supernatants from all Lactobacillus except the NA4 isolate produced food pathogen inhibitory molecules in biofilm. Moreover, TNF-alpha production by LPS-activated human monocytoid cells was suppressed by supernatants from Lactobacillus cultivated as biofilms but not by planktonic culture supernatants. However, only L. fermentum NA4 showed anti-inflammatory effects in zebrafish embryos fed with probiotic bacteria, as assessed by cytokine transcript level (TNF-alpha, IL-1 beta and IL-10). We conclude that the biofilm mode of life is associated with beneficial probiotic properties of lactobacilli, in a strain dependent manner. Those results suggest that characterization of isolate phenotype in the biofilm state could be additional valuable information for the selection of probiotic strains.
ano.nymous@ccsd.cnrs.fr.invalid (Nabil Aoudia) 11 Jan 2017
https://ube.hal.science/hal-01432554v1
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[hal-05268449] Therapeutic Manipulation of the Immune System: Enhancement of Innate and Adaptive Mucosal Immunity
The mucosal immune system has evolved alongside, but separate, from the general systemic immune system. As a major consequence of this dichotomy, only immune responses initiated in mucosal inductive sites can result in effective immunity in mucosal tissues themselves. Oral tolerance, as usually assessed as orally-induced systemic unresponsiveness, contributes to mucosal homoeostasis by preventing unwanted immune reactions to food or environmental antigens. It is now established that tolerance can also be induced by the nasal route and mucosally-induced tolerance is being actively investigated for immune therapy against a number of diseases. Nontoxic derivatives of cholera toxin and the heat labile toxin of Escherichia coli as well as chimeric enterotoxins have been developed. These molecules retain the mucosal adjuvant activity of native enterotoxins and are effective at inducing targeted Th1 or Th2- type immune responses. Mucosal delivery of cytokines as adjuvants represents a safer alternative to parenteral cytokine injection. Nasally administered cytokines such as IL-1 and IL-12 or chemokines including RANTES, lymphotactin, MIP-1 beta, all act as mucosal adjuvants for co-administered antigens. Each of these cytokines promote specific pattern of CD4(+) T helper cell cytokine responses that could be exploited for targeted immune therapy. Although GALT and NALT are both parts of the Common Mucosal Immune System, there are major differences between orally and nasally induced immune responses. Nasal vaccines more effectively promote protective immunity in the genitourinary tract than do oral vaccines. In addition, aging affects mucosal tolerance or immunity in GALT more than is seen in NALT. Therapeutic manipulation of mucosal immunity involves regulation of CD4(+) T cell cytokine responses and thus, should require a careful examination of the host status, including the occurrence of inflammatory bowel diseases.
ano.nymous@ccsd.cnrs.fr.invalid (Prosper Boyaka) 19 Sep 2025
https://hal.inrae.fr/hal-05268449v1
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[hal-01004227] First steps of bacteriophage SPP1 entry into Bacillus subtilis
The mechanism of genome transfer from the virion to the host cytoplasm is critical to understand and control the beginning of viral infection. The initial steps of bacteriophage SPP1 infection of the Gram-positive bacterium Bacillus subtilis were monitored by following changes in permeability of the cytoplasmic membrane (CM). SPP1 leads to a distinctively faster CM depolarization than the one caused by podovirus phi 29 or myovirus SP01 during B. subtilis infection. Depolarization requires interaction of SPP1 infective virion to its receptor protein YueB. The amplitude of depolarization depends on phage input and concentration of YueB at the cell surface. Sub-millimolar concentrations of Ca2+ are necessary and sufficient for SPP1 reversible binding to the host envelope and thus to trigger depolarization while DNA delivery to the cytoplasm depends on millimolar concentrations of this divalent cation. A model describing the early events of bacteriophage SPP1 infection is presented. (C) 2011 Elsevier Inc. All rights reserved.
ano.nymous@ccsd.cnrs.fr.invalid (Lina L. Jakutyte) 11 Jun 2014
https://hal.science/hal-01004227v1
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[hal-01001506] Bacteriophage SPP1 infection of [i]Bacillus subtilis[/i]: evidence for a preferential polar route for entry in a Gram-positive bacterium
absent
ano.nymous@ccsd.cnrs.fr.invalid (Lina L. Jakutyte) 04 Jun 2014
https://hal.science/hal-01001506v1
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[hal-01607430] Yamadazyma barbieri f.a. sp nov., an ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (-2300m) and marine coastal waters
Two yeast strains that are members of the same species were isolated from different marine habitats, i.e. one from Mid-Atlantic Ridge ocean water samples located in the direct vicinity of black smokers near the Rainbow deep-sea hydrothermal vent and one from Brazilian marine water samples off the Ipanema beach. Strains CLIB 1964(T) and CLIB 1965 are anamorphic ascomycetous yeasts affiliated to the Yamadazyma clade of Saccharomycetales. Interestingly, these strains were phylogenetically and distinctly positioned into a group of species comprising all species of the genus Yamadazyma isolated from marine habitats including deep-sea hydrothermal vents, i.e. Candida atmosphaerica, C. spencermartinsiae, C. atlantica, C. oceani and C. taylorii. These strains differed significantly in their D1/D2 domain sequences of the LSU rRNA gene from the closely related species mentioned above, by 2.6, 3.0, 3.4, 3.8 and 6.0 %, respectively. Internal transcribed spacer region sequence divergence was also significant and corresponded to 4.6, 4.7, 4.7, 12.0 and 24.7% with C. atlantica, C. atmosphaerica, C. spencermartinsiae, C. oceani and C. taylorii, respectively. Phenotypically, strains CLIB 1964(T) and CLIB 1965 could be distinguished from closely related species by their inability to assimilate L-sorbose. CLIB 1964(T) (= CBS 14301(T) = UBOCC-A-214001(T)) is the designated type strain for Yamadazyma barbieri sp. nov. The MycoBank number is MB 815884.
ano.nymous@ccsd.cnrs.fr.invalid (Gaetan Burgaud) 03 Oct 2017
https://hal.science/hal-01607430v1
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[hal-04792909] Enterobacterales carrying chromosomal AmpC β-lactamases in Europe (EuESCPM): Epidemiology and antimicrobial resistance burden from a cohort of 27 hospitals, 2020–2022
Introduction: The ESCPM group (Enterobacter species including Klebsiella aerogenes - formerly Enterobacter aerogenes, Serratia species, Citrobacter freundii complex, Providencia species and Morganella morganii) has not yet been incorporated into systematic surveillance programs. Methods: We conducted a multicentre retrospective observational study analysing all ESCPM strains isolated from blood cultures in 27 European hospitals over a 3-year period (2020-2022). Diagnostic approach, epidemiology, and antimicrobial susceptibility were investigated. Results: Our study comprised 6,774 ESCPM isolates. MALDI-TOF coupled to mass spectrometry was the predominant technique for bacterial identification. Susceptibility to new β-lactam/β-lactamase inhibitor combinations and confirmation of AmpC overproduction were routinely tested in 33.3% and 29.6% of the centres, respectively. The most prevalent species were E. cloacae complex (44.8%) and S. marcescens (22.7%). Overall, third-generation cephalosporins (3GC), combined third- and fourth-generation cephalosporins (3GC + 4GC) and carbapenems resistance phenotypes were observed in 15.7%, 4.6%, and 9.5% of the isolates, respectively. AmpC overproduction was the most prevalent resistance mechanism detected (15.8%). Among carbapenemase-producers, carbapenemase type was provided in 44.4% of the isolates, VIM- (22.9%) and OXA-48-enzyme (16%) being the most frequently detected. E. cloacae complex, K. aerogenes and Providencia species exhibited the most notable cumulative antimicrobial resistance profiles, with the former displaying 3GC, combined 3GC + 4GC and carbapenems resistance phenotypes in 15.2%, 7.4%, and 12.8% of the isolates, respectively. K. aerogenes showed the highest rate of both 3GC resistant phenotype (29.8%) and AmpC overproduction (32.1%), while Providencia species those of both carbapenems resistance phenotype (42.7%) and carbapenemase production (29.4%). ESCPM isolates exhibiting both 3GC and combined 3GC + 4GC resistance phenotypes displayed high susceptibility to ceftazidime/avibactam (98.2% and 95.7%, respectively) and colistin (90.3% and 90.7%, respectively). Colistin emerged as the most active drug against ESCPM species (except those intrinsically resistant) displaying both carbapenems resistance phenotype (85.8%) and carbapenemase production (97.8%). Conclusions: This study presented a current analysis of ESCPM species epidemiology in Europe, providing insights to inform current antibiotic treatments and guide strategies for antimicrobial stewardship and diagnostics.
ano.nymous@ccsd.cnrs.fr.invalid (Matteo Boattini) 20 Nov 2024
https://hal.science/hal-04792909v1
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[hal-01004585] Bacteriophage Infection in Rod-Shaped Gram-Positive Bacteria: Evidence for a Preferential Polar Route for Phage SPP1 Entry in Bacillus subtilis
Entry into the host bacterial cell is one of the least understood steps in the life cycle of bacteriophages. The different envelopes of Gram-negative and Gram-positive bacteria, with a fluid outer membrane and exposing a thick peptidoglycan wall to the environment respectively, impose distinct challenges for bacteriophage binding and (re)distribution on the bacterial surface. Here, infection of the Gram-positive rod-shaped bacterium Bacillus subtilis by bacteriophage SPP1 was monitored in space and time. We found that SPP1 reversible adsorption occurs preferentially at the cell poles. This initial binding facilitates irreversible adsorption to the SPP1 phage receptor protein YueB, which is encoded by a putative type VII secretion system gene cluster. YueB was found to concentrate at the cell poles and to display a punctate peripheral distribution along the sidewalls of B. subtilis cells. The kinetics of SPP1 DNA entry and replication were visualized during infection. Most of the infecting phages DNA entered and initiated replication near the cell poles. Altogether, our results reveal that the preferentially polar topology of SPP1 receptors on the surface of the host cell determines the site of phage DNA entry and subsequent replication, which occurs in discrete foci.
ano.nymous@ccsd.cnrs.fr.invalid (Lina L. Jakutyte) 11 Jun 2014
https://hal.science/hal-01004585v1
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[pasteur-01977322] Minimum Information about an Uncultivated Virus Genome (MIUViG)
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
ano.nymous@ccsd.cnrs.fr.invalid (Simon Roux) 10 Jan 2019
https://pasteur.hal.science/pasteur-01977322v1
