Publications

[hal-04099157] Microbiome-based solutions to address new and existing threats to food security, nutrition, health and agrifood systems' sustainability

In addition to challenges like climate change and biodiversity loss, the sustainability and resilience of agrifood systems worldwide are currently challenged by new threats, such as the COVID-19 pandemic and the Ukraine war. Furthermore, the resilience and sustainability of our agrifood systems need to be enhanced in ways that simultaneously increase agricultural production, decrease post-harvest food losses and food waste, protect the climate, environment and health, and preserve biodiversity. The precarious situation of agrifood systems is also illustrated by the fact that overall, around 3 billion people worldwide still do not have regular access to a healthy diet. This results in various forms of malnutrition, as well as increasing number of people suffering from overweight and obesity, and diet-related, non-communicable diseases (NCDs) around the world. Findings from microbiome research have shown that the human gut microbiome plays a key role in nutrition and diet-related diseases and thus human health. Furthermore, the microbiome of soils, plants, and animals play an equally important role in environmental health and agricultural production. Upcoming, microbiome-based solutions hold great potential for more resilient, sustainable, and productive agrifood systems and open avenues toward preventive health management. Microbiome-based solutions will also be key to make better use of natural resources and increase the resilience of agrifood systems to future emerging and already-known crises. To realize the promises of microbiome science and innovation, there is a need to invest in enhancing the role of microbiomes in agrifood systems in a holistic One Health approach and to accelerate knowledge translation and implementation.

ano.nymous@ccsd.cnrs.fr.invalid (Karel Callens) 16 May 2023

https://hal.inrae.fr/hal-04099157v1

[hal-04336557] BiochiMix, et si un jeu permettait de réaliser une mind map pour réviser ?

Introduction : Comment faire découvrir la base des molécules du vivant à des non biologistes ? Et si un jeu permettait de réaliser une mind map pour réviser ? BiochiMix a été mis en place dans le cadre d’enseignements de biochimie structurale destinés à des étudiants en licence professionnelle « Services clients en instrumentation et réactifs de laboratoire ». L’objectif pédagogique principal est de savoir reconnaitre les quatre grandes catégories de molécules biologiques : acides nucléiques, glucides, lipides et protéines. Ce jeu permet également aux étudiants de retenir les principales techniques d’analyses associées à ces molécules et faire la différence entre les monomères et les polymères de ces molécules biologiques. Public : Principalement destiné à des étudiants dans les premières années universitaires découvrant les molécules biologiques et leur analyse. Adaptable au grand public dans le cadre de médiation scientifique, BiochiMix peut aussi bien se jouer en mode collaboratif (une table de jeu de 3 ou 4 étudiants) ou qu’en mode tournoi (plusieurs tables en compétition). La durée d’une partie est estimée entre 10 à 20 minutes. L’objectif est d’associer correctement les cartes avec les catégories disponibles sur le plateau. L’équipe qui a le plus de bonnes réponses remporte la partie ! Avantages : Le jeu BiochiMix permet aux étudiants de faire un état rapide de leurs connaissances avant les examens et pour le grand public, il permet de découvrir la diversité des molécules du vivant. A l’issue du jeu (après vérification des combinaisons), il est possible de prendre en photo le plateau qui constitue ainsi une mind map de révision. La conception du jeu est telle qu’il est possible de rajouter de nouvelles cartes pour étendre/modifier les exemples présentés pour chacune des catégories. Conclusion : Le jeu BiochiMix est un outil ludique de formation et de communication sur les molécules du vivant, simple d’utilisation et adaptable à différents publics.

ano.nymous@ccsd.cnrs.fr.invalid (Anaïs Brosse) 11 Dec 2023

https://hal.science/hal-04336557v1

[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-05427912] Lung infection in orally inoculated SARS-CoV-2 hamsters

The digestive tropism of SARS-CoV-2 due to the presence of the same ACE2 receptor in the digestive system as in the respiratory system raised the question of the role of fecal-oral transmission in the pandemic. The aim of this study was to explore oral infection in hamsters model. SARS-CoV-2 inoculation via the oral and intranasal routes resulted in comparable infection in hamsters. In addition to implications for human health, oral infection could have implications for potential animal reservoirs.

ano.nymous@ccsd.cnrs.fr.invalid (Evelyne Picard-Meyer) 21 Dec 2025

https://hal.inrae.fr/hal-05427912v1

[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-05339375] Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech

Les "Premières Journées Scientifiques du Département des Sciences de la Vie et de la Santé" on eu lieu les 25 et 26 avril 2024 sur le campus de Palaiseau. Cet événement visait à présenter, partager et discuter des recherches actuellement menées par les équipes scientifiques du département. Afin de permettre à tous et toutes de découvrir les travaux en cours des scientifiques de SVS, à discuter des liens avec les enjeux actuels en sciences du vivant et en agronomie, et à voir comment ces recherches enrichissent les enseignements dispensés dans l’établissement.

ano.nymous@ccsd.cnrs.fr.invalid (Carmen Bessa-Gomes) 30 Oct 2025

https://hal.science/hal-05339375v1

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

The Red Fox (Vulpes vulpes) can be hunted as a game species. It may also be listed as a “species likely to cause damage” (ESOD – the acronym in French), for public health reasons among others. Conversely, benefits linked to the presence of foxes are also put forward, such as the predation of rodents carrying zoonotic agents. In this context, ANSES was asked to: (1) list the zoonoses present in France for which foxes play an epidemiological role, (2) identify other public health impacts associated with changes in fox populations, (3) explain the relative importance of the effects of changes in fox populations for humans and/or the environment, (4) analyse the feasibility of a cost‐benefit analysis (CBA) of the prevention and impacts associated with these zoonoses. In France, the fox is a source of zoonotic pathogens, with a major role for Echinococcus multilocularis, a parasite for which the fox is the main source of environmental contamination. However, reducing fox populations does not reduce the risk of transmission of E. multilocularis to humans or domestic animals, and may even have the opposite effect to the one intended. The main levers for action are those relating to exposure to environmental contamination. The fox is part of complex trophic networks, in which its specific role in regulating prey populations is impossible to determine because (i) several predators share the same prey, with a variable role for the fox among the predators, (ii) the dynamics of prey populations is also conditioned by factors other than predation. The relationship between the abundance of rodents and the risk of disease for humans has not been demonstrated either, due to the complexity of the trophic and epidemiological networks, their highly probable variability from one ecosystem to another, and the multiplicity of hosts. As a result, the data currently available does not allow any conclusions to be drawn about the epidemiological role of the fox as a predator of rodents hosting zoonotic agents. Finally, there is no public health justification for culling foxes, particularly for ESOD classification, except in the very specific and localised context of the fight against bovine tuberculosis, for which the selective culling of foxes in and around the livestock buildings of a domestic outbreak has been proposed. In addition, the expertise concluded to the feasibility of a CBA targeted at assessing the burden of alveolar echinococcosis and measures to prevent its transmission. The feasibility study shows the partial nature of a CBA targeting zoonoses, without taking into account other roles played by the fox in the ecosystem.

ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Gilot-Fromont) 18 Jul 2025

https://hal.science/hal-05124696v1

[hal-05447877] Bénéfices des aliments fermentés, de l’empirisme aux démonstrations scientifiques : l’apport de Ferments du Futur

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ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Roland) 08 Jan 2026

https://hal.science/hal-05447877v1

[hal-05447592] Pneumococcus uses COMMD2 to alter host cellular immunity

NF-κB driven cellular immunity is essential for both pro- and anti-inflammatory responses to microbes, which makes it one of the most frequently targeted pathways by bacteria during pathogenesis. How NF-κB tunes the epithelial response to Streptococcus pneumoniae across the spectrum of commensal to pathogenic outcomes is not fully understood. In this study, we compare a commensal-like 6B ST90 strain to an invasive TIGR4 isolate and demonstrate, through comparative mass spectrometry of the p65 interactome, TIGR4 challenge triggers a novel interaction of COMMD2 with p65 and p62. Mechanistically, we show this complex mediates export of p65 for degradation and COMMD2 is necessary for altering host cellular immunity. With these results, we reveal for the first time a new bacterial pathogenesis mechanism to repress host inflammatory response though COMMD2 and p65 degradation while presenting a paradigm for diverging NF-κB responses to pneumococcus.

ano.nymous@ccsd.cnrs.fr.invalid (Michael Connor) 08 Jan 2026

https://hal.science/hal-05447592v1

[inserm-02948958] Mucosal-associated invariant T cells promote inflammation and intestinal dysbiosis leading to metabolic dysfunction during obesity

Obesity is associated with low-grade chronic inflammation promoting insulin-resistance and diabetes. Gut microbiota dysbiosis is a consequence as well as a driver of obesity and diabetes. Mucosal-associated invariant T cells (MAIT) are innate-like T cells expressing a semi-invariant T cell receptor restricted to the non-classical MHC class I molecule MR1 presenting bacterial ligands. Here we show that during obesity MAIT cells promote inflammation in both adipose tissue and ileum, leading to insulin resistance and impaired glucose and lipid metabolism. MAIT cells act in adipose tissue by inducing M1 macrophage polarization in an MR1-dependent manner and in the gut by inducing microbiota dysbiosis and loss of gut integrity. Both MAIT cell-induced tissue alterations contribute to metabolic dysfunction. Treatment with MAIT cell inhibitory ligand demonstrates its potential as a strategy against inflammation, dysbiosis and metabolic disorders.

ano.nymous@ccsd.cnrs.fr.invalid (Amine Toubal) 25 Sep 2020

https://inserm.hal.science/inserm-02948958v1

[anses-04026020] Avis relatif à la représentativité de l’échantillonnage pour la recherche d’histamine dans les poissons

L’histamine est l’une des principales causes de toxi-infections alimentaires liées à la consommation de poisson. L’intoxication histaminique est majoritairement liée à la consommation de poissons riches en histidine. Le comité du Codex Alimentarius sur l’hygiène alimentaire (CCFH) a adopté en 2018, dans le Code d’usages pour les poissons et les produits de la pêche, des orientations de type HACCP pour la maîtrise par les opérateurs de la formation de l’histamine (CXC 52-2003). En parallèle, des discussions sur les normes pour les produits (tels que le thon en conserve ou les blocs de filets de poissons) ont été initiées notamment concernant l’échantillonnage des lots. Dans ce contexte, l’Union européenne a proposé de reprendre le plan à trois classes du règlement européen (CE) n°2073/2005. D’autres pays (USA, Japon notamment) proposent un plan à deux classes avec un échantillonnage plus élevé. Ces divergences d’approches n’ont pas permis d’adopter les sections relatives aux méthodes d’analyse et à l’échantillonnage des produits. Des éléments techniques sont attendus dans le cadre de la reprise des discussions. En outre, l’appréciation de la conformité des lots est rendue délicate par l’hétérogénéité de la contamination des poissons, associée au fait que seule une petite partie des poissons prélevés peut être analysée. Dans ce contexte, la DGAL souhaite disposer d’orientations afin d’améliorer, d’une part les dispositions pour les contrôles officiels, et d’autre part l’appréciation de la pertinence des plans mis en place par les professionnels. Les deux questions adressées dans le courrier de la saisine sont les suivantes : « - L’approche présentée dans les travaux du Codex qui compare la puissance statistique des plans d’échantillonnage de l’histamine entre la position UE et celle des USA/Japon est-elle jugée pertinente ? Quels arguments pourraient présenter l’UE/la France pour défendre son approche lors de la reprise des échanges ? - Dans l’objectif d’établir des recommandations sur l’échantillonnage pour la recherche d’histamine lors des contrôles officiels d’une part, et pour juger de la pertinence des plans mis en place par les professionnels pour les autocontrôles d’autre part, quelles seraient les propositions d’orientations de l’Anses (partie du poisson utilisée comme échantillon, définition du lot, analyse systématique ou non de tous les lots, nombre maximal d’unités d’un échantillonnage composite/pooling, etc.) ? » La première question a fait l’objet d’une note d’appui scientifique et technique (AST) du 30 novembre 2021, la seconde question est l’objet de cet avis.

ano.nymous@ccsd.cnrs.fr.invalid (Philippe Fravalo) 13 Mar 2023

https://anses.hal.science/anses-04026020v1

[hal-02641529] Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children

Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader-Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Ourmulti-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation. Research in context: Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children genetically obese with Prader-Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity. A diet rich in non-digestible but fermentable carbohydrates significantly promoted beneficial groups of bacteria and reduced toxin-producers, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces.

ano.nymous@ccsd.cnrs.fr.invalid (Chenhong Zhang) 28 May 2020

https://hal.inrae.fr/hal-02641529v1

[hal-01204455] Commensal microbiota influence systemic autoimmune responses

Antinuclear antibodies are a hallmark feature of generalized autoimmune diseases, including systemic lupus erythematosus and systemic sclerosis. However, the processes underlying the loss of tolerance against nuclear self-constituents remain largely unresolved. Using mice deficient in lymphotoxin and Hox11, we report that approximately 25% of mice lacking secondary lymphoid organs spontaneously develop specific antinuclear antibodies. Interestingly, we find this phenotype is not caused by a defect in central tolerance. Rather, cell-specific deletion and in vivo lymphotoxin blockade link these systemic autoimmune responses to the formation of gut-associated lymphoid tissue in the neonatal period of life. We further demonstrate antinuclear antibody production is influenced by the presence of commensal gut flora, in particular increased colonization with segmented filamentous bacteria, and IL-17 receptor signaling. Together, these data indicate that neonatal colonization of gut microbiota influences generalized autoimmunity in adult life.

ano.nymous@ccsd.cnrs.fr.invalid (Jens T. van Praet) 23 Sep 2015

https://hal.science/hal-01204455v1

[hal-03818233] Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

ano.nymous@ccsd.cnrs.fr.invalid (Andrey Yurkov) 17 Oct 2022

https://hal.inrae.fr/hal-03818233v1

[hal-04297527] Characterization and Whole Genome Sequencing of AR23, a Highly Toxic Bacillus thuringiensis Strain Isolated from Lebanese Soil

The demand for sustainable and eco-friendly control methods of pests and insects is increasing worldwide. From this came the interest in Bacillus thuringiensis, an entomopathogenic bacterium capable of replacing chemical pesticides. However, the possibility of pests developing resistance to a particular strain may impair its use, and there is a need to identify novel strains of this species as potential commercial biopesticides. B. thuringiensis sv. israelensis is one of the most successful serovars, widely commercialized for its activity against black fly and mosquito larvae. In this study, we isolated, characterized, and sequenced a new Lebanese B. thuringiensis sv. israelensis isolate, strain AR23. Compared to the commercialized reference strain AM65-52 (Vectobac®, Sumitomo), AR23 showed an increased activity against several mosquito species. The genomic analysis revealed that this strain, compared to AM65-52, possesses a simplified plasmid content and an additional functional cry4Ba coding gene that most likely accounts for the increased effectiveness of this strain in mosquito larvae killing.

ano.nymous@ccsd.cnrs.fr.invalid (Nancy Fayad) 06 Dec 2023

https://hal.inrae.fr/hal-04297527v1

[hal-01606175] Energy balance and obesity: what are the main drivers?

The aim of this paper is to review the evidence of the association between energy balance and obesity. In December 2015, the International Agency for Research on Cancer (IARC), Lyon, France convened a Working Group of international experts to review the evidence regarding energy balance and obesity, with a focus on Low and Middle Income Countries (LMIC). The global epidemic of obesity and the double burden, in LMICs, of malnutrition (coexistence of undernutrition and overnutrition) are both related to poor quality diet and unbalanced energy intake. Dietary patterns consistent with a traditional Mediterranean diet and other measures of diet quality can contribute to long-term weight control. Limiting consumption of sugar-sweetened beverages has a particularly important role in weight control. Genetic factors alone cannot explain the global epidemic of obesity. However, genetic, epigenetic factors and the microbiota could influence individual responses to diet and physical activity. Energy intake that exceeds energy expenditure is the main driver of weight gain. The quality of the diet may exert its effect on energy balance through complex hormonal and neurological pathways that influence satiety and possibly through other mechanisms. The food environment, marketing of unhealthy foods and urbanization, and reduction in sedentary behaviors and physical activity play important roles. Most of the evidence comes from High Income Countries and more research is needed in LMICs.

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Romieu) 27 May 2020

https://hal.science/hal-01606175v1

[hal-02154535] Le laboratoire international associé Bact-Inflam, l’aboutissement de 17 années de collaboration France-Brésil

Le laboratoire international associé (LIA) Bact-Inflam, dédié à l’étude des bactéries et des maladies inflammatoires en santé humaine et animale, offre un exemple exceptionnel de coopération réussie entre le Brésil et la France depuis le début du XXIe siècle.

ano.nymous@ccsd.cnrs.fr.invalid (Vasco Azevedo) 12 Jun 2019

https://hal.science/hal-02154535v1

[hal-01204337] Partindo de dados (meta)genômicos para entender as relações bactéria-hospedeiro no trato gastro intestinal

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ano.nymous@ccsd.cnrs.fr.invalid (Maarten van de Guchte) 23 Sep 2015

https://hal.science/hal-01204337v1

[hal-03752257] Intraspecific Diversity of Microbial Anti-Inflammatory Molecule (MAM) from Faecalibacterium prausnitzii

The commensal bacterium Faecalibacterium prausnitzii has unique anti-inflammatory properties, at least some of which have been attributed to its production of MAM, the Microbial Anti-inflammatory Molecule. Previous phylogenetic studies of F. prausnitzii strains have revealed the existence of various phylogroups. In this work, we address the question of whether MAMs from different phylogroups display distinct anti-inflammatory properties. We first performed wide-scale identification, classification, and phylogenetic analysis of MAM-like proteins encoded in different genomes of F. prausnitzii. When combined with a gene context analysis, this approach distinguished at least 10 distinct clusters of MAMs, providing evidence for functional diversity within this protein. We then selected 11 MAMs from various clusters and evaluated their anti-inflammatory capacities in vitro. A wide range of anti-inflammatory activity was detected. MAM from the M21/2 strain had the highest inhibitory effect (96% inhibition), while MAM from reference strain A2-165 demonstrated only 56% inhibition, and MAM from strain CNCM4541 was almost inactive. These results were confirmed in vivo in murine models of acute and chronic colitis. This study provides insights into the family of MAM proteins and generates clues regarding the choice of F. prausnitzii strains as probiotics for use in targeting chronic inflammatory diseases.

ano.nymous@ccsd.cnrs.fr.invalid (Sandrine Auger) 16 Aug 2022

https://hal.inrae.fr/hal-03752257v1

[hal-03690736] Genomic and probiotic traits of the commensal E. coli CEC15 strain.

Probiotics are microorganisms that can promote beneficial results to the host when administered in adequate quantities. Escherichia coli Nissle 1917 (EcN) is the most commonly known Gram-negative probiotic and its beneficial activities have been demonstrated in many studies since its discovery in the 20th century. We recently isolated from newborn rats’ feces a primo colonizer E. coli strain, called CEC15, with promising probiotic activities. It can colonize the gut of germ-free mice without modifying inflammatory parameters and displays substantial anti-inflammatory effects in a DSS-induced colitis model. In this work, we tested the potential probiotic activity of CEC15 in an in vivo model of intestinal mucositis induced by 5-fluorouracil (5-FU) administration. Bacteria were administered to BALB/c mice (male, 5 weeks old) daily in a 1.1010 CFU/animal dosage. EcN was administered as probiotic activity control. After 10-days of administration, the mucositis was induced by intraperitoneal injection of 5-FU (300mg/Kg), and the animals were sacrificed 72h later. Treatment was kept after mucositis induction. CEC15 promoted reduction of inflammatory histological scores, intestinal permeability, weight loss, and neutrophilic infiltrate, while EcN was only able to prevent an increase in intestinal permeability. An In vitro study of bacterial survival in the gastrointestinal tract (INFOGEST protocol) shows that both strains resist digestion conditions reaching a survival rate of 50% and 10% for CEC15 and EcN, respectively, in an initial dosage of 1.109 CFU/mL. Both strains also exhibit resistance to high concentrations of bile salts. Genomic analysis shows CEC15 belonging to the B1 phylogroup while EcN belongs to the B2 group. CEC15 genome contains 12 putative pathogenic islands against 25 on EcN and does not have the pks island, which encodes for the production of colibactin in EcN, a compound that has been associated with its genotoxicity side effect. Besides being necessary for more assays to confirm the safety and immunomodulation of the CEC15 strain, as well as the effects of its metabolites and extracellular vesicles produced, these results show a promising future for this strain for probiotic applications.

ano.nymous@ccsd.cnrs.fr.invalid (Tales da Silva) 08 Jun 2022

https://hal.inrae.fr/hal-03690736v1

[hal-01536568] Prospective uses of recombinant Lactococcus lactis expressing both listeriolysin O and mutated internalin A from Listeria monocytogenes as a tool for DNA vaccination

In this study, Lactococcus lactis was engineered to express mutated internalin A on its surface and to secrete large amounts of listeriolysin O (LLO) in order to improve its potential as a vehicle for DNA vaccination. Western blotting experiments demonstrated that the bacterium expressed LLO in both the cytoplasmic and extracellular compartments, with higher quantities found in the culture supernatants. A hemolytic assay showed that the recombinant strain secreted 250 ng active LLO/mg total protein. This mInlA/LLO-producing strain of L. lactis may be used as an alternative tool in DNA vaccination against a number of infectious diseases or in cancer therapy.

ano.nymous@ccsd.cnrs.fr.invalid (M. S. P. de Azevedo) 11 Jun 2017

https://hal.science/hal-01536568v1

[hal-01204308] Propriétés probiotiques de bactéries lactiques isolées du microbiote mammaire bovin : Des alliés potentiels contre les mammites

Les mammites bovines représentent un coût économique et sanitaire important pour la production laitière dans le monde. La prévention et le traitement des mammites reposent essentiellement sur l’usage d’antibiotiques qui affectent négativement la qualité de lait et dont l’efficacité est limitée, en particulier vis-à-vis de Staphylococcus aureus. En outre, l’usage massif d’antibiotiques pour contrôler les mammites contribue au risque de dissémination de l’antibiorésistance. Ces dernières années, l'utilisation de microorganismes probiotiques pour lutter contre les infections suscite un intérêt croissant en santé humaine et animale. Le but de cette étude était d'isoler des bactéries lactiques du microbiote mammaire bovin afin d’évaluer leur potentiel probiotique pour la prévention et le traitement des mammites. L'échantillonnage de l'écosystème du canal du trayon a permis l'isolement de 165 clones appartenant principalement aux genres Enterococcus, Streptococcus, Lactobacillus et Lactococcus. Parmi ces isolats, 11 souches appartenant aux genres non pathogènes Lactobacillus et Lactococcus, et non redondantes d’après leur profil PFGE, ont été retenues pour être caractérisées vis-à-vis de leurs propriétés de surface (hydrophobicité, autoaggrégation), leur capacité à produire des substances antimicrobiennes, leurs capacités d'adhésion et d’internalisation aux cellules épithéliales mammaires bovines MAC-T et leurs propriétés immunomodulatrices. Ce criblage in vitro a permis la sélection de 2 souches de L. brevis et 1 souche de L. plantarum pour leur capacité à coloniser le tissu épithélial mammaire bovin. Le potentiel immonumodulateur, determiné sur culture cellulaire, a révélé une tendance pro-inflammatoire pour deux souches appartenant aux espèces L. casei et L. brevis et une tendance antiinflammatoire de 2 souches de L. plantarum. Ce travail ouvre de nouvelles perspectives sur le développement de solutions alternatives et durables pour le contrôle des mammites bovines.

ano.nymous@ccsd.cnrs.fr.invalid (Bianca Seridan de Assis) 23 Sep 2015

https://hal.science/hal-01204308v1

[hal-02619666] Kurtzmaniella hittingeri f.a., sp. nov., isolated from rotting wood and fruits, and transfer of three candida species to the genus kurtzmaniella as new combinations

Twelve strains of a novel yeast species were isolated from rotting wood, mushrooms and fruit samples in Brazil and French Guiana. Analysis of the sequences of the internal transcribed spacer region and the D1/D2 domains of the large subunit rRNA gene showed that the novel species belongs to the Kurtzmaniella Clade. The novel species differed from its closest relative, Candida natalensis, by 12 substitutions in the D1/D2 sequences. The novel species could be distinguished from C. natalensis by its inability to assimilate cellobiose and salicin, and growth at 50 % (w/w) glucose. The name Kurtzmaniella hittingeri f.a., sp. nov. is proposed for the novel species. The type strain of K. hittingeri sp. nov. is CBS 13469(T) (=UFMG CM-Y272(T)). The MycoBank number is 827183. We also propose the transfer of Candida fragi, Candida quercitrusa and Candida natalensis to the genus Kurtzmaniella as new combinations.

ano.nymous@ccsd.cnrs.fr.invalid (Mariana R. Lopes) 25 May 2020

https://hal.inrae.fr/hal-02619666v1

[hal-01204404] Lactococcus lactis carrying the pValac DNA expression vector coding for IL-10 reduces inflammation in a murine model of experimental colitis

Background: Inflammatory bowel diseases (IBD) are intestinal disorders characterized by inflammation in the gastrointestinal tract. Interleukin 10 is one of the most important anti-inflammatory cytokines involved in the intestinal immune system and because of its role in downregulating inflammatory cascades, its potential for IBD therapy is under study. We previously presented the development of an invasive strain of Lactococcus lactis (L. lactis) producing Fibronectin Binding Protein A (FnBPA) which was capable of delivering, directly to host cells, a eukaryotic DNA expression vector coding for IL-10 of Mus musculus (pValac:il-10) and diminish inflammation in a trinitrobenzene sulfonic acid (TNBS)-induced mouse model of intestinal inflammation. As a new therapeutic strategy against IBD, the aim of this work was to evaluate the therapeutic effect of two L. lactis strains (the same invasive strain evaluated previously and the wild-type strain) carrying the therapeutic pValac:il-10 plasmid in the prevention of inflammation in a dextran sodium sulphate (DSS)-induced mouse model. Results: Results obtained showed that not only delivery of the pValac: il-10 plasmid by the invasive strain L. lactis MG1363 FnBPA+, but also by the wild-type strain L. lactis MG1363, was effective at diminishing intestinal inflammation (lower inflammation scores and higher IL-10 levels in the intestinal tissues, accompanied by decrease of IL-6) in the DSS-induced IBD mouse model. Conclusions: Administration of both L. lactis strains carrying the pValac: il-10 plasmid was effective at diminishing inflammation in this murine model of experimental colitis, showing their potential for therapeutic intervention of IBD.

ano.nymous@ccsd.cnrs.fr.invalid (Meritxell Zurita-Turk) 27 May 2020

https://hal.science/hal-01204404v1

[hal-01536533] Recombinant invasive Lactococcus lactis can transfer DNA vaccines either directly to dendritic cells or across an epithelial cell monolayer

Lactococcus laths (L, lactis), a generally regarded as safe (GRAS) bacterium has recently been investigated as a mucosa] delivery vehicle for DNA vaccines. Because of its GRAS status, L lactis represents an attractive alternative to attenuated pathogens. Previous studies showed that eukaryotic expression plasmids could be delivered into intestinal epithelial cells (IECs) by L. lactis, or recombinant invasive strains of L. lactis, leading to heterologous protein expression. Although expression of antigens in IECs might lead to vaccine responses, it would be of interest to know whether uptake of L. lactis DNA vaccines by dendritic cells (DCs) could lead to antigen expression as they are unique in their ability to induce antigen-specific T cell responses. To test this, we incubated mouse bone marrow-derived DCs (BMDCs) with invasive L laths strains expressing either Staphylococcus aureus Fibronectin Binding Protein A (LL-FnBPA+), or Lis teria monocytogenes mutated Internalin A (LL-mInlA+), both strains carrying a plasmid DNA vaccine (pValac) encoding for the cow milk allergen beta-lactoglobulin (BLG). We demonstrated that they can transfect BMDCs, inducing the secretion of the pro-inflammatory cytokine IL-12. We also measured the capacity of strains to invade a polarized monolayer of IECs, mimicking the situation encountered in the gastrointestinal tract. Gentamycin survival assay in these cells showed that LL-mInlA+ is 100 times more invasive than L. laths. The cross-talk between differentiated IECs, BMDCs and bacteria was also evaluated using an in vitro transwell co-culture model. Co-incubation of strains in this model showed that DCs incubated with LL-mInlA+ containing pValac:BLG could express significant levels of BLG. These results suggest that DCs could sample bacteria containing the DNA vaccine across the epithelial barrier and express the antigen.

ano.nymous@ccsd.cnrs.fr.invalid (Marcela de Azevedo) 19 Mar 2024

https://hal.science/hal-01536533v1

[hal-02735885] Propionibacterium freudenreichii secretes extracellular vesicles with anti-inflammatory activity via NF-κB pathway modulation

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Vinicius de Rezende Rodovalho) 02 Jun 2020

https://hal.inrae.fr/hal-02735885v1

[hal-01190702] In vitro and in vivo characterization of DNA delivery using recombinant Lactococcus lactis expressing a mutated form of L. monocytogenes Internalin A

Background: The use of food-grade Lactic Acid Bacteria (LAB) as DNA delivery vehicles represents an attractive strategy to deliver DNA vaccines at the mucosal surfaces as they are generally regarded as safe (GRAS). We previously showed that either native Lactococcus lactis (LL) or recombinant invasive LL expressing Fibronectin Binding Protein A of Staphylococcus aureus (LL-FnBPA+) or Internalin A of Listeria monocytogenes (LL-InlA+), were able to deliver and trigger DNA expression by epithelial cells, either in vitro or in vivo. InlA does not bind to its receptor, the murine E-cadherin, thus limiting the use of LL-InlA+ in in vivo murine models. Moreover, FnBPA binds to its receptors, integrins, via fibronectin introducing another limiting factor. In order to avoid the limitations of LL-InlA+ and LL-FnBPA+, a new L. lactis strain was engineered to produce a previously described mutated form of InlA (LL-mInlA+) allowing the binding of mInlA on murine E-cadherin. Results: After showing the expression of mInLA at the surface of LL-mInlA+ strain, in vitro gentamycin survival assay in Caco-2 cells showed that LL-mInlA+ is 1000 times more invasive than LL. LL-mInlA+ invasivity was also validated by fluorescence microscopy. LL and LL-mInlA+ were transformed with pValacBLG, a plasmid containing the cDNA of bovine beta-Lactoglobulin (BLG), resulting in strains LL-BLG and LL-mInlA+ BLG. The plasmid transfer in vitro using LL-mInlA+ BLG was increased 10 times compared to LL-BLG. Moreover, the number of mice producing BLG in isolated enterocytes after oral administration of LL-mInlA+ BLG in vivo was slightly higher than after oral administration of LL-BLG. Conclusions: We confirmed in this study that the production of mInlA at the surface of L. lactis is a promising strategy for plasmid transfer in vitro and in vivo.

ano.nymous@ccsd.cnrs.fr.invalid (Marcela de Azevedo) 29 May 2020

https://hal.science/hal-01190702v1

[hal-04297242] Over-production of exopolysaccharide by Lacticaseibacillus rhamnosus CNCM I-3690 strain cutbacks its beneficial effect on the host

Most lactobacilli produce extracellular polysaccharides that are considered to contribute to the probiotic effect of many strains. Lacticaseibacillus rhamnosus CNCM I-3690 is an anti-inflammatory strain able to counterbalance gut barrier dysfunction. In this study ten spontaneous variants of CNCM I-3690 with different EPS-production were generated and characterized by their ropy phenotype, the quantification of the secreted EPS and genetic analysis. Amongst them, two were further analysed in vitro and in vivo: an EPS over-producer (7292) and a low-producer derivative of 7292 (7358, with similar EPS levels than the wild type (WT) strain). Our results showed that 7292 does not have anti-inflammatory profile in vitro, and lost the capacity to adhere to the colonic epithelial cells as well as the protective effect on the permeability. Finally, 7292 lost the protective effects of the WT strain in a murine model of gut dysfunction. Notably, strain 7292 was unable to stimulate goblet cell mucus production and colonic IL-10 production, all key features for the beneficial effect of the WT strain. Furthermore, transcriptome analysis of colonic samples from 7292-treated mice showed a down-regulation of anti-inflammatory genes. Altogether, our results point out that the increase of EPS production in CNCM I-3690 impairs its protective effects and highlight the importance of the correct EPS synthesis for the beneficial effects of this strain.

ano.nymous@ccsd.cnrs.fr.invalid (R. Martín) 16 May 2025

https://hal.inrae.fr/hal-04297242v1

[hal-01204485] Milk Fermented with a 15-Lipoxygenase-1-Producing Lactococcus Lactis Alleviates Symptoms of colitis in a Murine Model

Inflammatory bowel diseases (IBD), such as Crohn's disease and ulcerative colitis, is characterized by extensive inflammation due to dysregulation of the innate and adaptive immune system whose exact etiology is not yet completely understood. Currently there is no cure for IBD, thus the search for new molecules capable of controlling IBD and their delivery to the site of inflammation are the goal of many researchers. The aim of this work was to evaluate the anti-inflammatory effect of the administration of milks fermented by a Lactococcus (L.) lactis strain producing 15-lipoxygenase-1 (15-LOX-1) using a trinitrobenzenesulfonic acid-induced IBD mouse model. The results obtained demonstrated that 15-LOX-1 producing L. lactis was effective in the prevention of the intestinal damage associated to inflammatory bowel disease in a murine model. The work also confirmed previous studies showing that fermented milk is an effective form of administration of recombinant lactic acid bacteria expressing beneficial molecules.

ano.nymous@ccsd.cnrs.fr.invalid (Tessalia D. L. Saraiva) 23 Sep 2015

https://hal.science/hal-01204485v1

[hal-02619713] Complete genome sequence of Francisella noatunensis subsp. orientalis strain F1 and prediction of vaccine candidates against warm and cold-water fish francisellosis

Francisella noatunensis subsp. orientalis (Fno) is a Gram-negative bacterium that causes granulomatous infections in fish reared at low water temperatures; it has been responsible for a large number of deaths in tilapia fish farms. Fno has been reported in many countries in the last decade. Studies on phylogenomic relationships among isolates are needed because of the increasing importance of this disease. Here, we present the complete genome of the Fno F1 strain isolated in 2015 from a tilapia farm in Sao Paulo state, Brazil. The genome is a circular chromosome with a length of 1,854,333 bp, containing 32.26% G+C DNA content, 1,448 protein-coding genes and 393 pseudogenes. In addition, a prediction of conserved vaccine targets was made between the two subspecies of F. noatunensis that cause disease in tropical and cold-water fish species. Five proteins conserved between Fno and Francisella noatunensis subsp. noatunensis were predicted to be good vaccine candidates for the development of a recombinant vaccine against francisellosis. This genome also provides useful data to help understand the pathogen evolution and epidemiology of this disease in Brazil.

ano.nymous@ccsd.cnrs.fr.invalid (C. T. Facimoto) 25 May 2020

https://hal.inrae.fr/hal-02619713v1

[hal-01506640] Contribution of sortase SrtA2 to Lactobacillus casei BL23 inhibition of Staphylococcus aureus internalization into bovine mammary epithelial cells

Probiotics have been considered as a promising strategy to prevent various diseases in both humans and animals. This approach has gained interest in recent years as a potential means to control bovine mastitis. In a previous study, we found that several L. casei strains, including BL23, were able to inhibit the internalization of S. aureus, a major etiologic agent of mastitis, into bovine mammary epithelial cells (bMEC). This antagonism required a direct contact between L. casei and bMEC or S. aureus, suggesting the inhibition relied on interactions between L. casei cell surface components and bMEC. In this study, we have investigated the impact of some candidates which likely influence bacteria host cell interactions. We have shown that L. casei BL23 fbpA retained its inhibitory potential, indicating that L. casei BL23 antagonism did not rely (solely) on competition between S. aureus and L. casei fibronectin-binding proteins for adhesion to bMEC. We have then investigated the impact of four sortase mutants, srtA1, srtA2, srtC1 and srtC2, and a double mutant (srtA1-srtA2) on L. casei BL23 inhibitory potential. Sortases are responsible for the anchoring on the bacterial cell wall of LPXTG-proteins, which reportedly play an important role in bacteria-host cell interaction. All the srt mutants tested presented a reduced inhibition capacity, the most pronounced effect being observed with the srtA2 mutant. A lower internalization capacity of L. casei srtA2 into bMEC was also observed. This was associated with several changes at the surface of L. casei BL23 srtA2 compared to the wild type (wt) strain, including altered abundance of some LPXTG- and moonlighting proteins, and modifications of cell wall structure. These results strongly support the role of sortase A2 in L. casei BL23 inhibition against S. aureus internalization. Deciphering the contribution of the cell surface components altered in srtA2 strain in the inhibition will require further investigation.

ano.nymous@ccsd.cnrs.fr.invalid (Renata Faria Silva Souza) 12 Apr 2017

https://hal.science/hal-01506640v1

[hal-01532545] Expression of fibronectin binding protein A (FnBPA) from Staphylococcus aureus at the cell surface of Lactococcus lactis improves its immunomodulatory properties when used as protein delivery vector

A recombinant strain of Lactococcus lactis displaying a cell-surface anchored fibronectin binding protein A (FnBPA) from Staphylococcus aureus (LL-FnBPA) had been shown to be more efficient in delivering plasmid than its wild-type counterpart both in vitro and in vivo, and have the ability to orientate the immune response toward a Th2 profile in a context of a DNA vaccination. The aim of this work was to test whether this LL-FnBPA strain could shape the immune response after mucosal administration in mice. For this, we used a mouse model of human papilloma virus (HPV)-induced cancer and a L. lactis strain displaying at its cell surface both HPV-16-E7 antigen (LL-E7) and FnBPA (LL-E7 + FnBPA). Our results revealed a more efficient systemic Th1 immune response with recombinant LL-E7 + FnBPA. Furthermore, mice vaccinated with LL-E7 + FnBPA were better protected when challenged with HPV-16-induced tumors. Altogether, the results suggest that FnBPA displays adjuvant properties when used in the context of mucosal delivery using L. lactis as a live vector. (C) 2016 Published by Elsevier Ltd.

ano.nymous@ccsd.cnrs.fr.invalid (Juliana Almeida Barros da Silva) 02 Jun 2017

https://hal.science/hal-01532545v1

[hal-01495114] Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp nov., Kazachstania serrabonitensis sp nov and Kazachstania australis sp nov Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov.

Five ascosporogenous yeast strains related to the genus Kazachstania were isolated. Two strains (CLIB 1764(T) and CLIB 1780) were isolated from French sourdoughs; three others (UFMG-CM-Y273(T), UFMG-CM-Y451 and UFMG-CM-Y452) were from rotting wood in Brazil. The sequences of the French and Brazilian strains differed by one and three substitutions, respectively, in the D1/D2 large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS). The D1/D2 LSU rRNA sequence of these strains differed by 0.5 and 0.7 % from Kazachstania exigua, but their ITS sequences diverged by 8.1 and 8.3%, respectively, from that of the closest described species Kazachstania barnettii. Analysis of protein coding sequences of RPB1, RPB2 and EF-1 alpha distinguished the French from the Brazilian strains, with respectively 3.3, 6 and 11.7 % substitutions. Two novel species are described to accommodate these newly isolated strains: Kazachstania saulgeensis sp. nov. (type strain CLIB 1764(T)=CBS 14374(T)) and Kazachstania serrabonitensis sp. nov. (type strain UFMG-CM-Y273(T)=CLIB 1783(T)=CBS 14236(T)). Further analysis of culture collections revealed a strain previously assigned to the K. exigua species, but having 3.8% difference (22 substitutions and 2 indels) in its ITS with respect to K. exigua. Hence, we describe a new taxon, Kazachstania australis sp. nov. (type strain CLIB 162(T)=CBS 2141(T)), to accommodate this strain. Finally, Candida humilis and Candida pseudohumilis are reassigned to the genus Kazachstania as new combinations. On the basis of sequence analysis, we also propose that Candida miller and Kazachstania humilis comb. nov. are conspecific.

ano.nymous@ccsd.cnrs.fr.invalid (Noémie Jacques) 24 Mar 2017

https://agroparistech.hal.science/hal-01495114v1

[hal-01617957] New Insights into the Diversity of the Genus Faecalibacterium

Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters—A, B, and C—composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.

ano.nymous@ccsd.cnrs.fr.invalid (Leandro Benevides) 17 Oct 2017

https://hal.sorbonne-universite.fr/hal-01617957v1

[hal-01190717] Production of Fibronectin Binding Protein A at the Surface of [i]Lactococcus lactis[/i] Increases Plasmid Transfer [i]In Vitro[/i] and[i] In Vivo[/i]

Lactococci are noninvasive lactic acid bacteria frequently used as protein delivery vectors and, more recently, as DNA delivery vehicles. We previously showed that Lactococcus lactis (LL) expressing the Fibronectin-Binding Protein A of Staphylococcus aureus (LL-FnBPA+) showed higher internalization rates in vitro in Caco-2 cells than the native (wt) lactococci and were able to deliver a eukaryotic Green Fluorescent Protein (GFP) expression plasmid in 1% of human Caco-2 cells. Here, using the bovine beta-lactoglobulin (BLG), one of the major cow's milk allergen, and GFP we characterized the potential of LL-FnBPA+ as an in vivo DNA vaccine delivery vehicle. We first showed that the invasive strain LL-FnBPA+ carrying the plasmid pValac:BLG (LL-FnBPA + BLG) was more invasive than LL-BLG and showed the same invasivity as LL-FnBPA+. Then we demonstrated that the Caco-2 cells, co-incubated with LL-FnBPA+ BLG produced up to 30 times more BLG than the Caco-2 cells co-incubated with the non invasive LL-BLG. Using two different gene reporters, BLG and GFP, and two different methods of detection, EIA and fluorescence microscopy, we showed in vivo that: i) in order to be effective, LL-FnBPA+ required a pre-coating with Fetal Calf Serum before oral administration; ii) plasmid transfer occurred in enterocytes without regard to the strains used (invasive or not); iii) the use of LL-FnBPA+ increased the number of mice producing BLG, but not the level of BLG produced. We thus confirmed the good potential of invasive recombinant lactic acid bacteria as DNA delivery vector in vivo.

ano.nymous@ccsd.cnrs.fr.invalid (Daniela Santos Pontes) 29 May 2020

https://hal.science/hal-01190717v1

[hal-01204459] Correlation between fibronectin binding protein A expression level at the surface of recombinant lactococcus lactis and plasmid transfer in vitro and in vivo

Background: Fibronectin Binding Protein A (FnBPA) is an invasin from Staphylococcus aureus that allows this pathogen to internalize into eukaryote cells. It was previously demonstrated that recombinant Lactococcus lactis expressing FnBPA were invasive and able to transfer a plasmid to eukaryotic cells in vitro and in vivo. In this study, the invasivity of recombinant strains of Lactococcus lactis that express FnBPA under the control of its constitutive promoter or driven by the strong nisin inducible expression system (NICE) were studied. Results: It was demonstrated that the nisA promoter allows an increase of FnBPA expression on the surface of Lactococcus lactis surface, as shown by flow cytometry, which subsequently enhanced internalization and plasmid transfer properties in vitro in Caco2 cells and Bone Marrow Dendritic Cells. In vivo, the use of nisA promoter increase the plasmid transfer in cells of both the small and large intestine of mice. Conclusion: FnBPA expression at the surface of recombinant L. lactis is positively correlated to internalization and DNA transfer properties. The recombinant strains of L. lactis that expresses FnBPA under the control of the nisin inducible expression system could thus be considered as an improved tool in the field of DNA transfer.

ano.nymous@ccsd.cnrs.fr.invalid (Juliana Franco Almeida) 27 May 2020

https://hal.science/hal-01204459v1

[hal-02623695] Wickerhamiella dianesei f.a., sp nov and Wickerhamiella kurtzmanii f.a., sp nov., two yeast species isolated from plants and insects

Six yeast strains representing two novel Wickerhamiella species were isolated from plants and insects collected in Costa Rica, Brazil, and French Guiana. They belong to a subclade containing Wickerhamiella domercqiae and Wickerhamiella bombiphila, and differ by approximately 12 % in the D1 /D2 sequences of the large subunit rRNA gene from these species. The intergenic spacer (ITS) regions of the two novel species differ by around 19 and 27%, respectively, from those of W. domercqiae. The novel species exhibit 5 % divergence in the D1 /D2 sequences among them (around 4 % in the ITS). The names Wickerhamiella dianesei f.a., sp. nov. and Wickerhamiella kurtzmanii f.a., sp. nov. are proposed to accommodate these species, for which a sexual cycle has not been observed. Wickerhamiella dianesei was isolated from the stingless bee, Trigona fulviventris, collected in an Asteraceae flower in Costa Rica, and from leaves of Sabicea brasiliensis (Rubiaceae) and a flower of Byrsonima crassifolia (Malpighiaceae) in Brazil. Wickerhamiellsa kurtzmanii was isolated from a flower of Ipomoea batatoides (Convolvulaceae) in Costa Rica, the surface of a fruit of B. crassifolia in Brazil, and flowers in French Guiana. The type strains are Wickerhamiella dianesei UWOPS 00-107.1(T) (=CBS 14185=NRRL Y-63789; Mycobank number MB 827008) and Wickerhamiella kurtzmanii UWOPS 00-192.1(T) (=CBS 15383=NRRL Y-63979; MB 827011).

ano.nymous@ccsd.cnrs.fr.invalid (Marc-Andre Lachance) 26 May 2020

https://hal.inrae.fr/hal-02623695v1

[hal-01607391] Secretion of biologically active pancreatitis-associated protein I ( PAP) by genetically modified dairy Lactococcus lactis NZ9000 in the prevention of intestinal mucositis

Background: Mucositis is one of the most relevant gastrointestinal inflammatory conditions in humans, generated by the use of chemotherapy drugs, such as 5-fluoracil (5-FU). 5-FU-induced mucositis affects 80% of patients undergoing oncological treatment causing mucosal gut dysfunctions and great discomfort. As current therapy drugs presents limitations in alleviating mucositis symptoms, alternative strategies are being pursued. Recent studies have shown that the antimicrobial pancreatitis-associated protein (PAP) has a protective role in intestinal inflammatory processes. Indeed, it was demonstrated that a recombinant strain of Lactococcus lactis expressing human PAP (LL-PAP) could prevent and improve murine DNBS-induced colitis, an inflammatory bowel disease (IBD) that causes severe inflammation of the colon. Hence, in this study we sought to evaluate the protective effects of LL-PAP on 5-FU-induced experimental mucositis in BALB/c mice as a novel approach to treat the disease. Results: Our results show that non-recombinant L. lactis NZ9000 have antagonistic activity, in vitro, against the enteroinvasive gastrointestinal pathogen L. monocytogenes and confirmed PAP inhibitory effect against Opportunistic E. faecalis. Moreover, L. lactis was able to prevent histological damage, reduce neutrophil and eosinophil infiltration and secretory Immunoglobulin-A in mice injected with 5-FU. Recombinant lactococci carrying antimicrobial PAP did not improve those markers of inflammation, although its expression was associated with villous architecture preservation and increased secretory granules density inside Paneth cells in response to 5-FU inflammation. Conclusions: We have demonstrated for the first time that L. lactis NZ9000 by itself, is able to prevent 5-FU-induced intestinal inflammation in BALB/c mice. Moreover, PAP delivered by recombinant L. lactis strain showed additional protective effects in mice epithelium, revealing to be a promising strategy to treat intestinal mucositis.

ano.nymous@ccsd.cnrs.fr.invalid (Rodrigo D. Carvalho) 26 May 2020

https://hal.science/hal-01607391v1

[hal-02637902] Current Review of Genetically Modified Lactic Acid Bacteria for the Prevention and Treatment of Colitis Using Murine Models

Inflammatory Bowel Diseases (IBD) are disorders of the gastrointestinal tract characterized by recurrent inflammation that requires lifelong treatments. Probiotic microorganisms appear as an alternative for these patients; however, probiotic characteristics are strain dependent and each probiotic needs to be tested to understand the underlining mechanisms involved in their beneficial properties. Genetic modification of lactic acid bacteria (LAB) was also described as a tool for new IBD treatments. The first part of this review shows different genetically modified L(GM-LAB) described for IBD treatment since 2000. Then, the two principally studied strategies are discussed (i) GM-Lproducing antioxidant enzymes and (ii) GM-Lproducing the anti-inflammatory cytokine IL-10. Different delivery systems, including protein delivery and DNA delivery, will also be discussed. Studies show the efficacy of GM-L(using different expression systems) for the prevention and treatment of IBD, highlighting the importance of the bacterial strain selection (with anti-inflammatory innate properties) as a promising alternative. These microorganisms could be used in the near future for the development of therapeutic products with anti-inflammatory properties that can improve the quality of life of IBD patients.

ano.nymous@ccsd.cnrs.fr.invalid (Alejandra de Moreno de Leblanc) 28 May 2020

https://hal.inrae.fr/hal-02637902v1

[hal-03790880] Lactococcus lactis engineered to deliver hCAP18 cDNA alleviates DNBS-induced colitis in C57BL/6 mice by promoting IL17A and IL10 cytokine expression

With its antimicrobial and immunomodulating properties, the cathelicidin (LL37) plays an important role in innate immune system. Here, we attempted to alleviate chemically induced colitis using a lactococci strain that either directly expressed the precursor to LL37, hCAP18 (LL-pSEC:hCAP18), or delivered hCAP18 cDNA to host cells under the control of the cytomegalovirus promoter (LL-Probi-H1:hCAP18). We also investigated whether the alleviation of symptoms could be explained through modification of the gut microbiota by hCAP18. Mice were administered daily doses of LL-pSEC:hCAP18 or LL-Probi-H1:hCAP18. On day 7, colitis was induced by DNBS. During autopsy, we assessed macroscopic tissue damage in the colon and collected tissue samples for the characterization of inflammation markers and histological analysis. Feces were collected at day 7 for 16S DNA sequencing. We also performed a fecal transplant experiment in which mice underwent colon washing and received feces from Lactococcus lactis -treated mice before DNBS-colitis induction. Treatment with LL-Probi-H1:hCAP18 reduced the severity of colitis symptoms. The protective effects were accompanied by increased levels of IL17A and IL10 in mesenteric lymph node cells. L. lactis administration altered the abundance of Lachnospiraceae and Muribaculaceae . However, fecal transplant from L. lactis -treated mice did not improve DNBS-induced symptoms in recipient mice.

ano.nymous@ccsd.cnrs.fr.invalid (Esther Borras Noguès) 28 Sep 2022

https://hal.inrae.fr/hal-03790880v1

[hal-01189501] Molecular basis of virulence in Staphylococcus aureus mastitis

Background: S. aureus is one of the main pathogens involved in ruminant mastitis worldwide. The severity of staphylococcal infection is highly variable, ranging from subclinical to gangrenous mastitis. This work represents an in-depth characterization of S. aureus mastitis isolates to identify bacterial factors involved in severity of mastitis infection. Methodology/Principal Findings: We employed genomic, transcriptomic and proteomic approaches to comprehensively compare two clonally related S. aureus strains that reproducibly induce severe (strain O11) and milder (strain O46) mastitis in ewes. Variation in the content of mobile genetic elements, iron acquisition and metabolism, transcriptional regulation and exoprotein production was observed. In particular, O11 produced relatively high levels of exoproteins, including toxins and proteases known to be important in virulence. A characteristic we observed in other S. aureus strains isolated from clinical mastitis cases. Conclusions/Significance: Our data are consistent with a dose-dependant role of some staphylococcal factors in the hypervirulence of strains isolated from severemastitis. Mobile genetic elements, transcriptional regulators, exoproteins and iron acquisition pathways constitute good targets for further research to define the underlying mechanisms of mastitis severity.

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Le Maréchal) 29 May 2020

https://hal.science/hal-01189501v1

[hal-03650997] Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation

Staphylococcus aureus is an opportunistic pathogen that causes a range of devastating diseases including chronic osteomyelitis, which partially relies on the internalization and persistence of S. aureus in osteoblasts. The identification of the mechanisms of the osteoblast response to intracellular S. aureus is thus crucial to improve the knowledge of this infectious pathology. Since the signal from specifically infected bacteria-bearing cells is diluted and the results are confounded by bystander effects of uninfected cells, we developed a novel model of long-term infection. Using a flow cytometric approach we isolated only S. aureus -bearing cells from mixed populations that allows to identify signals specific to intracellular infection. Here we present an in-depth analysis of the effect of long-term S. aureus infection on the transcriptional program of human osteoblast-like cells. After RNA-seq and KEGG and Reactome pathway enrichment analysis, the remodeled transcriptomic profile of infected cells revealed exacerbated immune and inflammatory responses, as well as metabolic dysregulations that likely influence the intracellular life of bacteria. Numerous genes encoding epigenetic regulators were downregulated. The later included genes coding for components of chromatin-repressive complexes ( e.g. , NuRD, BAHD1 and PRC1) and epifactors involved in DNA methylation. Sets of genes encoding proteins of cell adhesion or neurotransmission were also deregulated. Our results suggest that intracellular S. aureus infection has a long-term impact on the genome and epigenome of host cells, which may exert patho-physiological dysfunctions additionally to the defense response during the infection process. Overall, these results not only improve our conceptual understanding of biological processes involved in the long-term S. aureus infections of osteoblast-like cells, but also provide an atlas of deregulated host genes and biological pathways and identify novel markers and potential candidates for prophylactic and therapeutic approaches.

ano.nymous@ccsd.cnrs.fr.invalid (Aurélie Nicolas) 25 Apr 2022

https://hal.inrae.fr/hal-03650997v1

[hal-02885846] Extracellular vesicles produced by the probiotic Propionibacterium freudenreichii CIRM-BIA 129 mitigate inflammation by modulating the NF-κB pathway

Extracellular vesicles (EVs) are nanometric spherical structures involved in intercellular communication, whose production is considered to be a widespread phenomenon in living organisms. Bacterial EVs are associated with several processes that include survival, competition, pathogenesis, and immunomodulation. Among probiotic Gram-positive bacteria, some Propionibacterium freudenreichii strains exhibit antiinflammatory activity, notably via surface proteins such as the surface-layer protein B (SlpB). We have hypothesized that, in addition to surface exposure and secretion of proteins, P. freudenreichii may produce EVs and thus export immunomodulatory proteins to interact with the host. In order to demonstrate their production in this species, EVs were purified from cell-free culture supernatants of the probiotic strain P. freudenreichii CIRM-BIA 129, and their physicochemical characterization, using transmission electron microscopy and nanoparticle tracking analysis (NTA), revealed shapes and sizes typical of EVs. Proteomic characterization showed that EVs contain a broad range of proteins, including immunomodulatory proteins such as SlpB. In silico protein-protein interaction predictions indicated that EV proteins could interact with host proteins, including the immunomodulatory transcription factor NF-kB. This potential interaction has a functional significance because EVs modulate inflammatory responses, as shown by IL-8 release and NF-kB activity, in HT-29 human intestinal epithelial cells. Indeed, EVs displayed an anti-inflammatory effect by modulating the NF-kB pathway; this was dependent on their concentration and on the proinflammatory inducer (LPSspecific). Moreover, while this anti-inflammatory effect partly depended on SlpB, it was not abolished by EV surface proteolysis, suggesting possible intracellular sites of action for EVs. This is the first report on identification of P. freudenreichii-derived EVs, alongside their physicochemical, biochemical and functional characterization. This study has enhanced our understanding of the mechanisms associated with the probiotic activity of P. freudenreichii and identified opportunities to employ bacterial-derived EVs for the development of bioactive products with therapeutic effects.

ano.nymous@ccsd.cnrs.fr.invalid (Vinicius de Rezende Rodovalho) 01 Jul 2020

https://hal.inrae.fr/hal-02885846v1

[pasteur-03689605] Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids

Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. This bacterial species is subdominant in a healthy physiological state of the gut microbiota (eubiosis) in adults, but can become dominant and cause infections when the intestinal homeostasis is disrupted (dysbiosis). The relatively high concentrations of bile acids deoxycholate (DCA) and taurocholate (TCA) hallmark eubiosis and dysbiosis, respectively. This study aimed to better understand how E. faecalis adapts to DCA and TCA. We showed that DCA impairs E. faecalis growth and possibly imposes a continuous adjustment in the expression of many essential genes, including a majority of ribosomal proteins. This may account for slow growth and low levels of E. faecalis in the gut. In contrast, TCA had no detectable growth effect. The evolving transcriptome upon TCA adaptation showed the early activation of an oligopeptide permease system (opp2) followed by the adjustment of amino acid and nucleotide metabolisms. We provide evidence that TCA favors the exploitation of oligopeptide resources to fuel amino acid needs in limiting oligopeptide conditions. Altogether, our data suggest that the combined effects of decreased DCA and increased TCA concentrations can contribute to the rise of E. faecalis population during dysbiosis.

ano.nymous@ccsd.cnrs.fr.invalid (Francis Repoila) 07 Jun 2022

https://pasteur.hal.science/pasteur-03689605v1

[hal-05065122] Lactic Acid Bacteria Isolated from Bovine Mammary Microbiota: Potential Allies against Bovine Mastitis

Bovine mastitis is a costly disease in dairy cattle worldwide. As of yet, the control of bovine mastitis is mostly based on prevention by thorough hygienic procedures during milking. Additional strategies include vaccination and utilization of antibiotics. Despite these measures, mastitis is not fully under control, thus prompting the need for alternative strategies. The goal of this study was to isolate autochthonous lactic acid bacteria (LAB) from bovine mammary microbiota that exhibit beneficial properties that could be used for mastitis prevention and/or treatment. Sampling of the teat canal led to the isolation of 165 isolates, among which a selection of ten non-redundant LAB strains belonging to the genera Lactobacillus and Lactococcus were further characterized with regard to several properties: surface properties (hydrophobicity, autoaggregation); inhibition potential of three main mastitis pathogens, Staphylococcus aureus, Escherichia coli and Streptococcus uberis; colonization capacities of bovine mammary epithelial cells (bMEC); and immunomodulation properties. Three strains, Lactobacillus brevis 1595 and 1597 and Lactobacillus plantarum 1610, showed high colonization capacities and a medium surface hydrophobicity. These strains are good candidates to compete with pathogens for mammary gland colonization. Moreover, nine strains exhibited anti-inflammatory properties, as illustrated by the lower IL-8 secretion by E. coli-stimulated bMEC in the presence of these LAB. Full genome sequencing of five candidate strains allowed to check for undesirable genetic elements such as antibiotic resistance genes and to identify potential bacterial determinants involved in the beneficial properties. This large screening of beneficial properties while checking for undesirable genetic markers allowed the selection of promising candidate LAB strains from bovine mammary microbiota for the prevention and/or treatment of bovine mastitis.

ano.nymous@ccsd.cnrs.fr.invalid (Damien S Bouchard) 13 May 2025

https://normandie-univ.hal.science/hal-05065122v1

[hal-01123016] Production et sécrétion de L7/L12, un antigène de [i]Brucella abortus[/i], chez [i]Lactococcus lactis[/i] : vers de nouveaux vaccins oraux anti-brucellose ?

Brucella abortus est une bactérie pathogène à Gram négatif qui infecte le tube digestif de l'homme et des animaux. Nous développons des souches vaccinales de Lactococcus lactis contre la brucellose. L'antigène choisi est la protéine ribosomique L7/L12 de B. abortus. Nous avons produit L7/L12 sous forme cytoplasmique et sous forme sécrétée (après fusion avec un peptide signal). Chacune des formes a été exprimée sous la dépendance d'un promoteur constitutif (P59) et d'un promoteur inductible à la nisine (PnisA). L'utilisation de ces deux promoteurs conduit à des niveaux de production de L7/L12 équivalents : environ 0,5 mg/L pour la forme cytoplasmique et 3 mg/L pour la forme sécrétée. Dans les deux cas, on note une augmentation d'un facteur 6 du niveau de production de la forme sécrétée suggérant une protéolyse intracellulaire importante de L7/L12. Ces souches de lactocoques productrices de L7/L12, en cours d'essai chez la souris, constituent de nouvelles alternatives vaccinales contre la brucellose.

ano.nymous@ccsd.cnrs.fr.invalid (Luciana A. Ribeiro) 04 Mar 2015

https://hal.science/hal-01123016v1

[hal-03690660] Inflammasome activation and an involvement of Caspase-1 in a bacterial clearance during S. aureus infection.

Staphylococcus aureus is a highly versatile Gram-positive bacterium that is carried asymptomatically by up to fifty percent of healthy people, while being a major cause of hospital-acquired infections including bone and joint infections, such as osteomyelitis, which are prone to recurrence. S. aureus-caused bovine mastitis is also significant problem in veterinary medicine. The innate immune response plays a pivotal role in the defense against S. aureus. This response is initiated through pattern recognition receptors, and involves an activation of multi-protein signaling complexes known as inflammasomes. It activates proteases, most notably caspase-1 that proteolytically matures and promotes the secretion of mature IL-1β and IL-18. We investigated the role of inflammasomes and caspase-1 in the secretion of mature IL-1β and in the defence of S. aureus-infected osteoblast-like MG-63 cells. Using CRISPR-Cas9 technology, we demonstrated that MG-63 but not caspase-1 knock-out CASP1−/−MG-63 cells, activate the inflammasome as monitored by the release of mature IL-1β. The use of S. aureus deletion and complemented phenole soluble modulins (PSMs) mutants demonstrated a key role of PSMs in inflammasomes-related IL-1β production. Furthermore, we investigated the role of caspase-1in S. aureus clearance. We found that the lack of caspase-1 in CASP1−/−MG-63 cells impairs their defense functions, as bacterial clearance was drastically decreased in CASP1−/− MG-63 compared to wild-type cells. Using a flow cytometric approach we isolated only S. aureus-bearing cells from mixed populations that allows to identify signals specific to intracellular infection. After RNA-seq and KEGG and Reactome pathway enrichment analysis, the remodeled transcriptomic profile of infected cells revealed exacerbated immune and inflammatory responses, as well as metabolic and epigenetic dysregulations that likely influence the intracellular life of bacteria. Collectively, our results demonstrate that human osteoblast-like cells induce an immune response against S. aureus through inflammasomes activation and processing of IL-1β. The outcome of the infection depends on the balance between the host immune response and the action of main S. aureus virulence factors, such as PSMs, whose production differ among the S. aureus strains. Our results showed that the active caspase-1 prevents exacerbated intracellular replication of S. aureus in non-professional phagocytes in addition to professional phagocytes, suggesting the crucial role of caspase-1 in S. aureus clearance independently from the type of cells. Furthermore, our results provide an atlas of deregulated host genes and biological pathways and identify novel markers and potential candidates for prophylactic and therapeutic approaches.

ano.nymous@ccsd.cnrs.fr.invalid (Elma Lima Leite) 29 Jul 2022

https://hal.inrae.fr/hal-03690660v1

[hal-01352688] Evaluation of the biosafety of recombinant lactic acid bacteria designed to prevent and to treat colitis

Inflammatory Bowel Diseases or IBD affect the gastrointestinal tract and are characterized by recurrent inflammation that requires lifelong therapies. Probiotics such as lactic acid bacteria (LAB) have been proposed to complement current treatment protocols for these patients; however, their characteristics are strain dependent. In this regard certain novel characteristics are only possible through the genetic modification of these beneficial microorganisms. Different delivery systems, such as protein delivery of anti-oxidant enzymes and the anti-inflammatory cytokines such as IL-10 and DNA delivery have been shown to be effective for preventing and treating IBD in animal models. In this study, the safety of the recombinant LAB (recLAB) Streptococcus thermophilus (S.) CRL807:CAT, S. thermophilus CRL807: SOD, Lactococcus (L.) lactis NCDO2118 pXILCYT:IL-10, L. lactis MG1363 pValac:IL-10 and L. lactis MG1363 pGroESL:IL-10 with proven beneficial effects were compared to their progenitor strains S. thermophilus CRL807, L. lactis NCDO2118 or L. lactis MG1363. The prolonged administration of genetically modified strains evaluated in the present work showed that they were just as safe as the administration of the native strains from which they derive as demonstrated by normal animal growth and relative organ weights, absence of microbial translocation, altered blood parameters and modifications of intestinal histology. The results show the potential use of these recLAB in future therapeutic formulations; however, the use of modern bio-containment systems is required for the future acceptance of these recLAB by the medical community and patients suffering IBD.

ano.nymous@ccsd.cnrs.fr.invalid (Alejandra de Moreno de Leblanc) 28 May 2020

https://hal.science/hal-01352688v1

[hal-05156716] The Microbial Anti-Inflammatory Molecule (MAM) is a key protein processed and exported to Faecalibacterium duncaniae envelope

MAM (Microbial-Anti-Inflammatory Molecule) is a key effector protein with anti-inflammatory properties in Faecalibacterium duncaniae, a critical human gut microbiota species. Despite its importance, MAM function and molecular features remain poorly understood. This study elucidates MAM’s physiological importance by examining its cellular localization, secretion dynamics, and structural organization. Mass spectrometry and immunogold labeling confirmed MAM as the most abundant protein in the cell envelope and the second most abundant in the overall proteome, localizing it to the bacterial surface. Bioinformatic and in silico analyses suggest that MAM contains an N-terminal leader peptide with motifs recognized by a Peptidase-domain-Containing ABC Transporter (PCAT), enabling cargo transport to the cell envelope. After N-terminal excision, the cargo protein could be transported to the cell envelope via this PCAT, where it could assemble into a hexameric structure, as revealed by docking and AlphaFold3 modeling. Such results were supported by electron microscopy showing a lattice-like organization on the bacterial surface. This work introduces a novel discussion about the singular organization of the F. duncaniae cell envelope, having MAM as a key component for the bacteria, supporting the understanding of the unique biology of F. duncaniae and its potential as a next-generation probiotic or live biotherapeutic.

ano.nymous@ccsd.cnrs.fr.invalid (Thaís Vilela Rodrigues) 10 Jul 2025

https://hal.science/hal-05156716v1

[hal-04321441] Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell.

ano.nymous@ccsd.cnrs.fr.invalid (Liza Felicori) 04 Dec 2023

https://hal.science/hal-04321441v1

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PUBLICATIONS

> Click here to access the recent publication list from Micalis

HAL : Dernières publications

[hal-04099157] Microbiome-based solutions to address new and existing threats to food security, nutrition, health and agrifood systems' sustainability

[hal-04336557] BiochiMix, et si un jeu permettait de réaliser une mind map pour réviser ?

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

[hal-05427912] Lung infection in orally inoculated SARS-CoV-2 hamsters

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

[hal-05339375] Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech

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

[hal-05447877] Bénéfices des aliments fermentés, de l’empirisme aux démonstrations scientifiques : l’apport de Ferments du Futur

[hal-05447592] Pneumococcus uses COMMD2 to alter host cellular immunity

[inserm-02948958] Mucosal-associated invariant T cells promote inflammation and intestinal dysbiosis leading to metabolic dysfunction during obesity

[anses-04026020] Avis relatif à la représentativité de l’échantillonnage pour la recherche d’histamine dans les poissons

[hal-02641529] Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children

[hal-01204455] Commensal microbiota influence systemic autoimmune responses

[hal-03818233] Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

[hal-04297527] Characterization and Whole Genome Sequencing of AR23, a Highly Toxic Bacillus thuringiensis Strain Isolated from Lebanese Soil

[hal-01606175] Energy balance and obesity: what are the main drivers?

[hal-02154535] Le laboratoire international associé Bact-Inflam, l’aboutissement de 17 années de collaboration France-Brésil

[hal-01204337] Partindo de dados (meta)genômicos para entender as relações bactéria-hospedeiro no trato gastro intestinal

[hal-03752257] Intraspecific Diversity of Microbial Anti-Inflammatory Molecule (MAM) from Faecalibacterium prausnitzii

[hal-03690736] Genomic and probiotic traits of the commensal E. coli CEC15 strain.

[hal-01536568] Prospective uses of recombinant Lactococcus lactis expressing both listeriolysin O and mutated internalin A from Listeria monocytogenes as a tool for DNA vaccination

[hal-01204308] Propriétés probiotiques de bactéries lactiques isolées du microbiote mammaire bovin : Des alliés potentiels contre les mammites

[hal-02619666] Kurtzmaniella hittingeri f.a., sp. nov., isolated from rotting wood and fruits, and transfer of three candida species to the genus kurtzmaniella as new combinations

[hal-01204404] Lactococcus lactis carrying the pValac DNA expression vector coding for IL-10 reduces inflammation in a murine model of experimental colitis

[hal-01536533] Recombinant invasive Lactococcus lactis can transfer DNA vaccines either directly to dendritic cells or across an epithelial cell monolayer

[hal-02735885] <em>Propionibacterium freudenreichii</em> secretes extracellular vesicles with anti-inflammatory activity via NF-κB pathway modulation

[hal-01190702] In vitro and in vivo characterization of DNA delivery using recombinant Lactococcus lactis expressing a mutated form of L. monocytogenes Internalin A

[hal-04297242] Over-production of exopolysaccharide by Lacticaseibacillus rhamnosus CNCM I-3690 strain cutbacks its beneficial effect on the host

[hal-01204485] Milk Fermented with a 15-Lipoxygenase-1-Producing Lactococcus Lactis Alleviates Symptoms of colitis in a Murine Model

[hal-02619713] Complete genome sequence of Francisella noatunensis subsp. orientalis strain F1 and prediction of vaccine candidates against warm and cold-water fish francisellosis

[hal-01506640] Contribution of sortase SrtA2 to Lactobacillus casei BL23 inhibition of Staphylococcus aureus internalization into bovine mammary epithelial cells

[hal-01532545] Expression of fibronectin binding protein A (FnBPA) from Staphylococcus aureus at the cell surface of Lactococcus lactis improves its immunomodulatory properties when used as protein delivery vector

[hal-01617957] New Insights into the Diversity of the Genus Faecalibacterium

[hal-01190717] Production of Fibronectin Binding Protein A at the Surface of [i]Lactococcus lactis[/i] Increases Plasmid Transfer [i]In Vitro[/i] and[i] In Vivo[/i]

[hal-01204459] Correlation between fibronectin binding protein A expression level at the surface of recombinant lactococcus lactis and plasmid transfer in vitro and in vivo

[hal-02623695] <em>Wickerhamiella dianesei</em> f.a., sp nov and <em>Wickerhamiella kurtzmanii</em> f.a., sp nov., two yeast species isolated from plants and insects

[hal-01607391] Secretion of biologically active pancreatitis-associated protein I ( PAP) by genetically modified dairy Lactococcus lactis NZ9000 in the prevention of intestinal mucositis

[hal-02637902] Current Review of Genetically Modified Lactic Acid Bacteria for the Prevention and Treatment of Colitis Using Murine Models

[hal-03790880] Lactococcus lactis engineered to deliver hCAP18 cDNA alleviates DNBS-induced colitis in C57BL/6 mice by promoting IL17A and IL10 cytokine expression

[hal-01189501] Molecular basis of virulence in Staphylococcus aureus mastitis

[hal-03650997] Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation

[hal-02885846] Extracellular vesicles produced by the probiotic Propionibacterium freudenreichii CIRM-BIA 129 mitigate inflammation by modulating the NF-κB pathway

[pasteur-03689605] Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids

[hal-05065122] Lactic Acid Bacteria Isolated from Bovine Mammary Microbiota: Potential Allies against Bovine Mastitis

[hal-01123016] Production et sécrétion de L7/L12, un antigène de [i]Brucella abortus[/i], chez [i]Lactococcus lactis[/i] : vers de nouveaux vaccins oraux anti-brucellose ?

[hal-03690660] Inflammasome activation and an involvement of Caspase-1 in a bacterial clearance during S. aureus infection.

[hal-01352688] Evaluation of the biosafety of recombinant lactic acid bacteria designed to prevent and to treat colitis

[hal-05156716] The Microbial Anti-Inflammatory Molecule (MAM) is a key protein processed and exported to Faecalibacterium duncaniae envelope

[hal-04321441] Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

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