Publications

[hal-03975895] Harnessing the Vnn1 pantetheinase pathway boosts short chain fatty acids production and mucosal protection in colitis

Objective In the management of patients with IBD, there is a need to identify prognostic markers and druggable biological pathways to improve mucosal repair and probe the efficacy of tumour necrosis factor alpha biologics. Vnn1 is a pantetheinase that degrades pantetheine to pantothenate (vitamin B 5 , a precursor of coenzyme A (CoA) biosynthesis) and cysteamine. Vnn1 is overexpressed by inflamed colonocytes. We investigated its contribution to the tolerance of the intestinal mucosa to colitis-induced injury. Design We performed an RNA sequencing study on colon biopsy samples from patients with IBD stratified according to clinical severity and modalities of treatment. We generated the VIVA mouse transgenic model, which specifically overexpresses Vnn1 on intestinal epithelial cells and explored its susceptibility to colitis. We developed a pharmacological mimicry of Vnn1 overexpression by administration of Vnn1 derivatives. Results VNN1 overexpression on colonocytes correlates with IBD severity. VIVA mice are resistant to experimentally induced colitis. The pantetheinase activity of Vnn1 is cytoprotective in colon: it enhances CoA regeneration and metabolic adaptation of colonocytes; it favours microbiota-dependent production of short chain fatty acids and mostly butyrate, shown to regulate mucosal energetics and to be reduced in patients with IBD. This prohealing phenotype is recapitulated by treating control mice with the substrate (pantethine) or the products of pantetheinase activity prior to induction of colitis. In severe IBD, the protection conferred by the high induction of VNN1 might be compromised because its enzymatic activity may be limited by lack of available substrates. In addition, we identify the elevation of indoxyl sulfate in urine as a biomarker of Vnn1 overexpression, also detected in patients with IBD. Conclusion The induction of Vnn1/VNN1 during colitis in mouse and human is a compensatory mechanism to reinforce the mucosal barrier. Therefore, enhancement of vitamin B 5-driven metabolism should improve mucosal healing and might increase the efficacy of antiinflammatory therapy.

ano.nymous@ccsd.cnrs.fr.invalid (Virginie Millet) 06 Feb 2023

https://amu.hal.science/hal-03975895v1

[hal-04714371] Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories

Background: Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology. Results: We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. Conclusions:The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.

ano.nymous@ccsd.cnrs.fr.invalid (Florian Besnard) 30 Sep 2024

https://hal.inrae.fr/hal-04714371v1

[hal-05311416] Immunometabolic reprogramming of macrophages by gut microbiota-derived cadaverine controls colon inflammation

<div>Immunometabolic reprogramming of macrophages by gut microbiota</div>

ano.nymous@ccsd.cnrs.fr.invalid (Rodrigo de Oliveira Formiga) 13 Oct 2025

https://hal.inrae.fr/hal-05311416v1

[hal-04290181] Near-infrared co-illumination of fluorescent proteins reduces photobleaching and phototoxicity

Here we present a method to reduce the photobleaching of fluorescent proteins and the associated phototoxicity. It exploits a photophysical process known as reverse intersystem crossing, which we induce by near-infrared co-illumination during fluorophore excitation. This dual illumination method reduces photobleaching effects 1.5–9.2-fold, can be easily implemented on commercial microscopes and is effective in eukaryotic and prokaryotic cells with a wide range of fluorescent proteins.

ano.nymous@ccsd.cnrs.fr.invalid (Lucie Ludvikova) 22 Nov 2023

https://hal.science/hal-04290181v1

[hal-04565252] Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.

ano.nymous@ccsd.cnrs.fr.invalid (Katherine Kennedy) 01 May 2024

https://hal.inrae.fr/hal-04565252v1

[hal-03620811] Exploring the biosynthetic capacity of TsrM, a B12‐dependent Radical SAM Enzyme Catalyzing Non‐radical Reactions

B12 -dependent radical SAM enzymes are an emerging enzyme family with approximately 200,000 proteins. These enzymes have been shown to catalyze chemically challenging reactions such as methyl transfer to sp2- and sp3-hybridized carbon atoms. However, to date we have little information regarding their complex mechanisms and their biosynthetic potential. Here we show, using X-ray absorption spectroscopy, mutagenesis and synthetic probes that the vitamin B12 -dependent radical SAM enzyme TsrM catalyzes not only C- but also N-methyl transfer reactions further expanding its synthetic versatility. We also demonstrate that TsrM has the unique ability to directly transfer a methyl group to the benzyl core of tryptophan, including the least reactive position C4. Collectively, our study supports that TsrM catalyzes non-radical reactions and establishes the usefulness of radical SAM enzymes for novel biosynthetic schemes including serial alkylation reactions at particularly inert C-H bonds.

ano.nymous@ccsd.cnrs.fr.invalid (Feryel Soualmia) 08 Nov 2022

https://hal.science/hal-03620811v1

[hal-03624206] Capnocytophaga zoonotic infections: a 10-year retrospective study (the French CANCAN study)

Zoonotic species of Capnocytophaga genus belong to the oral microbiota of dogs and cats. They may be responsible for serious human infections, mainly after animal bites, with a high mortality rate. In France, only few cases have been reported and no multicenter study has been conducted. Our aim was to describe the French epidemiology of Capnocytophaga zoonosis. We conducted a multicenter (21 centers) retrospective non-interventional, observational study in France describing the epidemiology of Capnocytophaga zoonosis (C. canimorsus, C. cynodegmi, C. canis) over 10 years with regard to clinical and bacteriological data. From 2009 to 2018, 44 cases of Capnocytophaga zoonotic infections were described (C. canimorsus, n = 41; C. cynodegmi, n = 3). We observed an increase (2.5 times) in the number of cases over the study period (from the first to the last 5 years of the study). The most frequent clinical presentations were sepsis (n = 37), skin and soft tissue infections (n = 12), meningitis (n = 8), osteoarticular infections (n = 6), and endocarditis (n = 2). About one-third of patients with sepsis went into septic shock. Mortality rate was 11%. Mortality and meningitis rates were significantly higher for alcoholic patients (p = 0.044 and p = 0.006, respectively). Other comorbidities included smoking, splenectomy, diabetes mellitus, and immunosuppressive therapy are associated to zoonotic Capnocytophaga infection. Eighty-two percent of cases involved contact with dogs, mostly included bites (63%). Despite all isolates were susceptible to the amoxicillin-clavulanic acid combination, three of them were resistant to amoxicillin.

ano.nymous@ccsd.cnrs.fr.invalid (Clémence Beauruelle) 30 Mar 2022

https://hal.univ-reims.fr/hal-03624206v1

[hal-04316567] Contribution of the anaerobic blood culture vial for the recovery of Candida glabrata : A retrospective multicentric study

Abstract Although Candida spp are aerobic microorganisms, some Candida strains, mainly Candida glabrata, can be recovered from anaerobic blood culture vials. We assessed the contribution of the anaerobic vials for the diagnosis of candidemia, especially for C. glabrata. We conducted a multicenter retrospective study including eight university or regional hospitals. A single episode of monomicrobial candidemia per patient was included from September 1st, 2016, to August 31st, 2019. The characteristics of all aerobic and anaerobic blood culture vials sampled within 2 h before and after the first positive blood culture vials were recorded (type of vials, result, and for positive vials time-to-positivity and Candida species). Overall, 509 episodes of candidemia were included. The main species were C. albicans (55.6%) followed by C. glabrata (17.1%), C. parapsilosis (4.9%), and C. tropicalis (4.5%). An anaerobic vial was positive in 76 (14.9%) of all episodes of which 56 (73.8%) were due to C. glabrata. The number of C. glabrata infections only positive in anaerobic vials was 1 (2.6%), 1 (11.1%), and 15 (37.5%) with the BACT/ALERT 3D the BACT/ALERT VIRTUO and the BACTEC FX instrument, respectively (P &lt; 0.01). The initial positivity of an anaerobic vial was highly predictive of the isolation of C. glabrata with the BACTEC FX (sensitivity of 96.8%). C. glabrata time-to-positivity was shorter in anaerobic vial than aerobic vial with all instruments. Anaerobic blood culture vials improve the recovery of Candida spp mainly C. glabrata. This study could be completed by further analyses including mycological and pediatric vials. Lay summary Although Candida spp are aerobic microorganisms, C. glabrata is able to grow in anaerobic conditions. In blood culture, the time-to-positivity of C. glabrata is shorter in anaerobic than aerobic vials. Only the anaerobic vial was positive in up to 15 (37.5%) C. glabrata bloodstream infections.

ano.nymous@ccsd.cnrs.fr.invalid (Eric Farfour) 30 Nov 2023

https://hal.science/hal-04316567v1

[hal-01532602] Mass Spectrometry Analysis of the Extracellular Peptidome of Lactococcus lactis: Lines of Evidence for the Coexistence of Extracellular Protein Hydrolysis and Intracellular Peptide Excretion

We report here the use of a peptidomic approach to revisit the extracellular proteolysis of Lactococcus lactis. More than 1800 distinct peptides accumulate externally during growth of the plasmid-free protease-negative strain L. lactis IL1403 in a protein- and peptide-free medium. These peptides mainly originate from cell-surface- and cytoplasmic located proteins, despite the fact that no cell lysis could be evidenced. Positioning each identified peptide on its parental protein sequence demonstrated the involvement of exo- and endopeptidase activities. The endopeptidases responsible for the release of surface and cytoplasmic peptides had distinct specificities. The membrane-anchored protease HtrA was responsible for the release of only a part of the surface peptides, and its preference for branched-chain amino acids in the N-terminal side of the cleaved bond was established in situ. Other yet uncharacterized surface proteases were also involved. Several lines of evidence suggest that surface and cytoplasmic peptides were produced by different routes, at least part of the latter being most likely excreted as peptides from the cells. The mechanism by which these cytoplasmic peptides are excreted remains an open question, as it is still the case for excreted cytoplasmic proteins.

ano.nymous@ccsd.cnrs.fr.invalid (Alain Guillot) 02 Jun 2017

https://hal.science/hal-01532602v1

[hal-03593214] Microbial biofilms : Structural plasticity and emerging properties

Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation— from a single-cell to a multicellular scale— to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.

ano.nymous@ccsd.cnrs.fr.invalid (Arnaud A. Bridier) 03 Jan 2023

https://hal.inrae.fr/hal-03593214v1

[hal-04695580] Genomic pipeline for analysis of mutational events in bacteria

Unveiling the strategies of bacterial adaptation to stress constitute a challenging area of research. The understanding of mechanisms governing emergence of resistance to antimicrobials is of particular importance regarding the increasing threat of antibiotic resistance on public health worldwide. In the last decades, the fast democratization of sequencing technologies along with the development of dedicated bioinformatical tools to process data offered new opportunities to characterise genomic variations underlying bacterial adaptation. Thereby, research teams have now the possibility to dive deeper in the deciphering of bacterial adaptive mechanisms through the identification of specific genetic targets mediating survival to stress. In this chapter, we proposed a step-by-step bioinformatical pipeline enabling the identification of mutational events underlying biocidal stress adaptation associated to antimicrobial resistance development using Escherichia marmotae as an illustrative model.

ano.nymous@ccsd.cnrs.fr.invalid (Pierre Lemée) 12 Sep 2024

https://hal.science/hal-04695580v1

[hal-05323164] Enzymes Required for Maltodextrin Catabolism in Enterococcus faecalis Exhibit Novel Activities

Maltose and maltodextrins are formed during the degradation of starch or glycogen. Maltodextrins are composed of a mixture of maltooligosaccharides formed by α-1,4- but also some α-1,6-linked glucosyl residues. The α-1,6-linked glucosyl residues are derived from branching points in the polysaccharides. In Enterococcus faecalis , maltotriose is mainly transported and phosphorylated by a phosphoenolpyruvate:carbohydrate phosphotransferase system. The formed maltotriose-6″-phosphate is intracellularly dephosphorylated by a specific phosphatase, MapP. In contrast, maltotetraose and longer maltooligosaccharides up to maltoheptaose are taken up without phosphorylation via the ATP binding cassette transporter MdxEFG-MsmX. We show that the maltose-producing maltodextrin hydrolase MmdH (GenBank accession no. EFT41964 ) in strain JH2-2 catalyzes the first catabolic step of α-1,4-linked maltooligosaccharides. The purified enzyme converts even-numbered α-1,4-linked maltooligosaccharides (maltotetraose, etc.) into maltose and odd-numbered (maltotriose, etc.) into maltose and glucose. Inactivation of mmdH therefore prevents the growth of E. faecalis on maltooligosaccharides ranging from maltotriose to maltoheptaose. Surprisingly, MmdH also functions as a maltogenic α-1,6-glucosidase, because it converts the maltotriose isomer isopanose into maltose and glucose. In addition, E. faecalis contains a glucose-producing α-1,6-specific maltodextrin hydrolase (GenBank accession no. EFT41963 , renamed GmdH). This enzyme converts panose, another maltotriose isomer, into glucose and maltose. A gmdH mutant had therefore lost the capacity to grow on panose. The genes mmdH and gmdH are organized in an operon together with GenBank accession no. EFT41962 (renamed mmgT ). Purified MmgT transfers glucosyl residues from one α-1,4-linked maltooligosaccharide molecule to another. For example, it catalyzes the disproportionation of maltotriose by transferring a glucosyl residue to another maltotriose molecule, thereby forming maltotetraose and maltose together with a small amount of maltopentaose. IMPORTANCE The utilization of maltodextrins by Enterococcus faecalis has been shown to increase the virulence of this nosocomial pathogen. However, little is known about how this organism catabolizes maltodextrins. We identified two enzymes involved in the metabolism of various α-1,4- and α-1,6-linked maltooligosaccharides. We found that one of them functions as a maltose-producing α-glucosidase with relaxed linkage specificity (α-1,4 and α-1,6) and exo- and endoglucosidase activities. A third enzyme, which resembles amylomaltase, exclusively transfers glucosyl residues from one maltooligosaccharide molecule to another. Similar enzymes are present in numerous other Firmicutes , such as streptococci and lactobacilli, suggesting that these organisms follow the same maltose degradation pathway as E. faecalis .

ano.nymous@ccsd.cnrs.fr.invalid (Philippe Joyet) 21 Oct 2025

https://hal.science/hal-05323164v1

[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

[hal-05238241] One process applied to different cereals leads to specific microbial profiles: the case of traditional fermented couscous from Senegal.

Spontaneous fermentation is a process widely used around the world for millennia. Although studies have characterized the microbiota and the impact of fermentation on the nutritional composition of several traditional cereal-based fermented foods, they have not yet studied fermented couscous, a staple food in Senegal, made from a variety of cereals. Thus, this study aims to characterise the microbial composition of such fermented couscous from Senegal and the effect of the fermentation on their nutritional qualities. Forty samples from flours of different cereals (sorghum, maize, millet, and a mix of maize and millet) were collected in Senegal before and after fermentation (flours moistened into small balls, fermented for 8 hours). We analysed microbial diversity and metabolic functionalities using shotgun metagenomic sequencing. We also measured vitamin B9 content, as fermentation can significantly alter its levels. Each flour had a specific microbial diversity, with maize flours exhibiting the lowest diversity. Lactobacillaceae, especially from the genus Weissella, were in high proportions in all flours. Millet flour contained potentially pathogenic bacteria from Enterobacteriaceae family. Surprisingly, besides the expected presence of Lactobacillaceae after fermentation, a low proportion of species from Acinetobacter genera, previously undetected in flours, appeared. We detected only species of yeasts from the Saccharomycetales order in 28% of flour samples. Despite the presence of potential folate-producing microbes, vitamin B9 content decreased during the fermentation. Analysis of functions from metagenomic data will help better understand the metabolic interactions within the traditional microbial food ecosystem and help to know more about their potential nutritional properties.

ano.nymous@ccsd.cnrs.fr.invalid (Bastien Renard) 03 Sep 2025

https://hal.inrae.fr/hal-05238241v1

[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

[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

[hal-03751737] Contribution of omics to biopreservation: Toward food microbiome engineering

Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.

ano.nymous@ccsd.cnrs.fr.invalid (Frédéric Borges) 15 Aug 2022

https://hal.inrae.fr/hal-03751737v1

[anses-04453336] Avis de l'Anses relatif à un document d’appui aux lignes directrices de l’arrêté du 7 mars 2011 relatives à l’évaluation de l'efficacité antimicrobienne des auxiliaires technologiques utilisés comme agents de décontamination des denrées d’origine végétale

Un auxiliaire technologique est défini par le règlement (CE) n° 1333/2008 comme « toute substance : 1) non consommée comme ingrédient alimentaire en soi ; 2) volontairement utilisée dans la transformation de matières premières, de denrées alimentaires ou de leurs ingrédients pour répondre à un certain objectif technologique pendant le traitement ou la transformation ; et 3) pouvant avoir pour résultat la présence non intentionnelle mais techniquement inévitable de résidus de cette substance ou de ses dérivés dans le produit fini, à condition que ces résidus ne présentent pas de risque sanitaire et n’aient pas d’effets technologiques sur le produit fini ». Le décret n° 2011-509 du 10 mai 2011 fixe les conditions d’autorisation et d’utilisation des auxiliaires technologiques pouvant être employés dans la fabrication des denrées destinées à l'alimentation humaine. L’arrêté du 7 mars 2011 définit les prescriptions relatives à la constitution d’un dossier de demande d’autorisation d’emploi des auxiliaires technologiques dans une annexe intitulée « LIGNES DIRECTRICES POUR LA CONSTITUTION DES DOSSIERS […] ». La note d’appui scientifique et technique de l’Anses du 5 octobre 2018 (Anses 2018c) est également un document de référence et d’appui pour la constitution de ces dossiers. Elle apporte des précisions sur les données à fournir pour les aspects relatifs à l’innocuité et à la sécurité d’emploi, au regard des prescriptions susmentionnées. L’annexe de l’arrêté du 7 mars 2011 précise également qu’ « une justification de l'usage, de l'intérêt et de l'efficacité de la substance ou du mélange de substances, ainsi que l'explication du mode d'action et du rôle technologique dans le procédé de transformation, devraient être fournies, mentionnant les actions technologiques principales recherchées et secondaires éventuelles, si connues ». A cet égard, l’Afssa (Agence française de sécurité sanitaire des aliments) avait formulé en 2005 des « recommandations pour la présentation des données permettant d’évaluer l’efficacité des antimicrobiens appliqués sur, ou incorporés dans, les aliments » (Afssa 2005). L’expérience montre que les dossiers contiennent souvent des informations parcellaires et insuffisantes pour que l'Agence puisse évaluer l'efficacité antimicrobienne revendiquée par le pétitionnaire. Dans ce contexte, l’Anses a été saisie pour expliciter, par un document scientifique et technique, les termes des lignes directrices de l’arrêté relatives à l'efficacité antimicrobienne des auxiliaires technologiques. Ce document a vocation à se substituer aux recommandations publiées par l’Afssa en 2005. Cette expertise ne concerne que la catégorie d’auxiliaires technologiques « agents de décontamination des produits végétaux » mentionnée dans l’annexe 1 du décret n° 2011-509, c’est-à-dire les « substances utilisées pour réduire ou maîtriser la contamination des denrées alimentaires d’origine végétale inhérente à leur provenance. Leur utilisation ne doit en aucune manière se substituer aux bonnes pratiques d’hygiène et leur utilisation doit être suivie d’une élimination par rinçage » [Saisine liée n° 2003-SA-0363]

ano.nymous@ccsd.cnrs.fr.invalid (Régine Talon) 13 Feb 2024

https://anses.hal.science/anses-04453336v1

[hal-04345448] Hétérogénéités génotypique, physiologique et cellulaire des bactéries pathogènes alimentaires

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ano.nymous@ccsd.cnrs.fr.invalid (Florence Dubois-Brissonnet) 14 Dec 2023

https://hal.inrae.fr/hal-04345448v1

[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

[hal-04337407] Le microbiote et l’hôte: un duo dont les interactions évoluent en fonction des quantités de fer apportées par l’alimentation

La co-existence, la co-évolution, la tolérance, la coopération et la compétition régissent l’utilisation des ressources nutritionnelles entre l’écosystème microbien et les cellules de l’hôte. Le fer est un élément essentiel à tous les organismes vivants, ce qui fait que sa disponibilité peut modifier les interactions au sein du microbiote mais aussi les communications entre l’hôte et son microbiote. Il a été montré que la teneur en fer module la composition et l’activité du microbiote intestinal (1), mais l’impact du microbiote sur le métabolisme du fer est moins décrit. La comparaison d’animaux porteurs de microbiote sans pathogènes (SPF), avec des animaux axéniques (AX) dépourvus de microbiote ou des animaux gnotobiotiques (GNT) porteurs de microbiotes simplifiés a montré que les protéines DMT1 (transporteur apical) et ferritine (protéine intracellulaire de stockage) sont inversement modulées par le microbiote (2). Chez des animaux SPF et GNT en comparaison des animaux GF, la ferritine est augmentée, alors que DMT1 est inhibé (2). L’inhibition de DMT1 causée par certains métabolites bactériens implique la voie de signalisation dépendante de HIF2 (3). L’objectif de ce travail est de mieux comprendre les effets du microbiote sur le métabolisme du fer en cas de privation de fer en comparant une cinétique d’animaux SPF, GNT et AX qui reçoivent un régime contenant du fer ou pauvre en fer. Le numéro d’autorisation de l’étude est n° 20374- 2019060714134169V3. Toutes les souris (femelle C3H/HeN) GF (n=3 par point de cinétique), SPF (n=4 par point de cinétique), GNT (n=2 ou 3) reçoivent le même régime stérilisé par irradiation gamma (45 kGy). Le régime de privation contient < 6mg/kg de fer (U8958 Version 0176) et le régime de référence (U8958P Version 0176) contient + 65 mg/kg de fer (SAFE Nutrition, Augy, France). Après 15, 30, 45 ou 60 jours, les animaux ont été sacrifiés pour déterminer les paramètres sanguins (coefficient de saturation de la transferrine, ferritine, hepcidine, hémoglobine), les quantités de ferritine et de DMT1 dans le duodenum et le foie par western blot. La composition fécale du microbiote (séquençage 16S) et la production caecale d’acides gras à chaîne courte ont été determinés chez les animaux porteurs de microbiote en fonction du régime et du temps. Les differences significatives (p<0.05) sont établies par des tests anova et des T-tests non paramétriques Mann-Whitney en function du nombre de groupe considéré. Avec un régime contenant du fer, les animaux AX ont 10 fois moins de ferritine dans le duodenum en comparaison des SPF. Cela indique que la présence d’un microbiote favorise le stockage de fer par l’organisme quand le fer est disponible dans l’alimentation. En cas de régime pauvre en fer, les AX ayant moins de stocks initiaux, montrent une plus faible résistance, malgré des stocks hépatiques rapidement mobilisés et sur-expression rapide du transporteur apical DMT1. Sous un régime pauvre en fer, nous avons également observe une reduction de la quantité du transporteur DMT1 par l’inoculation d’un microbiote simplifié chez les AX. Ainsi, dans des conditions de privation de fer, l’installation d’un microbiote inhibe le transport du fer. La quantité de fer dans le régime module la composition et la production d’acides gras à chaîne courte en fonction du temps. Le fer de l’alimentation module le microbiote et fait évoluer les relations entre le microbiote et l’hôte d’une coopération en cas d’abondance à une competition en cas de privation.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Louise Noordine) 12 Dec 2023

https://hal.inrae.fr/hal-04337407v1

[anses-04027039] Évaluation des risques liés à la consommation de nitrates et nitrites

Le contexte de cette expertise est présenté ci-après selon les termes de la saisine émanant de la DGAL, la DGS et la DGCCRF . « La présence de nitrites dans l’organisme peut conduire à l’oxydation de l'hémoglobine réduisant la capacité des globules rouges à transporter l'oxygène. Elle peut également contribuer à la formation d’autres composés, tels que les nitrosamines, dont certains sont cancérogènes. Il existe différentes sources d’exposition des consommateurs aux nitrites et notamment : i) La conversion de nitrates présents dans certaines denrées alimentaires, en nitrites. Les nitrates se retrouvent dans l'eau notamment en raison de leur utilisation en production primaire. Ils sont naturellement présents dans certaines denrées alimentaires, en particulier dans les légumes-feuilles comme les épinards ou la laitue. Chez l’Homme, une partie des nitrates consommés peut être convertie en nitrites par les bactéries présentes dans la cavité buccale. ii) La présence non intentionnelle de nitrites dans les denrées alimentaires. Les nitrites peuvent notamment être présents dans les légumes mais à des teneurs généralement très inférieures aux nitrates. iii) L’utilisation de nitrites et de nitrates en tant qu’additifs dans les denrées alimentaires. Les nitrites de potassium et de sodium (E249, E250) et les nitrates de sodium et de potassium (E251, E252) sont couramment utilisés pour préserver la viande et d'autres produits périssables. Ils contribuent également à limiter la prolifération de microorganismes nuisibles, en particulier Clostridium botulinum, responsable du botulisme. Il s’agit d’additifs alimentaires autorisés dans l’Union européenne. A ce titre, ils ont fait l’objet de travaux scientifiques d’évaluation pour caractériser les risques liés à leur utilisation. Actuellement la réglementation européenne prévoit une teneur maximale d’incorporation de 150 mg/kg pour les produits de viande transformés, hors produits traditionnels. Pour les produits traditionnels dont la production est moindre en volume que les produits fabriqués par les industriels et qui contribuent donc moins à l’exposition des consommateurs, la réglementation prévoit une teneur de nitrites et nitrates résiduels pouvant aller jusqu’à 250 mg/kg. La teneur résiduelle varie selon différents facteurs liés au procédé de transformation (température de transformation, pH, présence d’acide ascorbique, etc.) et ne dépend pas uniquement de la teneur initialement incorporée. Les autorités danoises ont, pour leur part, souhaité maintenir un niveau d’emploi plus faible, à 60 mg/kg, qu’ils avaient fixé avant l’harmonisation européenne. L’association du fer-héminique avec les nitrites ajoutés a notamment été envisagée comme une explication du risque accru observé de développement de cancers du côlon ou du rectum lié à la consommation de certains produits carnés (données CIRC-INCa 2018)[2]. Le ferhéminique contenu dans la viande favoriserait la conversion des nitrites en nitrosamines, substances classées cancérogène probable (groupe 2A). Pour répondre à la demande des consommateurs, l’industrie a développé des solutions qu’elle présente comme alternatives à l’utilisation de sels nitrés (raccourcissement des DLC, bouillons de légumes, extraits de végétaux, etc.). En outre, des opérateurs s’engagent de manière plus globale à diminuer l’utilisation des additifs conformément aux objectifs définis par le programme national de l’alimentation et de la nutrition (PNAN). Dans le cadre de la réévaluation des additifs, l’Autorité européenne de sécurité des aliments (EFSA) a rendu des avis en juin 2017[3] et conclu, sur la base des éléments de preuve disponibles, que les niveaux de sécurité existants pour les nitrites et les nitrates ajoutés en tant qu’additifs à la viande et à d'autres aliments constituaient une protection adéquate pour les consommateurs. Plus précisément : ■ S’agissant des nitrates en tant qu’additif, et en ayant recours à des données dites réalistes (c’est-à-dire, les niveaux de concentration effectivement observés dans les aliments), les experts ont estimé que l'exposition des consommateurs aux nitrates utilisés comme additifs alimentaires était inférieure à 5% de l'exposition globale aux nitrates dans les aliments et ne dépassait pas la DJA ; ■ S’agissant des nitrites en tant qu’additif, les experts ont estimé que l'exposition se situait dans des limites sûres pour tous les groupes de population, à l'exception d'un léger dépassement chez les enfants dont le régime alimentaire est riche en aliments contenant ces additifs. De plus, le panel de l’EFSA soulignait, lorsque l’ensemble des sources d’expositions alimentaires (présence naturelle dans les aliments, contamination environnementale, utilisation en tant qu’additifs) étaient prises en compte : 1. pour les nitrates, des dépassements de la DJA pour l’ensemble des groupes d’âges (hypothèse d’exposition moyenne à haute) ; 2. pour les nitrites, des dépassements de la DJA pour l’ensemble des groupes d’âges sous l’hypothèse d’exposition haute, et pour des groupes d’âges spécifiques (nourrissons, jeunes enfants et enfants) sous l’hypothèse d’une exposition moyenne. L’EFSA a également émis des recommandations pour pallier certaines incertitudes. » En ce qui concerne les nitrates, des travaux ont été engagés à l’Anses afin de caractériser les expositions par voie alimentaire (notamment légumes et eau destinée à la consommation humaine) propres à la France dans le cadre de la saisine 2015-SA-0029. Ces travaux résultent d’une saisie de l’Anses par l’association Eaux et rivières de Bretagne (le 15/01/2015), par la Coordination rurale (le 19/01/2015) puis par la FNSEA (le 26/01/2015) sur les impacts sanitaires des nitrates présents dans l’alimentation et dans l’environnement. En effet, les habitudes alimentaires, de même que la présence de nitrates dans les aliments (légumes notamment) et l’eau, peuvent différer sensiblement des données européennes utilisées par l’EFSA. Cela est particulièrement vrai pour l’eau de consommation humaine distribuée dont les paramètres caractérisant sa qualité physico-chimique varient en fonction des ressources exploitées et des traitements mis en œuvre. Ces travaux avaient pour but d’apprécier, au plan national, la situation d’exposition de la population aux nitrates au regard des repères toxicologiques. Les résultats permettraient d’identifier les situations méritant attention, de façon à recommander des mesures, en particulier grâce à l’identification des aliments (y compris l’eau de boisson) les plus contributeurs à l’exposition aux nitrates en France. Ces travaux sont complétés par la présente expertise.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Louise Scippo) 13 Mar 2023

https://anses.hal.science/anses-04027039v1

[hal-05239660] Unlocking the potential of plant-based fermented foods through a Living Lab approach with consumers and stakeholders

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ano.nymous@ccsd.cnrs.fr.invalid (Ayité Adama-Hondegla) 04 Sep 2025

https://hal.inrae.fr/hal-05239660v1

[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

[hal-04727009] Quels sont les effets santé des produits fermentés ? Focus sur les végétaux fermentés

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ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Savary-Auzeloux) 09 Oct 2024

https://hal.inrae.fr/hal-04727009v1

[hal-04645842] The microbiota and the host organism switch between cooperation and competition based on dietary iron levels

The microbiota significantly impacts digestive epithelium functionality, especially in nutrient processing. Given the importance of iron for both the host and the microbiota, we hypothesized that host-microbiota interactions fluctuate with dietary iron levels. We compared germ-free (GF) and conventional mice (SPF) fed iron-containing (65 mg/Kg) or iron-depleted (&lt;6 mg/Kg) diets. The efficacy of iron privation was validated by iron blood parameters. Ferritin and Dmt1, which represent cellular iron storage and transport respectively, were studied in tissues where they are abundant: the duodenum, liver and lung. When the mice were fed an iron-rich diet, the microbiota increased blood hemoglobin and hepcidin and the intestinal ferritin levels, suggesting that the microbiota helps iron storage. When iron was limiting, the microbiota inhibited the expression of the intestinal Dmt1 transporter, likely via the pathway triggered by Hif-2 alpha. The microbiota assists the host in storing intestinal iron when it is abundant and competes with the host by inhibiting Dmt1 in conditions of iron scarcity. Comparison between duodenum, liver and lung indicates organ-specific responses to microbiota and iron availability. Iron depletion induced temporal changes in microbiota composition and activity, reduced alpha-diversity of microbiota, and led to Lactobacillaceae becoming particularly more abundant after 60 days of privation. By inoculating GF mice with a simplified bacterial mixture, we show that the iron-depleted host favors the gut fitness of Bifidobacterium longum

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Louise Noordine) 12 Jul 2024

https://hal.inrae.fr/hal-04645842v1

[hal-05240627] Du traditionnel vers le rationnel : utilisation d'approches omiques pour la conception d'écosystèmes microbiens sur mesures et la fabrication d'une boisson fermentée céréalière saine et durable

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Bastien Renard) 04 Sep 2025

https://hal.inrae.fr/hal-05240627v1

[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

[hal-02915539] Cycle biogéochimique du P organique : mécanismes mis en jeu dans la mobilisation du P du phytate par Bacillus subtilis et la boucle trophique

Dans le sol, les formes de P organique (Po), et particulièrement le phytate (myo-inositol 6P), peuvent constituer une proportion très importante du P total. Pour être utilisable par les organismes vivants, le groupement phosphate (Pi) des molécules de Po doit être libéré par des enzymes (phosphatases et phytases), étape primordiale du cycle du P. Contrairement aux plantes, de nombreuses espèces bactériennes sont capables d’utiliser le phytate comme seule source de P, grâce à leur production de phytase. Parmi ces espèces, celles produisant des phytases extracellulaires comme Bacillus subtilis sont potentiellement importantes pour la minéralisation du phytate. Nos travaux antérieurs [1] ont toutefois montré que la présence de nématodes bactérivores était indispensable pour que la plante bénéficie du P du phytate minéralisé par B. subtilis. L’objectif des travaux présentés ici est de mieux comprendre les mécanismes mis en jeu par la prédation par Acrobeloides sp. dans l’augmentation de la biodisponibilité de P à partir du phytate. Nous avons tout d’abord mesuré l’importance de la mobilité des nématodes, et ses conséquences sur la dispersion et la multiplication des populations bactériennes et la libération de Pi en milieu simplifié (boîte de Petri contenant de l’agarose et du phytate 1 mM), en localisant le dépôt des nématodes ou des bactéries seules. Dans une seconde étape, nous avons produit des souches de B. subtilis exprimant la GFP sous la dépendance du promoteur de la phytase bactérienne et nous les avons utilisées pour inoculer la rhizosphère de jeunes plantes de blé (Triticum durum), en absence ou en présence de nématodes. Les résultats montrent que la prédation améliore la minéralisation du phytate en augmentant (i) la dispersion des bactéries, (ii) l’expression du gène de la phytase de B. subtilis et (iii) la croissance du système racinaire du blé.

ano.nymous@ccsd.cnrs.fr.invalid (Mercedes Garcia-Sanchez) 14 Aug 2020

https://hal.science/hal-02915539v1

[hal-01004544] Food fermentations: Microorganisms with technological beneficial use

Microbial food cultures have directly or indirectly come under various regulatory frameworks in the course of the last decades. Several of those regulatory frameworks put emphasis on "the history of use", "traditional food", or "general recognition of safety". Authoritative lists of microorganisms with a documented use in food have therefore come into high demand. One such list was published in 2002 as a result of a joint project between the International Dairy Federation (IDF) and the European Food and Feed Cultures Association (EFFCA). The "2002 IDF inventory" has become a de facto reference for food cultures in practical use. However, as the focus mainly was on commercially available dairy cultures, there was an unmet need for a list with a wider scope. We present an updated inventory of microorganisms used in food fermentations covering a wide range of food matrices (dairy, meat, fish, vegetables, legumes, cereals, beverages, and vinegar). We have also reviewed and updated the taxonomy of the microorganisms used in food fermentations in order to bring the taxonomy in agreement with the current standing in nomenclature.

ano.nymous@ccsd.cnrs.fr.invalid (Francois F. Bourdichon) 11 Jun 2014

https://hal.science/hal-01004544v1

[hal-01594855] Human gut microbes impact host serum metabolome and insulin sensitivity

Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatusare identified as the main species driving the association between biosynthesis of BCAAs and insulin resistance, and in mice we demonstrate that P. copri can induce insulin resistance, aggravate glucose intolerance and augment circulating levels of BCAAs. Our findings suggest that microbial targets may have the potential to diminish insulin resistance and reduce the incidence of common metabolic and cardiovascular disorders.

ano.nymous@ccsd.cnrs.fr.invalid (Helle Krogh Pedersen) 26 Sep 2017

https://hal.science/hal-01594855v1

[hal-01189702] Genetic and biochemical characterization of the cell wall hydrolase activity of the major secreted protein of Lactobacillus rhamnosus GG

Lactobacillus rhamnosus GG (LGG) produces two major secreted proteins, designated here Msp1 (LGG_00324 or p75) and Msp2 (LGG_00031 or p40), which have been reported to promote the survival and growth of intestinal epithelial cells. Intriguingly, although each of these proteins shares homology with cell wall hydrolases, a physiological function that correlates with such an enzymatic activity remained to be substantiated in LGG. To investigate the bacterial function, we constructed knock-out mutants in the corresponding genes aiming to establish a genotype to phenotype relation. Microscopic examination of the msp1 mutant showed the presence of rather long and overly extended cell chains, which suggests that normal daughter cell separation is hampered. Subsequent observation of the LGG wild-type cells by immunofluorescence microscopy revealed that the Msp1 protein accumulates at the septum of exponential-phase cells. The cell wall hydrolyzing activity of the Msp1 protein was confirmed by zymogram analysis. Subsequent analysis by RP-HPLC and mass spectrometry of the digestion products of LGG peptidoglycan (PG) by Msp1 indicated that the Msp1 protein has D-glutamyl-L-lysyl endopeptidase activity. Immunofluorescence microscopy and the failure to construct a knock-out mutant suggest an indispensable role for Msp2 in priming septum formation in LGG.

ano.nymous@ccsd.cnrs.fr.invalid (Ingmar J. J. Claes) 29 May 2020

https://hal.science/hal-01189702v1

[hal-03753288] Modulation of skeletal muscle function by gut microbiota dysbiosis and reseeding

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ano.nymous@ccsd.cnrs.fr.invalid (Kevin Nay) 18 Aug 2022

https://hal.inrae.fr/hal-03753288v1

[hal-02180950] Aerobic glycerol dissimilation via the Enterococcus faecalis DhaK pathway depends on NADH oxidase and a phosphotransfer reaction from PEP to DhaK via EIIADha

Two pathways for glycerol dissimilation are present in <i>Enterococcus faecalis</i>. Either glycerol is first phosphorylated by glycerol kinase and then oxidized by glycerol-3-phosphate oxidase with molecular oxygen as the electron acceptor (GlpO/GlpK pathway), or it is first oxidized by glycerol dehydrogenase with NAD+ as the acceptor of the reduction equivalents and then phosphorylated by dihydroxyacetone kinase (GldA/DhaK pathway). The final end product in both cases is dihydroxyacetone phosphate (DHAP). The genes of the GldA/DhaK pathway are present in a four-gene operon structure encoding GldA, a small hypothetical protein (EF1359), and two subunits of dihydroxyacetone kinase (DhaK and DhaL). We demonstrate in this study that protein EF1359 is part of a phosphorylation cascade which phosphorylates dihydroxyacetone in a phosphoenolpyruvate (PEP)-dependent reaction via EI, HPr, EF1359 and DhaLK. Furthermore we show that aerobic dissimilation of glycerol via the GldA/DhaK pathway is dependent on active NADH oxidase to regenerate NADH in <i>Ent. faecalis</i>. A refined model of the aerobic metabolism of glycerol via the GldA/DhaK pathway is presented.

ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Sauvageot) 11 Jul 2019

https://normandie-univ.hal.science/hal-02180950v1

[hal-05334950] Two-phase model of ageing in mice for improved identification of age-related and late life metabolic decline

Living animals reach their end-of-life through a stereotypic set of fascinating but poorly understood processes. The discovery, first in flies and later in nematodes and zebrafish, of the “Smurf phenotype” has provided a valuable tool to investigate ageing and its associated physiological changes. Using the Smurfs, we have shown an evolutionarily conserved end-of-life transition across Drosophilids, nematodes, and zebrafish. This tool has been key to identify the discontinuous nature of ageing and predict impending death from natural causes as well as from environmental stresses. This phenotype led us to propose a two-phase perspective of ageing: a first phase where individuals are apparently healthy and have low risk of mortality, but show an age-dependent and increasing risk of entering a second phase, marked by more pronounced hallmarks of ageing and a markedly increased risk of death. Here, we test whether these two consecutive phases of ageing separated by the Smurf transition are a conserved feature of ageing in the mammals using Mus musculus as a model. We performed a longitudinal longevity study using both males and females from two different mouse genetic backgrounds and by integrating physiological, metabolic, and molecular measurements with the life history of approximately 150 mice. We show the existence of a phenotypic signature typical of the last phase of life, observable at any chronological age. Validating the two-phase ageing model in a mammalian organism allows better characterization of the high risk of imminent death and would extend its implications to a broader range of species for ageing research. The Stage 1 version of this Registered Report was submitted on 19th January 2022.

ano.nymous@ccsd.cnrs.fr.invalid (Céline Cansell) 04 Nov 2025

https://hal.science/hal-05334950v1

[hal-01004635] Structure, Adsorption to Host, and Infection Mechanism of Virulent Lactococcal Phage p2

Lactococcal siphophages from the 936 and P335 groups infect the Gram-positive bacterium Lactococcus lactis using receptor binding proteins (RBPs) attached to their baseplate, a large multiprotein complex at the distal part of the tail. We have previously reported the crystal and electron microscopy (EM) structures of the baseplates of phages p2 (936 group) and TP901-1 (P335 group) as well as the full EM structure of the TP901-1 virion. Here, we report the complete EM structure of siphophage p2, including its capsid, connector complex, tail, and baseplate. Furthermore, we show that the p2 tail is characterized by the presence of protruding decorations, which are related to adhesins and are likely contributed by the major tail protein C-terminal domains. This feature is reminiscent of the tail of Escherichia coli phage lambda and Bacillus subtilis phage SPP1 and might point to a common mechanism for establishing initial interactions with their bacterial hosts. Comparative analyses showed that the architecture of the phage p2 baseplate differs largely from that of lactococcal phage TP901-1. We quantified the interaction of its RBP with the saccharidic receptor and determined that specificity is due to lower k(off) values of the RBP/saccharidic dissociation. Taken together, these results suggest that the infection of L. lactis strains by phage p2 is a multistep process that involves reversible attachment, followed by baseplate activation, specific attachment of the RBPs to the saccharidic receptor, and DNA ejection.

ano.nymous@ccsd.cnrs.fr.invalid (Cecilia C. Bebeacua) 11 Jun 2014

https://hal.science/hal-01004635v1

[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

[hal-05289701] Atypical Replication Error Pattern and Limited Repair Efficiency Contribute to Elevated Mutation Rate in Phage lambda

Abstract Understanding the rate and nature of spontaneous mutations is crucial for understanding and modulating the pace and trajectory of evolution. Yet, both remain poorly characterized in double-stranded DNA (dsDNA) phages, despite their relevance for phage-based therapies. Here, we address this gap for the dsDNA phage lambda, using four complementary approaches: mutation accumulation assay combined with whole-genome sequencing, mutation visualization assay, duplex sequencing and fluctuation assay. We find that the mutation rate of wild-type phage lambda is 4.9 ± 1.8 x10 -9 per base per replication, approximately 15 times lower than previously estimated and about 20 times higher than that of its host, Escherichia coli ( E. coli ). Inactivation of Mismatch Repair (MMR), a major conserved cellular system for mutation avoidance, increases the lambda mutation rate by only 2-to 10-fold, in contrast to the approximately 150-fold increase in E. coli , however lambda does not exhibit the characteristic mutational bias associated with MMR deficiency. Interestingly replication of the lambda genome generates an error spectrum distinct from that of E. coli , characterized by a marked increase in transversions, poorly repaired by MMR. Together, these results reveal that lambda exhibits a replication error profile that is less amenable to repair, likely contributing to its elevated mutation rate.

ano.nymous@ccsd.cnrs.fr.invalid (Julien Lopez) 07 Oct 2025

https://hal.science/hal-05289701v1

[hal-05289461] Mutagenesis: Insights from Single-Cell, Real-Time Approaches

All genetic variation fueling evolution depends on mutations. Although mutations have been extensively studied for almost a century, until a decade ago the investigation of mutations was limited to population-level analysis. This constraint has hampered the exploration of cellular heterogeneity in mutation processes and its evolutionary implications. To overcome these limitations, quantitative visualization methods for studying mutations in the bacterium Escherichia coli at the single-cell level have been developed. These approaches offer the possibility of accessing a major source of mutations, i.e., DNA polymerase errors, and their fate, i.e., repair versus conversion to mutation. In addition, such methods allow for quantitative characterization of the effects of mutations on cell fitness. This article discusses insights into the mutation process derived from these new single-cell mutagenesis approaches.

ano.nymous@ccsd.cnrs.fr.invalid (Marina Elez) 30 Sep 2025

https://hal.science/hal-05289461v1

[hal-03344281] A bacterial prophage small peptide counteracts DnaA activities in B. subtilis

Abstract Bacteriophages are able to hijack host essential machineries to benefit their fitness and assemble their own progeny. Phage proteins targeting major bacterial pathways can be powerful tools to understand cell functions and have possible applications in human health and industry. Bacterial genomes also harbor cryptic prophages carrying genes that may contribute to their host fitness and properties. The cryptic prophages are mostly transcriptionally silent and most of the functions they encode are not annotated. In B. subtilis , the 48 kb-long skin element is a prophage carrying the yqaF-yqaN operon, which is tightly regulated by the Xre-like repressor sknR . The small yqaH gene potentially encodes the protein YqaH in absence of SknR. It was previously reported that YqaH interacts with the replication initiator DnaA in yeast two-hybrid assay and its expression in B. subtilis causes defects in the chromosomal cycle. In this study, we report that, in addition to DnaA, YqaH interacts with Spo0A, a master regulator of sporulation. To decipher yqaH mode of action, we used the yeast two-hybrid to isolate single mutations in yqaH that separate interactions with DnaA and Spo0A. We isolated mutations that caused loss-of-interaction (LOI) with DnaA but not Spo0A. However, all mutations disrupting the interaction with Spo0A were also DnaA-LOI functions, suggesting that these functions could not be separated. We found that expression YqaH carrying DnaA-LOI mutations affects both chromosome integrity and DnaA-mediated transcription, leading to growth inhibition as well as preventing bacterial development such as sporulation and biofilm formation. These results show that YqaH acts as an antimicrobial peptide in B. subtilis and pave the way for the structural design of mutants with improved antibacterial action.

ano.nymous@ccsd.cnrs.fr.invalid (Magali Ventroux) 14 Sep 2021

https://hal.inrae.fr/hal-03344281v1

[hal-05347177] Large-Scale Screening of a Targeted Enterococcus faecalis Mutant Library Identifies Envelope Fitness Factors

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Lionel Rigottier-Gois) 04 Nov 2025

https://hal.science/hal-05347177v1

[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

[hal-05343841] 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) 03 Nov 2025

https://hal.science/hal-05343841v1

[hal-03370372] A high content microscopy screening identifies new genes involved in cell width control in Bacillus subtilis

Abstract How cells control their shape and size is a fundamental question of biology. In most bacteria, cell shape is imposed by the peptidoglycan (PG) polymeric meshwork that surrounds the cell. Thus, bacterial cell morphogenesis results from the coordinated action of the proteins assembling and degrading the PG shell. Remarkably, during steady-state growth, most bacteria maintain a defined shape along generations, suggesting that error-proof mechanisms tightly control the process. In the rod-shaped model for Gram-positive bacteria Bacillus subtilis , the average cell length varies as a function of the growth rate but the cell diameter remains constant throughout the cell cycle and across growth conditions. Here, in an attempt to shed light on the cellular circuits controlling bacterial cell width, we developed a screen to identify genetic determinants of cell width in B. subtilis . Using high-content screening (HCS) fluorescence microscopy and semi-automated measurement of single-cell dimensions, we screened a library of ~ 4000 single knockout mutants. We identified 13 mutations significantly altering cell diameter, in genes that belong to several functional groups. In particular, our results indicate that metabolism plays a major role in cell width control in B. subtilis .

ano.nymous@ccsd.cnrs.fr.invalid (Dimitri Juillot) 08 Oct 2021

https://hal.inrae.fr/hal-03370372v1

[hal-04981805] Update of guidelines for management of Community Acquired pneumonia in adults by the French Infectious Disease Society (SPILF) and the French-Speaking Society of Respiratory Diseases (SPLF)

Community-Acquired Pneumonia (CAP) of Presumed Bacterial Origin: Updated Management Guidelines Community-acquired pneumonia (CAP) of presumed bacterial origin is a common condition with varying severity, requiring either outpatient, hospital, or even critical care management. The French Infectious Diseases Society (SPILF) and the French Language Pulmonology Society (SPLF), in collaboration with the French Societies of Microbiology (SFM), Emergency Medicine (SFMU), Radiology (SFR), and Intensive Care Medicine (SRLF), along with representatives of general practice, have coordinated an update of the previous management guidelines, which dated back to 2010. From a therapeutic perspective, the updated recommendations define the choice of initial empiric antibiotic therapy, indications for combination therapy, the use of anti-Pseudomonas beta-lactams, antibiotic treatment duration, and the indications and modalities for prescribing systemic corticosteroids. On a biological level, indications for biomarkers and microbiological investigations have been refined. Regarding imaging, the role of different modalities in the diagnosis and follow-up of CAP has been reassessed, including chest X-ray, pleuropulmonary ultrasound, and thoracic CT scan.

ano.nymous@ccsd.cnrs.fr.invalid (Aurélien Dinh) 29 Sep 2025

https://u-picardie.hal.science/hal-04981805v1

[hal-05322017] Deciphering the mechanisms of action underlying probiotic properties of Shouchella clausii by a functional genomics approach

Abstract Probiotics are widely used for their health promoting effects, though a lot remain to be discovered, particularly on their mechanisms of action at the molecular level. The functional genomic approach is an appropriate method to decipher how probiotics may influence human cell fate and therefore contribute to their health benefit. In the present work, we focused on Shouchella clausii (formerly named Bacillus then Alkalihalobacillus clausii ), a spore-forming bacterium that is commercially available as a probiotic for the prevention and the treatment of intestinal dysbiosis and related gastrointestinal disorders, such as diarrhoea. Several studies have demonstrated that S. clausii treatment modulated inflammatory and immune responses, as well as gut barrier functions. A functional genomic strategy was implemented to decipher the mechanisms by which S. clausii exerts its probiotic effects on human intestinal epithelial cells. To do so, a large genomic DNA fragment library was constructed for each of the four strains: O/C, N/R, SIN and T. A high throughput in vitro screening in human epithelial cells was then conducted, using the reporter gene strategy, targeting the nuclear factor kappa B (NF-κB) pathway and interleukin-10 (IL-10) gene expression. After an exhaustive in vitro screening of approximately a thousand clones per library, several clones modulating the NF-κB pathway in the HT-29 reporter cell line were identified. Among clone lysates, 1.1% (O/C), 1.4% (N/R), 2.0% (SIN), and 1.2% (T) were identified as biologically active on immune reporter systems (NF-κB and IL-10 expression). After transposon mutagenesis and a new set of screening and sequencing, 23 coding sequences (CDS) were identified, including one encoding for the glutamine synthetase, associated with NF-κB modulation, and six CDS for IL-10 modulation. The functional genomic strategy that was applied to S. clausii was an original approach to identify gene candidates that may explain the mechanisms of action of probiotics. However, further work is needed to validate the identified leads.

ano.nymous@ccsd.cnrs.fr.invalid (A. Lashermes) 20 Oct 2025

https://hal.science/hal-05322017v1

[hal-02620321] Alternative splicing events expand molecular diversity of camel CSN1S2 increasing its ability to generate potentially bioactive peptides

In a previous study on camel milk from Kazakhstan, we reported the occurrence of two unknown proteins (UP1 and UP2) with different levels of phosphorylation. Here we show that UP1 and UP2 are isoforms of camel αs2-CN (αs2-CNsv1 and αs2-CNsv2, respectively) arising from alternative splicing events. First described as a 178 amino-acids long protein carrying eight phosphate groups, the major camel αs2-CN isoform (called here αs2-CN) has a molecular mass of 21,906 Da. αs2-CNsv1, a rather frequent (35%) isoform displaying a higher molecular mass (+1,033 Da), is present at four phosphorylation levels (8P to 11P). Using cDNA-sequencing, αs2-CNsv1 was shown to be a variant arising from the splicing-in of an in-frame 27-nucleotide sequence encoding the nonapeptide ENSKKTVDM, for which the presence at the genome level was confirmed. αs2-CNsv2, which appeared to be present at 8P to 12P, was shown to include an additional decapeptide (VKAYQIIPNL) revealed by LC-MS/MS, encoded by a 3'-extension of exon 16. Since milk proteins represent a reservoir of biologically active peptides, the molecular diversity generated by differential splicing might increase its content. To evaluate this possibility, we searched for bioactive peptides encrypted in the different camel αs2-CN isoforms, using an in silico approach. Several peptides, putatively released from the C-terminal part of camel αs2-CN isoforms after in silico digestion by proteases from the digestive tract, were predicted to display anti-bacterial and antihypertensive activities.

ano.nymous@ccsd.cnrs.fr.invalid (Alma Ryskaliyeva) 26 May 2020

https://hal.inrae.fr/hal-02620321v1

[hal-02621893] Combining different proteomic approaches to resolve complexity of the milk protein fraction of dromedary, Bactrian camels and hybrids, from different regions of Kazakhstan

Nutritional suitability of milk is not only related to gross composition, but is also strongly affected by the microheterogeniety of the protein fraction. Hence, to go further into the evaluation of the potential suitability of non-bovine milks in human/infant nutrition it is necessary to have a detailed characterization of their protein components. Combining proven proteomic approaches (SDS-PAGE, LC-MS/MS and LC-ESI-MS) and cDNA sequencing, we provide here in depth characterization of the milk protein fraction of dromedary and Bactrian camels, and their hybrids, from different regions of Kazakhstan. A total 391 functional groups of proteins were identified from 8 camel milk samples. A detailed characterization of 50 protein molecules, relating to genetic variants and isoforms arising from post-translational modifications and alternative splicing events, belonging to nine protein families (κ-, αs1-, αs2-, β-; and γ-CN, WAP, α-LAC, PGRP, CSA/LPO) was achieved by LC-ESI-MS. The presence of two unknown proteins UP1 (22,939 Da) and UP2 (23,046 Da) was also reported as well as the existence of a β-CN short isoform (946 Da lighter than the full-length β-CN), arising very likely in both genetic variants (A and B) from proteolysis by plasmin. In addition, we report, for the first time to our knowledge, the occurrence of a αs2-CN phosphorylation isoform with 12P groups within two recognition motifs, suggesting thereby the existence of two kinase systems involved in the phosphorylation of caseins in the mammary gland. Finally, we demonstrate that genetic variants, which hitherto seemed to be species- specific (e.g. β-CN A for Bactrian and β-CN B for dromedary), are in fact present both in Camel dromedarius and C. bactrianus.

ano.nymous@ccsd.cnrs.fr.invalid (Alma Ryskaliyeva) 26 May 2020

https://hal.inrae.fr/hal-02621893v1

[hal-02624536] The main WAP isoform usually found in camel milk arises from the usage of an improbable intron cryptic splice site in the precursor to mRNA in which a GC-AG intron occurs

BACKGROUND: Whey acidic protein (WAP) is a major protein identified in the milk of several mammalian species with cysteine-rich domains known as four-disulfide cores (4-DSC). The organization of the eutherian WAP genes is highly conserved through evolution. It has been proposed that WAP could play an important role in regulating the proliferation of mammary epithelial cells. A bacteriostatic activity was also reported. Conversely to the other mammalian species expressing WAP in their milk, camel WAP contains 4 additional amino acid residues at the beginning of the second 4-DSC domain, introducing a phosphorylation site. The aim of this study was to elucidate the origin of this specificity, which possibly impacts its physiological functions. RESULTS: Using LC-ESI-MS, we identified in Camelus bactrianus from Kazakhstan a phosphorylated whey protein, exhibiting a molecular mass (12,596 Da), 32 Da higher than the original WAP (12,564 Da) and co-eluting with WAP. cDNA sequencing revealed a transition G/A, which modifies an amino acid residue of the mature protein (V12 M), accounting for the mass difference observed between WAP genetic variants. We also report the existence of two splicing variants of camel WAP precursors to mRNA, arising from an alternative usage of the canonical splice site recognized as such in the other mammalian species. However, the major camel WAP isoform results from the usage of an unlikely intron cryptic splice site, extending camel exon 3 upstream by 12-nucleotides encoding the 4 additional amino acid residues (VSSP) in which a potentially phosphorylable Serine residue occurs. Combining protein and cDNA sequences with genome data available (NCBI database), we report another feature of the camel WAP gene which displays a very rare GC-AG type intron. This result was confirmed by sequencing a genomic DNA fragment encompassing exon 3 to exon 4, suggesting for the GC donor site a compensatory effect in terms of consensus at the acceptor exon position. CONCLUSIONS: Combining proteomic and molecular biology approaches we report: the characterization of a new genetic variant of camel WAP, the usage of an unlikely intron cryptic splice site, and the occurrence of an extremely rare GC-AG type of intron.

ano.nymous@ccsd.cnrs.fr.invalid (Alma Ryskaliyeva) 26 May 2020

https://hal.inrae.fr/hal-02624536v1

[hal-05244825] 3D imaging-driven assembly of multi-species biofilms with antagonistic activity against undesirable bacteria

Engineered synthetic microbial communities (SynComs) forming biofilms with antagonistic activity offer a promising strategy in biotechnology to prevent harmful bacterial settlement and reduce reliance on chemical antimicrobials. However, strain selection criteria and antagonistic mechanisms remain unclear. This study presents a bottom-up approach integrating 3D fluorescence imaging with high-throughput analysis of multi-strain biofilms. Our findings reveal that competitive strains against undesirable bacteria may also exclude desirable community members, highlighting the need for compatibility control in SynCom assembly. SynComs composed of B. velezensis and Pediococcus spp. 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 dynamics (prey-predator Lotka-Volterra model). Furthermore, pre-established SynComs significantly increased pathogen inhibition, indicating a distinct biofilm-associated exclusion effect. These insights provide a framework for SynCom assembly and refine our understanding of interaction dynamics driving antagonistic biofilm applications.

ano.nymous@ccsd.cnrs.fr.invalid (Virgile Guéneau) 08 Sep 2025

https://hal.inrae.fr/hal-05244825v1

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PUBLICATIONS

> Click here to access the recent publication list from Micalis

HAL : Dernières publications

[hal-03975895] Harnessing the Vnn1 pantetheinase pathway boosts short chain fatty acids production and mucosal protection in colitis

[hal-04714371] Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories

[hal-05311416] Immunometabolic reprogramming of macrophages by gut microbiota-derived cadaverine controls colon inflammation

[hal-04290181] Near-infrared co-illumination of fluorescent proteins reduces photobleaching and phototoxicity

[hal-04565252] Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

[hal-03620811] Exploring the biosynthetic capacity of TsrM, a B12‐dependent Radical SAM Enzyme Catalyzing Non‐radical Reactions

[hal-03624206] Capnocytophaga zoonotic infections: a 10-year retrospective study (the French CANCAN study)

[hal-04316567] Contribution of the anaerobic blood culture vial for the recovery of Candida glabrata : A retrospective multicentric study

[hal-01532602] Mass Spectrometry Analysis of the Extracellular Peptidome of Lactococcus lactis: Lines of Evidence for the Coexistence of Extracellular Protein Hydrolysis and Intracellular Peptide Excretion

[hal-03593214] Microbial biofilms : Structural plasticity and emerging properties

[hal-04695580] Genomic pipeline for analysis of mutational events in bacteria

[hal-05323164] Enzymes Required for Maltodextrin Catabolism in Enterococcus faecalis Exhibit Novel Activities

[hal-04297740] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les enfants de 0 à 3 ans

[hal-05238241] One process applied to different cereals leads to specific microbial profiles: the case of traditional fermented couscous from Senegal.

[hal-04314263] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les femmes enceintes ou allaitantes

[anses-04171242] Évaluation des impacts sur la santé publique de la dynamique des populations de renards

[hal-03751737] Contribution of omics to biopreservation: Toward food microbiome engineering

[anses-04453336] Avis de l'Anses relatif à un document d’appui aux lignes directrices de l’arrêté du 7 mars 2011 relatives à l’évaluation de l'efficacité antimicrobienne des auxiliaires technologiques utilisés comme agents de décontamination des denrées d’origine végétale

[hal-04345448] Hétérogénéités génotypique, physiologique et cellulaire des bactéries pathogènes alimentaires

[hal-02790439] Avis de l'Anses relatif à l’actualisation des repères alimentaires du PNNS pour les enfants de 4 à 17 ans

[hal-04337407] Le microbiote et l’hôte: un duo dont les interactions évoluent en fonction des quantités de fer apportées par l’alimentation

[anses-04027039] Évaluation des risques liés à la consommation de nitrates et nitrites

[hal-05239660] Unlocking the potential of plant-based fermented foods through a Living Lab approach with consumers and stakeholders

[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

[hal-04727009] Quels sont les effets santé des produits fermentés ? Focus sur les végétaux fermentés

[hal-04645842] The microbiota and the host organism switch between cooperation and competition based on dietary iron levels

[hal-05240627] Du traditionnel vers le rationnel : utilisation d'approches omiques pour la conception d'écosystèmes microbiens sur mesures et la fabrication d'une boisson fermentée céréalière saine et durable

[hal-05124696] Impacts sur la santé publique de la dynamique des populations de renards

[hal-02915539] Cycle biogéochimique du P organique : mécanismes mis en jeu dans la mobilisation du P du phytate par Bacillus subtilis et la boucle trophique

[hal-01004544] Food fermentations: Microorganisms with technological beneficial use

[hal-01594855] Human gut microbes impact host serum metabolome and insulin sensitivity

[hal-01189702] Genetic and biochemical characterization of the cell wall hydrolase activity of the major secreted protein of Lactobacillus rhamnosus GG

[hal-03753288] Modulation of skeletal muscle function by gut microbiota dysbiosis and reseeding

[hal-02180950] Aerobic glycerol dissimilation via the Enterococcus faecalis DhaK pathway depends on NADH oxidase and a phosphotransfer reaction from PEP to DhaK via EIIADha

[hal-05334950] Two-phase model of ageing in mice for improved identification of age-related and late life metabolic decline

[hal-01004635] Structure, Adsorption to Host, and Infection Mechanism of Virulent Lactococcal Phage p2

[hal-05347161] Intestinal hepcidin overexpression promotes iron deficiency anemia and counteracts iron overload via DMT1 downregulation

[hal-05289701] Atypical Replication Error Pattern and Limited Repair Efficiency Contribute to Elevated Mutation Rate in Phage lambda

[hal-05289461] Mutagenesis: Insights from Single-Cell, Real-Time Approaches

[hal-03344281] A bacterial prophage small peptide counteracts DnaA activities in B. subtilis

[hal-05347177] Large-Scale Screening of a Targeted Enterococcus faecalis Mutant Library Identifies Envelope Fitness Factors

[hal-02941029] Sulfiredoxin Protects Mice from Lipopolysaccharide-Induced Endotoxic Shock

[hal-05343841] MAIT cells monitor intestinal dysbiosis and contribute to host protection during colitis

[hal-03370372] A high content microscopy screening identifies new genes involved in cell width control in Bacillus subtilis

[hal-04981805] Update of guidelines for management of Community Acquired pneumonia in adults by the French Infectious Disease Society (SPILF) and the French-Speaking Society of Respiratory Diseases (SPLF)

[hal-05322017] Deciphering the mechanisms of action underlying probiotic properties of Shouchella clausii by a functional genomics approach

[hal-02620321] Alternative splicing events expand molecular diversity of camel CSN1S2 increasing its ability to generate potentially bioactive peptides

[hal-02621893] Combining different proteomic approaches to resolve complexity of the milk protein fraction of dromedary, Bactrian camels and hybrids, from different regions of Kazakhstan

[hal-02624536] The main WAP isoform usually found in camel milk arises from the usage of an improbable intron cryptic splice site in the precursor to mRNA in which a GC-AG intron occurs

[hal-05244825] 3D imaging-driven assembly of multi-species biofilms with antagonistic activity against undesirable bacteria

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