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[hal-05142580] Rapid adaptation of Bacillus thuringiensis to alkaline environments via the L-lactate metabolism pathway regulated by the CRP/FNR family regulator LtmR
Bacillus thuringiensis (Bt) is an entomopathogenic bacterium. During infection, Bt often encounters alkaline conditions in the insect midgut and adaptation to this alkaline environment is crucial for its survival and establishment. Here, we investigated the mechanisms of rapid adaptation of Bt to an alkaline environment. DNA microarray revealed 739 downregulated genes and 662 upregulated genes in the presence of 28 mM NaOH for 10 min relative to the condition without alkaline treatment. The activities of some primary metabolic pathways of Bt were enhanced under alkaline conditions, and many genes related to synthesis and transportation of amino acids, nucleic acids, and cell surfaces were significantly induced. In particular, ldh2 (HD73_5189) and lpm1 (HD73_0686), which encode lactate dehydrogenase and lactate permease, respectively, were significantly upregulated. Transcription of ldh2 and lpm1 was directly regulated by the CRP/FNR family transcriptional regulator, LtmR (L-lactate transport and metabolism regulator), through binding between LtmR and their promoters. The intracellular concentration of pyruvate increased and that of lactate decreased under alkaline conditions. Following deletion of ldh2, the concentration of pyruvate decreased, and that of lactate increased, suggesting that ldh2 catalyzes the conversion of lactate to pyruvate. ltmR, ldh2, and lpm1 were shown to contribute to Bt virulence in Ostrinia furnacalis. Collectively, these data indicate that the pyruvate-L-lactate metabolic pathway is important for Bt adaptation and virulence in alkaline environments. Homologues of LtmR are highly conserved in B. cereus group, suggesting that they share a similar strategy for pH adaptation.
ano.nymous@ccsd.cnrs.fr.invalid (Qi Peng) 03 Jul 2025
https://hal.inrae.fr/hal-05142580v1
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[hal-04754706] Le microbiome humain à l’épreuve de l’anthropocène
Si les effets délétères des activités humaines sur la biodiversité du monde végétal et animal et sur le climat sont un fait acquis, leur impact sur la biodiversité microbienne doit être urgemment considéré, particulièrement sur le microbiome humain. La révolution métagénomique permet une large analyse et un suivi spatio-temporels jusqu’à présent inenvisageables. Une réduction de la richesse et de la diversité des microbiotes humains, en particulier intestinaux, est maintenant avérée, surtout dans les aires industrialisées de la planète. Utilisation inconsidérée des antibiotiques, changements drastiques des régimes alimentaires et éléments restant à déterminer de l’exposome environnemental sont le plus souvent incriminés. En découlent des situations de dysbioses caractérisées par une érosion du cœur d’espèces microbiennes communes à tous les individus et une prolifération de pathobiontes opportunistes, sans doute due à un affaiblissement de l’effet de barrière du microbiome. Le défi actuel est d’établir un lien de causalité entre ces dysbioses et des maladies en émergence épidémique, bien que non transmissibles, comme l’asthme, l’allergie, les maladies auto-immunes, l’obésité, le diabète et certains cancers. Modèles expérimentaux et études cliniques contrôlées prospectives et interventionnelles sont indispensables pour consolider cette causalité, d’autant que dans le déchiffrage des altérations de la symbiose homme-microbiome se profile un nouveau chapitre de la médecine : la « médecine microbienne »
ano.nymous@ccsd.cnrs.fr.invalid (Philippe J Sansonetti) 26 Oct 2024
https://hal.science/hal-04754706v1
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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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[hal-05168922] A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research
The gut microbiome comprises trillions of microorganisms and profoundly influences human health by modulating metabolism, immune responses and neuronal functions. Disruption in gut microbiome composition is implicated in various inflammatory conditions, metabolic disorders and neurodegenerative diseases. However, determining the underlying mechanisms and establishing cause and effect is extremely difficult. Preclinical models offer crucial insights into the role of the gut microbiome in diseases and help identify potential therapeutic interventions. The Human Microbiome Action Consortium initiated a Delphi survey to assess the utility of preclinical models, including animal and cell-based models, in elucidating the causal role of the gut microbiome in these diseases. The Delphi survey aimed to address the complexity of selecting appropriate preclinical models to investigate disease causality and to study host–microbiome interactions effectively. We adopted a structured approach encompassing a literature review, expert workshops and the Delphi questionnaire to gather insights from a diverse range of stakeholders. Experts were requested to evaluate the strengths, limitations, and suitability of these models in addressing the causal relationship between the gut microbiome and disease pathogenesis. The resulting consensus statements and recommendations provide valuable insights for selecting preclinical models in future studies of gut microbiome-related diseases.
ano.nymous@ccsd.cnrs.fr.invalid (Amira Metwaly) 18 Jul 2025
https://hal.inrae.fr/hal-05168922v1
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[hal-05193143] Hematopoietic MyD88 orchestrates the control of gut colonization by segmented filamentous bacteria
Host-microbiota cooperation is critical for successful intestinal homeostasis. The commensal segmented filamentous bacteria (SFB) are crucial for orchestrating the post-natal maturation of the host gut immune system and establishing a healthy state of physiological inflammation, which largely depends on their intimate attachment to the ileal mucosa. However, the signaling pathways used by SFB to induce gut immune responses and how such responses ultimately control SFB colonization remain controversial. Using gnotobiotic approaches, we showed that SFB load is controlled by complex interactions involving the gut microbiota and the host immune system. Therefore, to clearly determine the role of host immune responses induced by SFB in directly controlling their growth, immunodeficient mice monocolonized with SFB were used. Here, we show that in the absence of a complex microbiota, the humoral immune response is dispensable to control SFB growth in the jejunum and ileum, shortly and later after colonization. In contrast, MyD88 signaling in myeloid cells is critical for licensing interleukin (IL)-22 production by type 3 innate lymphoid cells (ILC3) and CD4 + T cells, which ultimately limits SFB expansion. Thus, by revisiting the hierarchy of immune mechanisms that directly control SFB growth, our results emphasize the necessary and sufficient role of a hematopoietic MyD88/IL-22 axis.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Cherrier) 30 Jul 2025
https://hal.inrae.fr/hal-05193143v1
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[hal-05191105] Complementary killing activities of Pbunavirus LS1 and Bruynoghevirus LUZ24 phages on planktonic and sessile Pseudomonas aeruginosa PAO1 derivatives
Four active against a representative panel of Pseudomonas aeruginosa strains were chosen with the goal of using them for phage therapy. Two were belonging to the Pbunavirus LS1 species, and two to the Bruynoghevirus LUZ24 species. The receptor of the P. LS1 phage Ab27 had already been characterized as the O-antigen chain of the lipopolysaccharides, whereas no information was available at the onset of this work on the receptor used by the B. LUZ24 phages. We show that this receptor is the surface polysaccharide Psl, an important component of the biofilm matrix. Remarkably, the B. LUZ24 phages were more active against PAO1 in minimal medium compared to rich medium. This was correlated with larger amounts of Psl bound at the bacterial surface during exponential growth in minimal medium, compared to the rich medium. Phages prevented biofilm growth when applied early after biofilm formation on a medical endotracheal tube, as well as in 96-well plates, and acted more slowly on mature biofilms. No biofilm overgrowth was observed when applying the two phage species combination, over a 48 h period of imaging by confocal microscopy. Genetic mutants resistant to each phage arose at a frequency of 10 −5 to 10 −6 per generation, and most P. LS1 -resistant mutants were sensitized to the B. LUZ24 phage. The combination of the selected phages has promising properties that are relevant in the framework of phage therapy.
ano.nymous@ccsd.cnrs.fr.invalid (Maud Billaud) 29 Jul 2025
https://hal.inrae.fr/hal-05191105v1
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[hal-03351311] Enterococcus faecalis Maltodextrin Gene Regulation by Combined Action of Maltose Gene Regulator MalR and Pleiotropic Regulator CcpA
Enterococcus faecalis represents a leading cause of hospital-acquired infections worldwide. Several studies highlighted the importance of carbohydrate metabolism in the infection process of this bacterium. The genes required for maltodextrin metabolism are particularly induced during mouse infection and, therefore, should play an important role for pathogenesis. Since no data were hitherto available concerning the regulation of expression of the maltodextrin operons, we have conducted experiments to study the underlying mechanisms.
ano.nymous@ccsd.cnrs.fr.invalid (Maxime Grand) 22 Sep 2021
https://hal.inrae.fr/hal-03351311v1
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[hal-05133341] Adaptation factors of SalmonellaTyphimurium, 1,4,[5],12:i:-and Dublin serovars to disinfection in the pig/pork and dairy industries : characterization of strain diversity and mechanisms of persistence
Biocides are routinely used in food processing industries to control microbial contamination. Despite their proven effectiveness, some Salmonella spp. strains exhibit environmental persistence, surviving and reappearing even after stringent sanitation measures. Various tolerance mechanisms and adaptative pathways have been described for Enterobacteriaceae, particularly in foodborne pathogens. However, the specific mechanisms of Salmonella adaptation to these environments and the genetic determinants associated with its persistence despite cleaning and disinfection remain unclear. The current study aims 1/to decipher the increased potential of Salmonella strains for biocides tolerance and biofilm formation, and 2/develop a fast molecular tool to identify the strains with high survival potential. The genomic and phenotypical diversity of three distinct serovars of Salmonella (Typhimurium, its monophasic variant and Dublin) will be examined using a collection of 935 strains isolated in France between 2017 and 2024 from both the pig/pork and dairy production chains. Genes known as involved in biocides tolerance and biofilm production will be identified and characterized. Building on these results, a representative panel of 300 strains will be selected to investigate their phenotypic response to biocides in biofilm models, close to conditions undergone by bacteria on food processing chains. Finally, Association Studies will be conducted to identify possible new genetic markers involved in strain adaptation in food processing plants. The results will shed light on the potential presence of persistent Salmonella strains (Typhimurium, 1,4,[5],12:i:-, and Dublin) which are prevalent in the French pig/pork and dairy product sectors. This study will identify and describe genes implicated in persistence within the Salmonella populations of both sectors. The genetic markers identified will then be used to develop a molecular tool detecting strains capable of surviving in food processing plants. This test will assist the food industry in decision-making to improve sanitation measures and control Salmonella in the pig/pork and dairy product industries.
ano.nymous@ccsd.cnrs.fr.invalid (Grandjean Hugo) 04 Jul 2025
https://hal.science/hal-05133341v1
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[hal-04820676] Guided assembly of multispecies positive biofilms targeting undesirable bacteria
The use of synthetic microbial communities (SynComs) engineered to form positive biofilms that prevent the settlement of harmful bacteria is emerging as a promising strategy in biotechnology, particularly in reducing reliance on chemical antimicrobials. Despite this potential, the rationale for selecting specific strains in SynComs and the mechanisms underlying their antagonistic effects remains insufficiently understood. In this study, we present a bottom-up approach integrating live-cell imaging with high-throughput analysis of multi-strain biofilms across diverse scenarios. Through this method, we identified beneficial strains based on their superior ability to exclude undesirable bacteria and form mixed biofilms. Notably, our findings revealed that competitive strains against undesirable bacteria could also exclude other beneficial strains, emphasising the need for compatibility control in SynComs design. SynComs composed of B. velezensis and Pediococcus spp. demonstrated enhanced pathogen exclusion compared to single strains. Temporal analysis of biofilm interactions, supported by mathematical models, showed that pathogen exclusion was primarily driven by nutritional competition (Jameson effect) with additional specific interference mechanisms (prey-predator Lotka-Volterra model). Furthermore, pre-establishing SynComs to surfaces significantly increased pathogen inhibition, indicating a distinct biofilm-associated exclusion effect. These insights offer a framework for rational SynCom design and deepen our understanding of the mechanisms underpinning positive biofilm applications.
ano.nymous@ccsd.cnrs.fr.invalid (Virgile Guéneau) 05 Dec 2024
https://hal.inrae.fr/hal-04820676v1
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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-05193373] ZnO-nanostructured electrochemical sensor for efficient detection of glyphosate in water
Glyphosate is a widely used broad-spectrum herbicide for controlling grassy weeds, despite having potential health hazards. Herein, we report on a solid-state electrochemical sensor based on ZnO nanoparticles (ZnO NPs) for on-site detection of glyphosate. Accordingly, ZnO NPs was drop-cast on the surface of a disposable screenprinted carbon electrode. Eco-friendly ZnO NPs of only 7 nm crystallite sizes were obtained by green sol-gel synthesis using lemon (Citrus limon) waste aqueous extract as the green reducing and capping/stabilizing agent and Zn nitrate precursor as evidenced by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction and diffuse reflectance. SEM confirmed successful electrode functionalization with the synthesized nanoparticles. Under laboratory conditions in acetate buffer (pH 5), the sensor demonstrated excellent selectivity and sensitivity, with a detection limit of 0.648 µM, a wide linear detection range (0.5 µM to 7.5 mM), and a rapid detection time of 30 min. When tested in river water, the sensor achieved a detection limit of 0.96 µM using differential pulse voltammetry. It also exceptionally tolerated interference from similar organophosphorus compounds and ions commonly found in river water. The excellent detection performance of the sensor was attributed to the strong coordination interactions between Zn atoms and phosphonate/carboxylate groups that are enhanced by a hydrogen bond at acidic pH, as determined by chemical calculations. This disposable sensor offers a cost-effective, efficient, and environmentally friendly solution for monitoring glyphosate in water systems.
ano.nymous@ccsd.cnrs.fr.invalid (Zorica Novakovic) 30 Jul 2025
https://hal.inrae.fr/hal-05193373v1
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[hal-05193026] Novel RNA viruses in a commercial colony of Tenebrio molitor
Insect mass rearing for food and feed purposes is rapidly expanding in response to the current increase in protein demand. The mass reared insect strains are characterized by interactions with microorganisms, including viruses, that can be either beneficial or pathogenic and might lead to improved or decreased host health. The yellow mealworm, Tenebrio molitor, is a coleopteran species mainly reared for food and feed purposes showing high susceptibility to the Tenebrio molitor densovirus (TmDNV), which can lead to the loss of the entire population in a few days. The potential effect of viruses on mass-reared yellow mealworm highlights the need to screen for additional insect viruses associated with this insect species. In this study, we described and characterized five novel viruses associated with a European commercial T. molitor strain: Tenebrio molitor virga-like virus 1 (TmViLV1), Tenebrio molitor virga-like virus 2 (TmViLV2), Tenebrio molitor iflavirus 1 (TmIV1), Tenebrio molitor tombusvirus 1 (with two segments) (TmToV1), and Tenebrio molitor associated narnavirus 1 (TmAsNaV1). Then, we assessed the prevalence of these viruses in T. molitor samples derived from T. molitor rearings located worldwide. Assessing host-virus interactions aids in unravelling the effect of viruses on insect development, giving insights into possible implications for mass-rearing facilities.
ano.nymous@ccsd.cnrs.fr.invalid (Luis Hernández-Pelegrín) 30 Jul 2025
https://hal.inrae.fr/hal-05193026v1
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[anses-05192491] To be rough or not to be? An overview of Salmonella Agona genome and biofilm diversity
Background: Salmonella enterica serovar Agona ranks among the 30 most commonly isolated food Salmonella serovars globally and has been linked to recent outbreaks in Europe, United States and Australia. Known for its biofilm-forming capabilities, S. Agona poses a significant threat to food safety. This study explored the genomic diversity and biofilm forming ability of major S. Agona clones isolated in France along the food chain, from poultry and dairy products until humans. Methods : From a collection of 233 strains S. Agona isolates, we performed core SNP phylogeny (Snippya) and pangenome characterization (Panaroob), with a focus on the resistome (Abricatec) and plasmidome (MOBsuited). For macroscopy assays, a representative panel of S. Agona strains were grown on Luria–Bertani medium (LB) without NaCl (WS), supplemented with Congo red and Coomassie. Confocal laser scanning microscopy was performed on submerged biofilms in diluted (1/20) LB-WS. Results and discussion : Genomic analyses revealed that the French poultry sector and the dairy products are dominated by a clonal population of S. Agona strains belonging to the MLST profile ST13 with some clones capable to infect humans. This clonal group exhibited high genome plasticity, with some strains carrying up to three different plasmids and elements such as the Salmonella Genomic Island 4. Furthermore, poultry-associated strains harbored a higher prevalence of antibiotic resistance genes, likely reflecting greater antibiotic exposure in poultry farming compared to dairy production. The macroscopic biofilm assays demonstrated an equal proportion of cellulose-producing and deficient morphotypes, with only a small fraction of strains lacking curli production. The microscopic assays revealed planktonic cells motility and adhesion differences correlated to cellulose secretion between strains, along with variations in the three-dimensional biofilm structure. Interestingly, the planktonic cells motility was associated to isolates origins with human strains more mobile than non-humans, possibly indicating adaptation of the S. Agona strains to their environment. This study highlighted the presence within food environments of persistent clones with a virulence potential. Biofilm formation appeared as an element associated to virulence and persistence of the clones circulating in France. These findings highlight the transmission of S. Agona through agro-food systems to human, providing insights for control strategies and public health risk reduction.
ano.nymous@ccsd.cnrs.fr.invalid (Grandjean Hugo) 30 Jul 2025
https://anses.hal.science/anses-05192491v1
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[hal-05192588] Chemometric study of the effects of the geographical origin and the collection period on the chemical compositions and the antimicrobial activities of Pituranthos tortuosus essential oils
The present study aims to analyze the chemometric variation of the chemical composition of the aerial part’s essential oils of Pituranthos tortuosus , collected from different regions from Tunisia (Majoura and Sened (Gafsa), Sbeitla (Kasserine), and Eljem (Mahdia)) during the period from February to June and to assess their antimicrobial activity. The different samples of the aerial parts of P. tortuosus were hydrodistillated during 4 h. The obtained essential oils were analyzed by GC/FID and GC/MS techniques. The antimicrobial activity of these essential oils samples was evaluated in vitro using Petri dishes against Staphylococcus aureus subsp . aureus , Pseudomonas aeruginosa , Escherichia coli , and Candida albicans . The obtained results showed that the yields of all essential oils were ranging from 0.42 to 0.77 %. They differ significantly ( p ≤ 0.01) with the regions of collection. The chromatographic analysis of these essential oils displayed different chemical compositions leading to the identification of eight chemotypes. The majority of their chemical compounds differ significantly with the collection regions ( p ≤ 0.05). The studied antimicrobial effects of the essential oils revealed significant differences ( p ≤ 0.02) with the collection region. All the essential oils displayed an important antimicrobial effect against S. aureus and C. albicans .
ano.nymous@ccsd.cnrs.fr.invalid (Zina Benissa) 30 Jul 2025
https://hal.inrae.fr/hal-05192588v1
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[hal-05192923] Turning residues into valuable compounds: organic waste conversion into odd-chain fatty acids via the carboxylate platform by recombinant oleaginous yeast
Environmental concerns are rising the need to find cost-effective alternatives to fossil oils. In this sense, short-chain fatty acids (SCFAs) are proposed as carbon source for microbial oils production that can be converted into oleochemicals. This investigation took advantage of the outstanding traits of recombinant Yarrowia lipolytica strains to assess the conversion of SCFAs derived from real digestates into odd-chain fatty acids (OCFA). High yeast OCFAs content was aimed by using two engineered strains (Y. lipolytica JMY7780 and JMY7782). Batch and two-step batch fermentations were performed, reaching high lipid content (40.8% w/w) and lipid yield (0.07 g/g) with JMY7782, which overexpresses propionyl-CoA synthase. Fed-batch fermentation with an acetic acid pulse after 24 h was also carried out to promote SCFAs consumption and OCFAs production. In this case, SCFAs consumption rate increased and JMY7782 was able to accumulate up to 60.4% OCFAs of the total lipids produced from food waste-derived carbon sources.
ano.nymous@ccsd.cnrs.fr.invalid (Marta de Vicente) 30 Jul 2025
https://hal.inrae.fr/hal-05192923v1
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[hal-05193443] Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts
Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.
ano.nymous@ccsd.cnrs.fr.invalid (Tamsin A Redgwell) 30 Jul 2025
https://hal.inrae.fr/hal-05193443v1
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[hal-05192522] Extracellular DNA filaments associated with surface polysaccharide II give Clostridioides difficile biofilm matrix a network-like structure
Clostridioides difficile is an anaerobic, spore-forming, Gram-positive bacterium, and a leading cause of healthcare-associated intestinal infections. Recurrences occur frequently, most of them being relapses. Apart from spores, C. difficile biofilm is hypothesized as a reservoir for relapses. Thus, increased knowledge on in vitro biofilm formation and characteristics is required. We finely characterized the matrix components in 4 C. difficile strains. Confocal microscopy revealed for the first time the presence of eDNA filaments connecting bacteria, with a spider's web-like organization. Biofilm disruption with DNase I suggests that eDNA, even in low abundance, plays a key role in the biofilm scaffold, maintaining biofilm cohesion by connecting bacteria. Observation of strong overlapping staining, particularly in the highest biofilm-producing strain tested between eDNA and polysaccharide II or lipoprotein CD1687, suggests that interactions between these components may enhance biofilm cohesion. Whereas autolysis does not appear to be a major way of matrix component release under our conditions, eDNA was sometimes associated with lipidic round shapes that can evoke vesicle structures. Together, these results suggest that the bacterial aggregation and structuring of the C. difficile biofilm involve several components of the matrix, including eDNA, interacting with each other to build the scaffold of biofilm.
ano.nymous@ccsd.cnrs.fr.invalid (Tania Kamwouo) 30 Jul 2025
https://hal.inrae.fr/hal-05192522v1
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[hal-03343060] Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases which can substitute the classical, bacterial RecA and manage the DNA metabolism at different steps of phage propagation. SSAPs have been shown to efficiently promote recombination between short and rather divergent DNA sequences and were exploited for in vivo genetic engineering mainly in Gram-negative bacteria. In opposition to the conserved and almost universal bacterial RecA protein, SSAPs display great sequence diversity. The importance for SSAPs in phage biology and phage-bacteria evolution is underlined by their role as key players in events of horizontal gene transfer (HGT). All of the above provoke a constant interest for the identification and study of new phage recombinase proteins in vivo , in vitro as well as in silico . Despite this, a huge body of putative ssap genes escapes conventional classification, as they are not properly annotated. In this work, we performed a wide-scale identification, classification and analysis of SSAPs encoded by the Firmicutes bacteria and their phages. By using sequence similarity network and gene context analyses, we created a new high quality dataset of phage-related SSAPs, substantially increasing the number of annotated SSAPs. We classified the identified SSAPs into seven distinct families, namely RecA, Gp2.5, RecT/Redβ, Erf, Rad52/22, Sak3, and Sak4, organized into three superfamilies. Analysis of the relationships between the revealed protein clusters led us to recognize Sak3-like proteins as a new distinct SSAP family. Our analysis showed an irregular phylogenetic distribution of ssap genes among different bacterial phyla and specific phages, which can be explained by the high rates of ssap HGT. We propose that the evolution of phage recombinases could be tightly linked to the dissemination of bacterial phage-resistance mechanisms (e.g., abortive infection and CRISPR/Cas systems) targeting ssap genes and be a part of the constant phage-bacteria arms race.
ano.nymous@ccsd.cnrs.fr.invalid (P. Nicolas) 13 Sep 2021
https://hal.inrae.fr/hal-03343060v1
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[hal-05156716] The Microbial Anti-Inflammatory Molecule (MAM) is a key protein processed and exported to Faecalibacterium duncaniae envelope
MAM (Microbial-Anti-Inflammatory Molecule) is a key effector protein with anti-inflammatory properties in Faecalibacterium duncaniae, a critical human gut microbiota species. Despite its importance, MAM function and molecular features remain poorly understood. This study elucidates MAM’s physiological importance by examining its cellular localization, secretion dynamics, and structural organization. Mass spectrometry and immunogold labeling confirmed MAM as the most abundant protein in the cell envelope and the second most abundant in the overall proteome, localizing it to the bacterial surface. Bioinformatic and in silico analyses suggest that MAM contains an N-terminal leader peptide with motifs recognized by a Peptidase-domain-Containing ABC Transporter (PCAT), enabling cargo transport to the cell envelope. After N-terminal excision, the cargo protein could be transported to the cell envelope via this PCAT, where it could assemble into a hexameric structure, as revealed by docking and AlphaFold3 modeling. Such results were supported by electron microscopy showing a lattice-like organization on the bacterial surface. This work introduces a novel discussion about the singular organization of the F. duncaniae cell envelope, having MAM as a key component for the bacteria, supporting the understanding of the unique biology of F. duncaniae and its potential as a next-generation probiotic or live biotherapeutic.
ano.nymous@ccsd.cnrs.fr.invalid (Thaís Vilela Rodrigues) 10 Jul 2025
https://hal.science/hal-05156716v1
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[hal-05137649] Effect of bacterial nanocellulose and plant-containing facial serum on hyperpigmentation in in-vitro conditions
This study investigated the effect of some herbal extracts, such as licorice root, white mulberry leaf, green tea leaf, and grape seed, with a combination of bacterial nanocellulose and some bioactive materials, such as ascorbic acid, niacinamide, hexylresorcinol, and alpha-arbutin, on treatment of hyperpigmentation. The effect of the prepared emulsions on hyperpigmentation was revealed by analyzing their tyrosinase inhibition properties, their ability to stop melanin production, or their properties of whitening the brown spot on the skin. In addition to the physicochemical properties of the 5 different emulsions obtained, tyrosinase, collagenase, and elastase enzyme activities, antioxidant properties, cytotoxicity, and microbiological analyzes were performed by cell-culture modelling. Finally, a dermocosmetic facial serum was designed that is compatible with skin pH, is homogeneously mixed, has good spreading properties, does not cause any microbiological growth, does not inhibit elastase activity while stimulating collagenase activity, reduces melanin production by inhibiting the tyrosinase enzyme, and does not have any toxic effects.
ano.nymous@ccsd.cnrs.fr.invalid (Sibel Dikmen Kucuk) 01 Jul 2025
https://hal.science/hal-05137649v1
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[hal-03732430] Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology.
ano.nymous@ccsd.cnrs.fr.invalid (Tyler W. Doughty) 21 Jul 2022
https://hal.science/hal-03732430v1
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[hal-05107337] An anti-virulence drug targeting the evolvability protein Mfd protects against infections with antimicrobial resistant ESKAPE pathogens
The increasing incidence of antibiotic resistance and the decline in the discovery of novel antibiotics have resulted in a global health crisis, particularly, for the treatment of infections caused by Gram-negative bacteria, for which therapeutic dead-ends are alarming. Here, we identify and characterize a molecule, NM102, that displays antimicrobial activity exclusively in the context of infection. NM102 inhibits the activity of the non-essential Mutation Frequency Decline (Mfd) protein by competing with ATP binding to its active site. Inhibition of Mfd by NM102 sensitizes pathogenic bacteria to the host immune response and blocks infections caused by the clinically-relevant bacteria Klebsiella pneumoniae and Pseudomonas aeruginosa, without inducing host toxicity. Finally, NM102 inhibits the mutation and evolvability function of Mfd, thus reducing the bacterial capacity to develop antimicrobial resistance. These data provide a potential roadmap for the development of drugs to combat antimicrobial resistance.
ano.nymous@ccsd.cnrs.fr.invalid (Seav-Ly Tran) 11 Jun 2025
https://hal.science/hal-05107337v1
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[anses-05157590] Marked reduction of SARS-CoV-2 infection and improved recovery following supplementation with a probiotic mix of four strains and two strains of Bifidobacterium breve in hamsters
Only a few studies have shown that certain probiotics have beneficial effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In this study, two strains of Bifidobacterium breve , CNCM I-5644 and CNCM I-5979, selected for their in vitro immunomodulatory properties demonstrated in a screening of 20 strains and a mixture of 4 probiotic strains selected based on its immunomodulatory and antiviral properties were evaluated in a hamster model of SARS-CoV-2 infection. Supplementation with these probiotics (7 days before plus 7 days after infection) reduced SARS-CoV-2 infection with a significantly reduced viral load in the upper respiratory tract and lungs and improved weight recovery. Probiotics also counteracted the increase in inflammatory markers and intestinal permeability. The impact of these probiotics was independent of microbiota composition and short-chain fatty acid production. Overall, these data suggest that the probiotics tested, in particular the mix containing Bifidobacterium longum LA101, Lactobacillus helveticus LA102, Lactococcus lactis LA103, and Streptococcus thermophilus LA104, can facilitate recovery from SARS-CoV-2 infection (as shown by weight regain in infected hamsters) by reducing viral load and inflammation. Our study investigated the potential benefits of specific probiotics in fighting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19). We tested two strains of Bifidobacterium breve selected based on their immune-boosting properties, along with a commercial mix of four probiotic strains chosen for its antiviral and immune-modulating effects. These probiotics were administered to hamsters over a week before and a week after infection. Supplementation with these probiotics significantly reduced the viral load in the upper respiratory tract and lungs, promoting recovery as demonstrated by the weight regain observed. In addition to reducing viral presence, the probiotics also helped lower inflammation and improved gut health by counteracting increased intestinal permeability. Our findings suggest that probiotics, particularly the mix of four strains, could support recovery from SARS-CoV-2 infection by reducing inflammation, viral load, and enhancing overall health.
ano.nymous@ccsd.cnrs.fr.invalid (Edgar Torres-Maravilla) 11 Jul 2025
https://anses.hal.science/anses-05157590v1
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[hal-05191232] Prevalence and Characterization of Staphylococcus aureus Isolated from Meat and Milk in Northeastern Italy
Staphylococcus aureus is a pathogenic microorganism often found in animal-derived foods and is known for its ability to readily develop resistance to antibiotic treatments. This study was designed to determine the prevalence of S. aureus strains in raw milk and meat in Italy and to evaluate their antibiotic resistance profiles and biofilm production. Among the meat isolates, 41.67% were resistant to ampicillin, and 25% were methicillin-resistant S. aureus (MRSA). In milk, 20% of the isolates were resistant to gentamycin, while 5.71% were MRSA. The prevalence of multidrug-resistant strains was higher in meat (16.67%) compared to milk (5.71%). The biofilm formation capability was assessed in most of the isolates (80% in milk and 100% in meat). Representative strains exhibiting different antibiotic resistance profiles were all negative for the enterotoxin genes sea, seb, sec, sed, and see, but harbored potential virulence factors such as hemolytic activity, high pigmentation, low cell envelop permeability, charged and hydrophobicity. Finally, the interaction of representative strains with human Caco-2 intestinal cell line showed that most strains had an adhesion capacity. Our findings reveal that foodborne isolates of S. aureus present a considerable threat to consumers due to their production of virulence factors, which enhance their pathogenicity and increase the likelihood of antibiotic treatment failures.
ano.nymous@ccsd.cnrs.fr.invalid (Debora Pinamonti) 29 Jul 2025
https://hal.inrae.fr/hal-05191232v1
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[hal-05191306] Histoire naturelle des allergies alimentaires non IgE-médiées
Non-IgE-mediated food allergies are adverse immune reactions to certain food allergens that are spe- cific for a given individual, but do not involve specific serum IgE antibodies. They mainly affect infants and young children. They include allergic proctocolitis, food protein-induced enterocolis syndrome (FPIES), allergic enteropathy, aspecific digestive dysmotility (e.g., severe reflux, constipation) and certain eosinophilic oesophagitis (EoE) responding to the avoidance diet. The most common allergen involved is cow’s milk, but other foods may be responsible, particularly in breast-fed infants, although this is rare. The main symptoms are haematochezia in allergic proctocolitis, acute vomiting with pallor and hypotonia in FPIES, stunted growth and chronic diarrhoea in allergic enteropathy, and reflux with feeding difficulties in infantile EoE. Eviction-reintroduction of the suspected allergen is used as a diagnostic test in aller- gic proctocolitis and enteropathy. In FPIES, there is a clinical definition. For EoE, histological analysis of oesophageal biopsies makes the diagnosis after elimination of differential diagnoses. Treatment involves avoiding the allergen responsible until tolerance is acquired. With the exception of EoE, the course of the disease is favourable in the first 2–3 years of life. There is a risk of developing functional intestinal disorders and atopic diseases. EoE is a chronic disease, with possible cases of remission in paediatrics. The main complications are oesophageal stenosis, food impaction and oesophageal perforation.
ano.nymous@ccsd.cnrs.fr.invalid (A Lemoine) 29 Jul 2025
https://hal.inrae.fr/hal-05191306v1
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[hal-03900002] Contribution of Tiltmeters and Extensometers to Monitor Piton de la Fournaise Activity
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Aline Peltier) 15 Dec 2022
https://hal.science/hal-03900002v1
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[hal-04786672] Unlocking the potential of biofilm properties in beneficial microbes for one health advancements
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Virgile Guéneau) 16 Nov 2024
https://hal.inrae.fr/hal-04786672v1
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[hal-05191616] Metabolic engineering of Yarrowia lipolytica for the production and secretion of the saffron ingredient crocetin
Background Crocetin is a multifunctional apocarotenoid natural product derived from saffron, holding significant promises for protection against various diseases and other nutritional applications. Historically, crocetin has been extracted from saffron stigmas, but this method is hindered by the limited availability of high-quality raw materials and complex extraction processes. To overcome these challenges, metabolic engineering and synthetic biology can be applied to the sustainable production of crocetin. Results We constructed a Yarrowia lipolytica strain using hybrid promoters and copy number adjustment, which was able to produce 2.66 g/L of β-carotene, the precursor of crocetin. Next, the crocetin biosynthetic pathway was introduced, and we observed both the production and secretion of crocetin. Subsequently, the metabolite profiles under varied temperatures were studied and we found that low temperature was favorable for crocetin biosynthesis in Y. lipolytica. Therefore, a two-step temperature-shift fermentation strategy was adopted to optimize yeast growth and biosynthetic enzyme activity, bringing a 2.3-fold increase in crocetin titer. Lastly, fermentation media was fine-tuned for an optimal crocetin output of 30.17 mg/L, bringing a 51% higher titer compared with the previous highest report in shake flasks. Concomitantly, we also generated Y. lipolytica strains capable of achieving substantial zeaxanthin production, yielding 1575.09 mg/L, doubling the previous highest reported titer. Conclusions Through metabolic engineering and fermentation optimization, we demonstrated the first de novo biosynthesis of crocetin in the industrial yeast Yarrowia lipolytica. In addition, we achieved a higher crocetin titer in flasks than all our known reports. This work not only represents a high production of crocetin, but also entails a significant simultaneous zeaxanthin production, setting the stage for sustainable and cost-effective production of these valuable compounds.
ano.nymous@ccsd.cnrs.fr.invalid (Tingan Zhou) 29 Jul 2025
https://hal.inrae.fr/hal-05191616v1
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[hal-05191678] Substrate-dependent lipid and β-carotene production in engineered Yarrowia lipolytica: a comparative study
This study evaluates the influence of various substrates (glucose, glycerol, and acetic acid) on the growth and metabolite production of Yarrowia lipolytica in fed-batch bioreactors. The primary aim is to understand how substrate choice impacts lipid and β-carotene production, critical for bioenergy and bioproducts. The study demonstrates that the choice of substrate significantly influences biomass yield, lipid content, and β-carotene levels. Among the substrates tested, glycerol yielded the highest biomass concentration of 5.31 g/L. Glucose led to the highest lipid content, with a yield of 35.8% (g lipids/g biomass), while acetic acid resulted in the highest lipid concentration, reaching 1.42 g/L. In terms of β-carotene production, glucose showed the highest content per cell at 63.3 mg/g, whereas glycerol led to the highest overall concentration of 202 mg/L. These findings highlight Y. lipolytica's versatility and potential as a flexible platform to produce lipids and β-carotene, which are essential for developing sustainable biofuels and bioproducts. The study underscores the significant variations in metabolite production based on substrate choice, emphasizing on the importance of tailored strategies to optimize industrial applications. Further research may explore optimizing fermentation conditions to enhance production yields, making this yeast a viable option for various biotechnological applications. Key points Y. lipolytica produces biodiesel and β-carotene from low-cost substrates. Glucose, glycerol, or acetic acid act differently as substrates on Y. lipolytica. Cheap substrates derived from pollutants can be used for biofuels and bioproducts.
ano.nymous@ccsd.cnrs.fr.invalid (Raúl Robles-Iglesias) 29 Jul 2025
https://hal.inrae.fr/hal-05191678v1
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[hal-05191495] Spectroscopic and Biochemical Characterization of the Noncanonical Radical SAM Enzyme ArsL, Involved in Arsinothricin Biosynthesis
Radical SAM enzymes are the most widespread biocatalysts. These metalloenzymes, using S-adenosyl-l-methionine (SAM) and a [4Fe-4S] cluster as central cofactors, catalyze a broad range of chemically challenging transformations. The vast majority of radical SAM enzymes initiate their reaction by the homolytic cleavage of the SAM C5'-S bond and the generation of the central 5'-deoxyadenosyl radical (5'-dA·). In this study, by combining spectroscopic approaches with labeling and biochemical analyses, we show that ArsL, the key enzyme in the biosynthesis of the arsenic-containing antibiotic arsinothricin, catalyzes a unique reaction: the addition of the 3-amino-3-carboxypropyl radical (ACP·) to As(III). Remarkably, by exploiting several radical trapping strategies, we demonstrate that in sharp contrast to canonical radical SAM enzymes ArsL cleaves the SAM Cγ-S bond. In addition, using electron paramagnetic resonance (EPR) and hyperfine sublevel correlation (HYSCORE) spectroscopies, we establish that ArsL has a unique SAM binding mode, consistent with its catalytic properties and predicted structure. Notably, EPR and HYSCORE analyses support that SAM interacts with the radical SAM [4Fe-4S] cluster in an uncharacteristic conformation to form ACP·. Collectively, our study reveals that members of the superfamily of radical SAM enzymes are able to finely tune the binding of the SAM cofactor in order to perform unique chemistries.
ano.nymous@ccsd.cnrs.fr.invalid (Mickaël Mauger) 29 Jul 2025
https://hal.inrae.fr/hal-05191495v1
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[hal-05191245] Synbiotic Microencapsulation of Lactobacillus Strains from Mexican Fermented Beverages for Enhanced Probiotic Functionality
Synbiotics, which combine probiotics and prebiotics, represent an innovative approach to developing functional foods with enhanced health benefits compared to their individual components. This study focuses on the production of synbiotics through the microencapsulation of Lactobacillus strains isolated from traditional Mexican fermented beverages, contributing to the advancement of technologies for functional food development. Three Lactobacillus strains (Lacticaseibacillus rhamnosus LM07, Lactiplantibacillus plantarum LM19, and Levilactobacillus brevis LBH1070) were microencapsulated by spray-drying using a mixture of maltodextrin and gum arabic as wall materials and inulin as a prebiotic. The microencapsulation process achieved high survival rates (>90%), low moisture content (~5%), and low water activity (~0.3), ensuring long-term stability. Notably, the microencapsulated strains demonstrated improved tolerance to gastrointestinal conditions, enhanced adhesion properties, and increased antioxidant activity compared to non-microencapsulated strains. These results highlight the potential of microencapsulation as an innovative technology not only to preserve but also to enhance probiotic properties, facilitating the development of functional foods with improved health-promoting properties, extended shelf life, and stability at room temperature.
ano.nymous@ccsd.cnrs.fr.invalid (Morayma Ramírez-Damián) 29 Jul 2025
https://hal.inrae.fr/hal-05191245v1
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[hal-04275845] Hybrid models for neural computations with metabolism
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ano.nymous@ccsd.cnrs.fr.invalid (Léon Faure) 08 Nov 2023
https://hal.science/hal-04275845v1
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[hal-01000245] Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis
Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature.We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.
ano.nymous@ccsd.cnrs.fr.invalid (Pierre P. Nicolas) 04 Jun 2014
https://hal.science/hal-01000245v1
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[hal-03968015] Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
Outside In Acquisition and analysis of large data sets promises to move us toward a greater understanding of the mechanisms by which biological systems are dynamically regulated to respond to external cues. Now, two papers explore the responses of a bacterium to changing nutritional conditions (see the Perspective by Chalancon et al. ). Nicolas et al. (p. 1103 ) measured transcriptional regulation for more than 100 different conditions. Greater amounts of antisense RNA were generated than expected and appeared to be produced by alternative RNA polymerase targeting subunits called sigma factors. One transition, from malate to glucose as the primary nutrient, was studied in more detail by Buescher et al. (p. 1099 ) who monitored RNA abundance, promoter activity in live cells, protein abundance, and absolute concentrations of intracellular and extracellular metabolites. In this case, the bacteria responded rapidly and largely without transcriptional changes to life on malate, but only slowly adapted to use glucose, a shift that required changes in nearly half the transcription network. These data offer an initial understanding of why certain regulatory strategies may be favored during evolution of dynamic control systems.
ano.nymous@ccsd.cnrs.fr.invalid (Joerg Martin Buescher) 10 Mar 2023
https://hal.inrae.fr/hal-03968015v1
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[hal-03089431] Biochemical characteristics of a diffusible factor that induces gametophyte to sporophyte switching in the brown alga Ectocarpus
The haploid-diploid life cycle of the filamentous brown alga Ectocarpus involves alternation between two independent and morphologically distinct multicellular generations, the sporophyte and the gametophyte. Deployment of the sporophyte developmental program requires two TALE homeodomain transcription factors OUROBOROS and SAMSARA. In addition, the sporophyte generation has been shown to secrete a diffusible factor that can induce uni-spores to switch from the gametophyte to the sporophyte developmental program. Here, we determine optimal conditions for production, storage and detection of this diffusible factor and show that it is a heat-resistant, high molecular weight molecule. Based on a combined approach involving proteomic analysis of sporophyte-conditioned medium and the use of biochemical tools to characterize arabinogalactan proteins, we present evidence that sporophyte-conditioned medium contains AGP epitopes and suggest that the diffusible factor may belong to this family of glycoproteins.
ano.nymous@ccsd.cnrs.fr.invalid (Haiqin Yao) 28 Dec 2020
https://cnrs.hal.science/hal-03089431v1
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[anses-04171242] Évaluation des impacts sur la santé publique de la dynamique des populations de renards
Le Renard roux (Vulpes vulpes) est une espèce de la faune sauvage. En tant que gibier, il peut être chassé par différents moyens. Il est de plus susceptible d’être inscrit, dans certains territoires, comme espèce susceptible d’occasionner des dégâts (ESOD) par arrêté ministériel triennal pris en application de l’article R.427-6 du Code de l’environnement. Nonobstant les restrictions sur les périodes de chasse, les animaux classés ESOD peuvent être éliminés toute l’année. En 2019 et pour trois ans, suite à des consultations départementales et un arbitrage ministériel, le renard a été classé ESOD dans 90 départements français. La décision de classement doit être motivée. Plusieurs arguments sont avancés pour ce classement : pertes dans les élevages avicoles ou de gibier, raisons sanitaires (par ex. : échinococcose alvéolaire, gale sarcoptique). Inversement, des bénéfices liés à la présence des renards sont également avancés, tels que la prédation de rongeurs (campagnols notamment), porteurs d’agents zoonotiques, la réduction d’utilisation de raticides, etc. ... Dans un rapport et avis sur le rôle épidémiologique du renard dans le système multihôtes de la tuberculose bovine (Anses 2021), l’Anses notait que l’importance des nuisances attribuées aux renards faisait l’objet de controverses et de polémiques en France. La présente saisine s’inscrit ainsi dans un contexte sociétal sensible impliquant notamment les associations de protection de la nature et les chasseurs ou les éleveurs. Les réponses à cette saisine visent à clarifier le rôle du renard dans l’épidémiologie de certaines zoonoses pour lesquelles il est présenté comme premier responsable de la transmission à l’humain, ce qui motive certains acteurs à proposer son classement en tant qu’ESOD.
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Gilot-Fromont) 04 Mar 2025
https://anses.hal.science/anses-04171242v1
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[hal-05191251] Characterization of Foodborne Pathogens in Biofilms: A Four-Dimensional Structural Dynamics Approach Using HCS-CLSM
The functional properties of biofilms are intimately related to their spatial architecture. Structural data are therefore of prime importance to dissect the complex social and survival strategies of biofilms and ultimately to improve their control. Confocal laser scanning microscopy (CLSM) is the most widespread microscopic tool to decipher biofilm structure, enabling noninvasive three-dimensional investigation of their dynamics down to the single-cell scale. The emergence of fully automated high content screening (HCS) systems, associated with large-scale image analysis, has radically amplified the flow of available biofilm structural data. In this contribution, we present a HCS-CLSM protocol used to analyze biofilm four-dimensional structural dynamics at high throughput. Meta-analysis of the quantitative variables extracted from HCS-CLSM will contribute to a better biological understanding of biofilm traits.
ano.nymous@ccsd.cnrs.fr.invalid (Alexis Canette) 29 Jul 2025
https://hal.inrae.fr/hal-05191251v1
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[hal-04575931] Prebiotics supplementation during pregnancy leads to the transmission of microbial and immune factors from mother to child, preventing from food allergy
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Brosseau C.) 15 May 2024
https://hal.science/hal-04575931v1
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[hal-02625174] Nutritional strategies and gut microbiota composition as risk factors for necrotizing enterocolitis in very-preterm infants
Background: The pathophysiology of necrotizing enterocolitis (NEC) remains poorly understood. Objective: We assessed the relation between feeding strategies, intestinal microbiota composition, and the development of NEC. Design: We performed a prospective nationwide population-based study, EPIPAGE 2 (Etude Epidemiologique sur les Petits Ages Ges-tationnels), including preterm infants born at,32 wk of gestation in France in 2011. From individual characteristics observed during the first week of life, we calculated a propensity score for the risk of NEC (Bell's stage 2 or 3) after day 7 of life. We analyzed the relation between neonatal intensive care unit (NICU) strategies concerning the rate of progression of enteral feeding, the direct-breastfeeding policy, and the onset of NEC using general linear mixed models to account for clustering by the NICU. An ancillary propensitymatched case-control study, EPIFLORE (Etude Epidemiologique de la flore), in 20 of the 64 NICUs, analyzed the intestinal microbiota by culture and 16S ribosomal RNA gene sequencing. Results: Among the 3161 enrolled preterm infants, 106 (3.4%; 95% CI: 2.8%, 4.0%) developed NEC. Individual characteristics were significantly associated with NEC. Slower and intermediate rates of progression of enteral feeding strategies were associated with a higher risk of NEC, with an adjusted OR of 2.3 (95% CI: 1.2, 4.5; P = 0.01) and 2.0 (95% CI: 1.1, 3.5; P = 0.02), respectively. Less favorable and intermediate direct-breastfeeding policies were associated with higher NEC risk as well, with an adjusted OR of 2.5 (95% CI: 1.1, 5.8; P = 0.03) and 2.3 (95% CI: 1.1, 4.8; P = 0.02), respectively. Microbiota analysis performed in 16 cases and 78 controls showed an association between Clostridium neonatale and Staphylococcus aureus with NEC (P = 0.001 and P = 0.002). Conclusions: A slow rate of progression of enteral feeding and a less favorable direct-breastfeeding policy are associated with an increased risk of developing NEC. For a given level of risk assessed by propensity score, colonization by C. neonatale and/or S. aureus is significantly associated with NEC. This trial (EPIFLORE study) was registered at clinicaltrials.gov as NCT01127698.
ano.nymous@ccsd.cnrs.fr.invalid (Jean-Christophe Rozé) 04 Sep 2024
https://hal.inrae.fr/hal-02625174v1
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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-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-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-02735602] Maternal obesogenic microbiota modified central neural circuits leading to eating behavior modulations in transplanted rat pups
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Lise Pocheron) 02 Jun 2020
https://hal.inrae.fr/hal-02735602v1
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[hal-01204239] Degraded Carrageenan Causing Colitis in Rats Induces TNF Secretion and ICAM-1 Upregulation in Monocytes through NF-kappa B Activation
Carrageenan (CGN) is a high molecular weight sulphated polysaccharide derived from red seaweeds. In rodents, its degraded forms (dCGN) can induce intestinal inflammation associated with macrophage recruitment and activation. The aim of this study was: 1) to analyze the size-dependent effects of dCGN on colon inflammation in vivo, and 2) to correlate these effects with monocyte/macrophage proliferation, cytokine production and expression of various cell surface antigens including ICAM-1 adhesion molecule. Peripheral blood monocytes (PBM) and THP-1 monocytic cells were cultured in the presence of either 10 or 40 kDa, dCGN. The 40 kDa, but not the 10 kDa dCGN, induced colitis in in vivo. Degraded CGN inhibited THP-1 cell proliferation in vitro, arresting the cells in G1 phase. In addition, dCGN increased ICAM-1 expression in both PBM and THP-1 cells with a major effect seen after 40 kDa dCGN exposure. Also, dCGN stimulated monocyte aggregation in vitro that was prevented by inc! ubation with anti-ICAM-1 antibody. Finally, dCGN stimulated TNF-alpha expression and secretion by both PBM and THP-1 cells. All these effects were linked to NF-kappa B activation. These data strongly suggest that the degraded forms of CGN have a pronounced effect on monocytes, characteristic of an inflammatory phenotype.
ano.nymous@ccsd.cnrs.fr.invalid (Claudine Benard) 30 May 2020
https://hal.science/hal-01204239v1
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[hal-01204439] Perinatal high-fat diet increases hippocampal vulnerability to the adverse effects of subsequent high-fat feeding
Epidemiological observations report an increase in fat consumption associated with low intake of n-3 relative to n-6 polyunsaturated fatty acids (PUFAs) in women of childbearing age. However, the impact of these maternal feeding habits on cognitive function in the offspring is unknown. This study aims to investigate the impact of early exposure to a high-fat diet (HFD) with an unbalanced n-6/n-3 PUFAs ratio on hippocampal function in adult rats. Furthermore, we explored the effects of perinatal HFD combined with exposure to HFD after weaning. Dams were fed a control diet (C, 12% of energy from lipids, n-6/n-3 PUFAs ratio: 5) or HFD (HF, 39% of energy from lipids, n-6/n-3 PUFAs ratio: 39) throughout gestation and lactation. At weaning, offspring were placed either on control (C-C, HF-C) or high-fat (HF-HF) diets. In adulthood, hippocampus-dependent memory was assessed using the water-maze task and potential hippocampal alterations were determined by studying PUFA levels, gene expression, neurogenesis and astrocyte morphology. Perinatal HFD induced long-lasting metabolic alterations and some changes in gene expression in the hippocampus, but had no effect on memory. In contrast, spatial memory was impaired in animals exposed to HFD during the perinatal period and maintained on this diet. HF-HF rats also exhibited low n-3 and high n-6 PUFA levels, decreased neurogenesis and downregulated expression of several plasticity-related genes in the hippocampus. To determine the contribution of the perinatal diet to the memory deficits reported in HF-HF animals, an additional experiment was conducted in which rats were only exposed to HFD starting at weaning (C-HF). Interestingly, memory performance in this group was similar to controls. Overall, our results suggest that perinatal exposure to HFD with an unbalanced n-6/n-3 ratio sensitizes the offspring to the adverse effects of subsequent high-fat intake on hippocampal function.
ano.nymous@ccsd.cnrs.fr.invalid (Amandine L. Lepinay) 23 Sep 2015
https://hal.science/hal-01204439v1
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[hal-05170246] Cell-free genome-wide transcriptomics through machine learning optimization
Despite advances in transcriptomics, understanding of genome regulation remains limited by the complex interactions within living cells. To address this, we performed cell-free transcriptomics by developing a platform using an active learning workflow to explore over 1,000,000 buffer conditions. This enabled us to identify a buffer that increased mRNA yield by 20-fold, enabling cell-free transcriptomics. By employing increasingly complex conditions, our approach untangles the regulatory layers controlling genome expression. Main<p>Lysate-based cell-free systems (CFS) are valuable platform for studying the living and elucidating molecular mechanisms 1-3 . Transcription and translation are restored in bacterial lysates by supplementing with a buffer containing ATP regeneration substrates, crowding agents, salts, and essential precursors such as nucleotides and amino acids. As such, CFS are simpler than living cells in terms of molecular interactions as they eliminate complex and interfering biological processes such as cell division and membrane-related functions. For example, previous experiments showed that production and metabolic burdens can be untangled using cell-free compared with in vivo measurements 4 . CFS provide an open platform ideally suited for protein production, highthroughput prototyping of genetic circuits and parts, biosensing biomanufacturing and gene expression analysis and modelling 5-7 . Genome expression in living cells is routinely analyzed using RNA-seq 8 ; however, low transcript yields in CFS have so far limited the application of this technique in vitro 9 . Here, we developed a general methodological pipeline that integrates active learning loops with high-throughput experimentation to optimize mRNA production in Escherichia coli BL21(DE3) CFS. This approach enabled transcript abundances sufficient for RNA-seq-based, genome-wide transcriptomic analysis. As proof of concept, we applied the pipeline to enhance RNA synthesis by T7 RNA polymerase (T7 RNAP) and performed in vitro transcriptomic profiling of the phage T7 genome.
ano.nymous@ccsd.cnrs.fr.invalid (Léa Wagner) 18 Jul 2025
https://hal.science/hal-05170246v1
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[hal-05156875] Postbiotic Effect of Escherichia coli CEC15 and Escherichia coli Nissle 1917 on a Murine Model of 5-FU-induced Intestinal Mucositis
<div><p>Postbiotics are preparations of inanimate microorganisms and/or their components that confers a health bene t on the host. The Escherichia coli strains Nissle 1917 (EcN) and CEC15 have shown bene cial effects, in their live form, in murine models of intestinal in ammation, such as colitis and mucositis. However, the use of live bacteria, in special by immunocompromised individuals, had raised concerns. Based on this, the present study evaluated the effects as postbiotic of heat-inactivated, and cell-free supernatant preparations of EcN and CEC15 in attenuating 5-uorouracil (5-FU)-induced intestinal mucositis in mice and compared them with the probiotic effects of the live preparations.</p><p>BALB/c mice were fed daily, by gavage, with 10 10 CFU of live or inactivated bacteria, or with 300 µL of cell-free supernatant for 12 days. On the 10th day, all animals, except for the control group, received an intraperitoneal injection of 5-FU (300 mg/kg). After 72 h of 5-FU administration, animals were euthanized, and the ileum and blood were collected for analysis. Treatments with live and heat-inactivated CEC15 mitigated weight loss, preserved intestinal length, reduced histological damage, maintained goblet cells, decreased neutrophil in ltration, and modulated expression of in ammatory and barrier genes, when compared to 5-FU mucositis controls. EcN showed more limited effects. CEC15 upregulated mRNA expression of the mucin MUC2 and tight junction protein TJP1. Overall, CEC15 demonstrated protective effects against 5-FU-induced mucositis, whatever the way it was administered: live bacteria, heatinactivated bacteria, or cell-free supernatant. This suggests CEC15 mediates a protective response via secreted metabolites and does not require viability.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Rafael de Assis Glória) 21 Jul 2025
https://hal.science/hal-05156875v1
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[hal-01768437] Host–microbe interactions in distal airways: relevance to chronic airway diseases
This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways.
ano.nymous@ccsd.cnrs.fr.invalid (Clémence Martin) 17 Apr 2018
https://hal.umontpellier.fr/hal-01768437v1
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[hal-05124696] Impacts sur la santé publique de la dynamique des populations de renards
Le Renard roux (Vulpes vulpes) est une espèce de la faune sauvage. En tant que gibier, il peut être chassé par différents moyens. Il est de plus susceptible d’être inscrit, dans certains territoires, comme espèce susceptible d’occasionner des dégâts (ESOD) par arrêté ministériel triennal pris en application de l’article R.427-6 du Code de l’environnement. Nonobstant les restrictions sur les périodes de chasse, les animaux classés ESOD peuvent être éliminés toute l’année. En 2019 et pour trois ans, suite à des consultations départementales et un arbitrage ministériel, le renard a été classé ESOD dans 90 départements français. La décision de classement doit être motivée. Plusieurs arguments sont avancés pour ce classement : pertes dans les élevages avicoles ou de gibier, raisons sanitaires (par ex. : échinococcose alvéolaire, gale sarcoptique). Inversement, des bénéfices liés à la présence des renards sont également avancés, tels que la prédation de rongeurs (campagnols notamment), porteurs d’agents zoonotiques, la réduction d’utilisation de raticides, etc. ... Dans un rapport et avis sur le rôle épidémiologique du renard dans le système multihôtes de la tuberculose bovine (Anses 2021)1, l’Anses notait que l’importance des nuisances attribuées aux renards faisait l’objet de controverses et de polémiques en France. La présente saisine s’inscrit ainsi dans un contexte sociétal sensible impliquant notamment les associations de protection de la nature et les chasseurs ou les éleveurs. Les réponses à cette saisine visent à clarifier le rôle du renard dans l’épidémiologie de certaines zoonoses pour lesquelles il est présenté comme premier responsable de la transmission à l’humain, ce qui motive certains acteurs à proposer son classement en tant qu’ESOD. Dans une approche « une seule santé » (One Health), il est demandé d’identifier les risques pour la santé publique associés à des évolutions significatives, à la hausse et à la baisse, de populations de renards, i.e. : 1) « lister des zoonoses présentes en France pour lesquelles les renards ont un rôle épidémiologique, direct ou indirect (par les populations de proies qu’il élimine) et décrire ce rôle épidémiologique ; 2) identifier, le cas échéant, d’autres familles d’impacts en santé publique (par exemple l’effet indirect sur l’emploi des pesticides tels que les raticides) associés à l’évolution des populations de renards ; 3) expliciter, en fonction des connaissances disponibles (publications, données disponibles ou mécanismes de collecte mobilisables), l’importance relative des effets identifiés aux points 1 et 2, pour l’humain et/ou l’environnement, de l’évolution des populations de renards ; 4) analyser la faisabilité d’une évaluation socio-économique de type coût/bénéfice de la prévention et des impacts associés à ces zoonoses dans lesquels les renards ont des rôles différents, pour l’être humain et/ou l’environnement ». La saisine concerne exclusivement la France métropolitaine. En outre, n’entrent pas dans le champ de la saisine (i) les renards en tant que proies des loups, lynx et grands ducs principalement, ce qui ne constitue pas un enjeu de santé publique, (ii) l’impact des renards prédateurs sur les populations de volailles (basse-cours, élevages aviaires), d’oiseaux sauvages (notamment le gibier), sujet très large qui rejoint un critère de classement ESOD, et (iii) l’impact des renards prédateurs de micromammifères (souris, campagnols, mulots, etc.) à l’origine de dégâts aux cultures, l’expertise se limitant aux populations de proies susceptibles de transmettre des agents de zoonoses.
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Gilot-Fromont) 18 Jul 2025
https://hal.science/hal-05124696v1
