Publications

[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-04739209] Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease

Objective There is substantial inter-individual diversity in the susceptibility of alcoholics to liver injury. Alterations of intestinal microbiota (IM) have been reported in alcoholic liver disease (ALD), but the extent to which they are merely a consequence or a cause is unknown. We aimed to demonstrate that a specific dysbiosis contributes to the development of alcoholic hepatitis (AH). Design We humanised germ-free and conventional mice using human IM transplant from alcoholic patients with or without AH. The consequences on alcohol-fed recipient mice were studied. Results A specific dysbiosis was associated with ALD severity in patients. Mice harbouring the IM from a patient with severe AH (sAH) developed more severe liver inflammation with an increased number of liver T lymphocyte subsets and Natural Killer T (NKT) lymphocytes, higher liver necrosis, greater intestinal permeability and higher translocation of bacteria than mice harbouring the IM from an alcoholic patient without AH (noAH). Similarly, CD45+ lymphocyte subsets were increased in visceral adipose tissue, and CD4(+) T and NKT lymphocytes in mesenteric lymph nodes. The IM associated with sAH and noAH could be distinguished by differences in bacterial abundance and composition. Key deleterious species were associated with sAH while the Faecalibacterium genus was associated with noAH. Ursodeoxycholic acid was more abundant in faeces from noAH mice. Additionally, in conventional mice humanised with the IM from an sAH patient, a second subsequent transfer of IM from an noAH patient improved alcohol-induced liver lesions. Conclusions Individual susceptibility to ALD is substantially driven by IM. It may, therefore, be possible to prevent and manage ALD by IM manipulation.

ano.nymous@ccsd.cnrs.fr.invalid (M Llopis) 16 Oct 2024

https://hal.science/hal-04739209v1

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

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

ano.nymous@ccsd.cnrs.fr.invalid (Aurélien Dinh) 07 Mar 2025

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

[hal-04009559] Polysaccharide II Surface Anchoring, the Achilles’ Heel of Clostridioides difficile

Cell wall glycopolymers (CWPGs) in Gram-positive bacteria have been reported to be involved in several bacterial processes. These polymers, pillars for proteins and S-layer, are essential for the bacterial surface setup, could be essential for growth, and, in pathogens, participate most often in virulence. CWGPs are covalently anchored to peptidoglycan by proteins that belong to the LytR-CpsA-PSr (LCP) family. This anchoring, important for growth, was reported as essential for some bacteria such as Bacillus subtilis, but the reason why CWGP anchoring is essential remains unknown. We studied LcpA and LcpB of Clostridioides difficile and showed that they have a redundant activity. To delete both lcp genes, we set up the first conditional-lethal mutant method in C. difficile and showed that polysaccharide II (PSII) anchoring at the bacterial surface is essential for C. difficile survival. In the conditional-lethal mutant, C. difficile morphology was impaired, suggesting that peptidoglycan synthesis was affected. Because Lcp proteins are transferring CWPGs from the C55-undecaprenyl phosphate (also needed in the peptidoglycan synthesis process), we assumed that there was competition between PSII and peptidoglycan synthesis pathways. We confirmed that UDP-MurNAc-pentapeptide precursor was accumulated, showing that peptidoglycan synthesis was blocked. Our results provide an explanation for the essentiality of PSII anchoring in C. difficile and suggest that the essentiality of the anchoring of CWPGs in other bacteria can also be explained by the blocking of peptidoglycan synthesis. To conclude, our results suggest that Lcps are potential new targets to combat C. difficile infection. IMPORTANCE Cell wall glycopolymers (CWGPs) in Gram-positive bacteria have been reported to be involved in several bacterial processes. CWGP anchoring to peptidoglycan is important for growth and virulence. We set up the first conditional-lethal mutant method in Clostridioides difficile to study LcpA and LcpB involved in the anchoring of CWPGs to peptidoglycan. This study offers new tools to reveal the role of essential genes in C. difficile. LcpA and LcpB activity was shown to be essential, suggesting that they are potential new targets to combat C. difficile infection. In this study, we also showed that there is competition between the polysaccharide II synthesis pathway and peptidoglycan synthesis that probably exists in other Gram-positive bacteria. A better understanding of these mechanisms allows us to define the Lcp proteins as a therapeutic target for potential design of novel antibiotics against pathogenic Gram-positive bacteria.

ano.nymous@ccsd.cnrs.fr.invalid (Jeanne Malet-Villemagne) 01 Mar 2023

https://hal.inrae.fr/hal-04009559v1

[hal-04764203] Outcomes of Enterococcus faecalis infective endocarditis according to MIC of amoxicillin: a multicentric study

Abstract Background The incidence of Enterococcus faecalis infective endocarditis is increasing over time. Data on the impact of minimum inhibitory concentration (MIC) of amoxicillin on treatment outcomes are scarce. The objective of this study was to describe the epidemiology of E. faecalis infective endocarditis and to evaluate whether the MIC of amoxicillin might influence mortality. Materials We retrospectively included all consecutive patients diagnosed with definite E. faecalis infective endocarditis between 2013 and 2020 in 11 French hospitals. We extracted data from the local diagnosis-related group (DRG) database and matched these data with microbiological results. Amoxicillin MIC was determined by Etest strip. The primary endpoints were endocarditis-related mortality and risk factors for endocarditis-related mortality including amoxicillin MIC. Results A total of 403 patients with definite E. faecalis infective endocarditis were included. Patients were predominantly male (76.4%) with a median age of 74 years (67–82). Embolic complications occurred in 170 (42.1%) patients. Cardiac surgery was performed in 158 (61.5%) patients. The endocarditis-related mortality rate was 28.3% and the median delay between mortality and onset of hospitalization was 24 (9; 41) days. E. faecalis MIC of amoxicillin was available for 246 (61%) patients. The median MIC was 0.5 mg/L (0.4–0.7). Amoxicillin MIC was not found to be associated with in-hospital mortality. None of the variables included in the multivariate model were identified as a risk factor for mortality and there was no correlation between mortality and the duration of treatment for 4 weeks versus 6 weeks. Conclusions Higher amoxicillin MIC was not a risk factor leading to endocarditis-related mortality in definite E. faecalis infective endocarditis. However, further studies are needed to assess the effect of amoxicillin MIC on relapse.

ano.nymous@ccsd.cnrs.fr.invalid (Hermann Do Rego) 08 Nov 2024

https://hal.inrae.fr/hal-04764203v1

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

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

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

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

[inserm-03962400] Evaluation of ceftolozane-tazobactam susceptibility on a French nationwide collection of Enterobacterales

Objectives: Ceftolozane-tazobactam (C/T) proved its efficacy for the treatment of infections caused by non-carbapenemase producing Pseudomonas aeruginosa and Enterobacterales. Here, we aimed to provide susceptibility data on large series of Enterobacterales since the revision of EUCAST categorization breakpoints in 2020.Methods: First, C/T susceptibility was determined on characterized Enterobacterales resistant to 3rd generation cephalosporins (3GC) (ESBL production or different levels of AmpC overexpression) (n=213) and carbapenem resistant Enterobacterales (CRE) (n=259) including 170 carbapenemase producers (CPE). Then, 1,632 consecutive clinical Enterobacterales responsible for infection were prospectively collected in 23 French hospitals. C/T susceptibility was determined by Etest® (biomérieux) and broth microdilution (BMD) (Sensititre™, Thermo Scientific) to perform method comparison.Results: Within the collection isolates, 88% of 3GC resistant strains were susceptible to C/T, with important variation depending on the resistance mechanism: 93% vs 13% susceptibility for CTX-M and SHV-ESBL producers, respectively. Only 20% of the CRE were susceptible to C/T. Among CPE, 80 % of OXA-48-like producers were susceptible to C/T, whereas all metallo-β-lactamase producers were resistant. The prospective study revealed that 95.6% of clinical isolates were susceptible to C/T. Method comparison performed on these 1,632 clinical isolates demonstrated 99 % of categorization agreement between MIC to C/T determined by Etest® compared to BMD (reference) and only 74% of essential agreement.Conclusion: Overall, C/T showed good activity against wild-type Enterobacterales, AmpC producers and ESBL-producing E. coli but is less active against ESBL-producing K. pneumoniae and CRE. Etest® led to an underestimation of the MICs in comparison to BMD.

ano.nymous@ccsd.cnrs.fr.invalid (Agnès Jousset) 30 Jan 2023

https://inserm.hal.science/inserm-03962400v1

[hal-03216705] Temocillin susceptibility among Enterobacterales strains recovered from blood culture in France

Temocillin is used for several years in some European countries but, only since 2015 in France. We assessed the susceptibility of Enterobacterales strains isolated from blood culture 1 year before (2014) and 2 years after (2017) its use in France. 1,387 strains were included by 17 clinical laboratories located throughout France: 363 in 2014 and 1,024 in 2017. The rate of resistance to temocillin was 4.6% and 26.7% in 3rd generation cephalosporin (3GC) susceptible and resistant strains respectively. Cephalosporinase-overproducer (COPE) strains were significantly more resistant to temocillin (37.7%) than ESBL-producer (ESBL-PE) (23.5%) (P < 0.01). The rate of temocillin resistance was correlated to the number of inactive beta-lactams. The rate of resistance to temocillin trend to increase from 13.9% in 2014 to 23.9% in 2017 (P < 0.01). Temocillin remains highly active against Enterobacterales but the trend in resistance should be assessed over time.

ano.nymous@ccsd.cnrs.fr.invalid (Eric Farfour) 27 May 2021

https://hal.univ-reims.fr/hal-03216705v1

[hal-04833227] Alteration of Cardiolipin-Dependent Mitochondrial Coupling in Muscle Protects against Obesity

Summary The tubular shape of mitochondrial cristae depends upon a specific composition of the inner mitochondrial membrane, including cardiolipin that allows strong curvature and promotes optimal organization of ATP synthase. Here we identify Hacd1, which encodes an enzyme involved in very long chain fatty acid biosynthesis, as a key regulator of composition, structure and functional properties of mitochondrial membranes in muscle. In Hacd1 -deficient mice, the reduced cardiolipin content was associated with dilation of cristae and caused defective phosphorylating respiration, characterized by absence of proton leak and oxidative stress. The skeletal muscle-specific mitochondrial coupling defect produced a global elevation in basal energy expenditure with increased carbohydrate and lipid catabolism, despite decreased muscle mass and locomotor capacities. Mice were protected against diet-induced obesity despite reduced muscle activity, providing an in vivo proof of concept that reducing mitochondrial coupling efficiency in skeletal muscle might be an actionable mechanism in metabolic disease conditions.

ano.nymous@ccsd.cnrs.fr.invalid (Alexandre Prola) 12 Dec 2024

https://cnrs.hal.science/hal-04833227v1

[hal-03105418] Cardiolipin content controls mitochondrial coupling and energetic efficiency in muscle

Unbalanced energy partitioning participates in the rise of obesity, a major public health concern in many countries. Increasing basal energy expenditure has been proposed as a strategy to fight obesity yet raises efficiency and safety concerns. Here, we show that mice deficient for a muscle-specific enzyme of very-long-chain fatty acid synthesis display increased basal energy expenditure and protection against high-fat diet–induced obesity. Mechanistically, muscle-specific modulation of the very-long-chain fatty acid pathway was associated with a reduced content of the inner mitochondrial membrane phospholipid cardiolipin and a blunted coupling efficiency between the respiratory chain and adenosine 5′-triphosphate (ATP) synthase, which was restored by cardiolipin enrichment. Our study reveals that selective increase of lipid oxidative capacities in skeletal muscle, through the cardiolipin-dependent lowering of mitochondrial ATP production, provides an effective option against obesity at the whole-body level.

ano.nymous@ccsd.cnrs.fr.invalid (Alexandre Prola) 26 Jan 2021

https://institut-agro-dijon.hal.science/hal-03105418v1

[hal-01594853] One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial beta-tubulin II (TUB2); iv) gamma-actin (ACT); v) translation elongation factor 1-alpha (TEF1 alpha); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1 alpha. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1 alpha, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.

ano.nymous@ccsd.cnrs.fr.invalid (J.B. Stielow) 26 Sep 2017

https://hal.science/hal-01594853v1

[hal-02914082] Détermination de la souplesse hors plan d’un assemblage de composites boulonnés à l’aide d’une démarche d’homogénéisation

Dans de nombreux secteurs industriels, les matériaux composites tissés à fibres de carbone et matrices thermoplastiques semblent être une alternative prometteuse aux matériaux métalliques pour alléger les structures. Les matrices composites thermoplastiques ont un coût plus adapté à la fabrication de pièces composites avec de grandes cadences. Les assemblages de structures peuvent être des jonctions mécaniques à base de rivets, de vis ou de boulons. Dans cette étude, nous proposons de développer une approche expérimentale et numérique pour identifier les souplesses hors plan des constituants élémentaires d’un assemblage boulonné. Il n’y a actuellement aucune règle de conception pour prédire la rupture des liaisons boulonnées constituées de substrats composites thermoplastiques. Par conséquent, une étude expérimentale d’une liaison boulonnée utilisant la technique de corrélation d’images est présentée. Simultanément, des modèles éléments finis tridimensionnels d’assemblages associés à une approche d’équivalence en énergie ont été développés afin de déterminer la souplesse des éléments de l’assemblage. Ces modèles éléments finis ont ensuite été comparés avec succès à des résultats expérimentaux.

ano.nymous@ccsd.cnrs.fr.invalid (Laurent Gornet) 11 Aug 2020

https://hal.science/hal-02914082v1

[hal-04918234] Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs

Background: Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic alterations, often present in aging PWH, has been poorly investigated. Methods: In this study, we compared fecal metagenomes of 25 antiretroviral-treatment (ART)-controlled PWH to three independent control groups of 25 non-infected matched individuals by means of univariate analyses and machine learning methods. Moreover, we used two external datasets to validate predictive models of PWH classification. Next, we searched for associations between clinical and biological metabolic parameters with taxonomic and functional microbiome profiles. Finally, we compare the gut microbiome in 7 PWH after a 17-week ART switch to raltegravir/maraviroc. Results: Three major enterotypes (Prevotella, Bacteroides and Ruminococcaceae) were present in all groups. The first Prevotella enterotype was enriched in PWH, with several of characteristic lineages associated with poor metabolic profiles (low HDL and adiponectin, high insulin resistance (HOMA-IR)). Conversely butyrate-producing lineages were markedly depleted in PWH independently of sexual preference and were associated with a better metabolic profile (higher HDL and adiponectin and lower HOMA-IR). Accordingly with the worst metabolic status of PWH, butyrate production and amino-acid degradation modules were associated with high HDL and adiponectin and low HOMA-IR. Random Forest models trained to classify PWH vs. control on taxonomic abundances displayed high generalization performance on two external holdout datasets (ROC AUC of 80-82%). Finally, no significant alterations in microbiome composition were observed after switching to raltegravir/maraviroc. Conclusion: High resolution metagenomic analyses revealed major differences in the gut microbiome of ART-controlled PWH when compared with three independent matched cohorts of controls. The observed marked insulin resistance could result both from enrichment in Prevotella lineages, and from the depletion in species producing butyrate and involved into amino-acid degradation, which depletion is linked with the HIV infection.

ano.nymous@ccsd.cnrs.fr.invalid (Eugeni Belda) 29 Jan 2025

https://hal.sorbonne-universite.fr/hal-04918234v1

[hal-03153762] IBISBA-FR : Une infrastructure en soutien au développement de la biotechnologie industrielle comme technologie clef pour l’industrie du futur et pour accompagner la bioéconomie et l’économie circulaire

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ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Bernet) 26 Feb 2021

https://hal.inrae.fr/hal-03153762v1

[hal-03973514] MATERNAL MICROBIOTAS TRANSFER IMPACTS MICROBIOTA-GUT-BRAIN AXIS IN OFFSPRING

Content: Introduction. The intestinal microbiota is a major player in the physiology of the host, particularly through its interactions with the intestinal epithelium. Initially transmitted from mother to child, the metabolism of primocolonizing bacteria can have an immediate and future impact on health. We previously demonstrated that neonatal transfer of different microbiota from obese-resistant (OR) or obese-prone (OP) dams has short-and long-term effects on the feeding behavior of offspring, supporting a risk of overweight. Regulation of food intake by the gut-brain axis involves enteroendocrine cells capable of detecting bacterial metabolites. Objectives. We looked for potential relationships between the composition and activity of transferred microbiota and gut endocrine function as a hypothesis for an early impact of microbiota-gut-brain on neurodevelopment and further eating behavior. Method. Microbiota (vaginal, fecal, and milk-derived) from OP and OR dams, which differed in taxonomic composition, were inoculated into pups born to conventional Fischer F344 dams from birth to day 15 of life, constituting three groups: F-OP, FOR , and F-Sham. Results. At 21 days of age, principal component analysis of caecocolic contents showed a discriminant separation of the 3 groups by metagenomic species and associated functions, which was reflected by only minor differences in metabolite abundance (NMR) in caecocolic supernatants. In vivo transcriptomic analysis of ileum and colon (RT-qPCR) and in vitro on the enteroendocrine STC-1 line incubated with the supernatants revealed differences in expression of some endocrine markers between the treated and F-Sham groups. The identification of the bacterial markers involved (short-chain fatty acids, neurotransmitters, bacterial peptides) is in progress via the search for statistical correlations. Conclusion. Maternal microbiotas tranfserred at birth altered the microbiota-gut-brain axis at leat in part via the enteroendocrine function.

ano.nymous@ccsd.cnrs.fr.invalid (Gwenola Le Dréan) 04 Feb 2023

https://hal.inrae.fr/hal-03973514v1

[hal-03981886] Impact d'un transfert de microbiotes maternels et de leurs métabolites sur l'expression de marqueurs entéroendocrines chez le raton

Le microbiote intestinal est un acteur majeur de la physiologie de l’hôte notamment via ses interactions avec l’épithélium intestinal. Initialement transmis de la mère à l’enfant, le métabolisme des bactéries primocolonisatrices peut avoir un impact immédiat et futur sur la santé. Ainsi, le transfert néonatal de microbiotes différents issus de rates résistantes (obese-resistant, OR) ou prédisposées (obese-prone, OP) à l’obésité a des effets à court et long terme sur le comportement alimentaire de la descendance (Pocheron et al. Frontiers in Microbiology, 2021), en faveur d’un risque de surpoids. La régulation de la prise alimentaire par l’axe intestin-cerveau fait intervenir les cellules entéroendocrines capables de détecter les métabolites bactériens. Nous avons recherché des relations potentielles entre la composition et l’activité des microbiotes transférés et la fonction endocrine intestinale. Les microbiotes (vaginaux, fécaux et issus du lait) de mères OP et OR, dont la composition taxonomique différait, ont été inoculés à des ratons nés de mères conventionnelles Fischer F344 de la naissance au 15ème jour de vie, constituant ainsi trois groupes : F-OP, F-OR, et F-Sham. A 21 jours, l’analyse métagénomique des contenus caecoliques révélait une composition taxonomique et un potentiel fonctionnel significativement différents entre les groupes traités et le groupe F-Sham, qui ne se traduisait que par des différences mineures dans l’abondance des métabolites (RMN) dans les surnageants caecocoliques. De même, l’analyse transcriptomique in vivo des iléons et côlons (qPCR) et in vitro sur la lignée STC-1 incubée en présence des surnageants a révélé des différences d’expression de certains marqueurs endocrines uniquement entre les groupes traités et F-Sham. Le transfert néonatal de microbiote impacterait donc les cellules entéroendocrines indépendamment des différences taxonomiques (OP/OR). L’identification des marqueurs bactériens impliqués est en cours via la recherche de corrélations statistiques.

ano.nymous@ccsd.cnrs.fr.invalid (Gwenola Le Dréan) 10 Feb 2023

https://hal.inrae.fr/hal-03981886v1

[hal-02180624] Enzymes Required for Maltodextrin Catabolism in Enterococcus faecalis Exhibit Novel Activities

Maltose and maltodextrins are formed during the degradation of starch or glycogen. Maltodextrins are composed of a mixture of maltooligosaccharides formed by α-1,4- but also some α-1,6-linked glucosyl residues. The α-1,6-linked glucosyl residues are derived from branching points in the polysaccharides. In Enterococcus faecalis, maltotriose is mainly transported and phosphorylated by a phosphoenolpyruvate:carbohydrate phosphotransferase system. The formed maltotriose-6″-phosphate is intracellularly dephosphorylated by a specific phosphatase, MapP. In contrast, maltotetraose and longer maltooligosaccharides up to maltoheptaose are taken up without phosphorylation via the ATP binding cassette transporter MdxEFG-MsmX. We show that the maltose-producing maltodextrin hydrolase MmdH (GenBank accession no. EFT41964) in strain JH2-2 catalyzes the first catabolic step of α-1,4-linked maltooligosaccharides. The purified enzyme converts even-numbered α-1,4-linked maltooligosaccharides (maltotetraose, etc.) into maltose and odd-numbered (maltotriose, etc.) into maltose and glucose. Inactivation of mmdH therefore prevents the growth of E. faecalis on maltooligosaccharides ranging from maltotriose to maltoheptaose. Surprisingly, MmdH also functions as a maltogenic α-1,6-glucosidase, because it converts the maltotriose isomer isopanose into maltose and glucose. In addition, E. faecalis contains a glucose-producing α-1,6-specific maltodextrin hydrolase (GenBank accession no. EFT41963, renamed GmdH). This enzyme converts panose, another maltotriose isomer, into glucose and maltose. A gmdH mutant had therefore lost the capacity to grow on panose. The genes mmdH and gmdH are organized in an operon together with GenBank accession no. EFT41962 (renamed mmgT). Purified MmgT transfers glucosyl residues from one α-1,4-linked maltooligosaccharide molecule to another. For example, it catalyzes the disproportionation of maltotriose by transferring a glucosyl residue to another maltotriose molecule, thereby forming maltotetraose and maltose together with a small amount of maltopentaose.

ano.nymous@ccsd.cnrs.fr.invalid (Philippe Joyet) 11 Jul 2019

https://normandie-univ.hal.science/hal-02180624v1

[hal-03352896] Blockage of bacterial FimH prevents mucosal inflammation associated with Crohn’s disease

Background An Escherichia coli (E. coli) pathotype with invasive properties, first reported by Darfeuille-Michaud and termed adherent-invasive E. coli (AIEC), was shown to be prevalent in up to half the individuals with Crohn’s Disease (CD), suggesting that these bacteria could be involved in the pathophysiology of CD. Among the genes related to AIEC pathogenicity, fim has the potential to generate an inflammatory reaction from the intestinal epithelial cells and macrophages, as it interacts with TLR4, inducing the production of inflammatory cytokines independently of LPS. Therefore, targeting the bacterial adhesion of FimH-expressing bacteria seems a promising therapeutic approach, consisting of disarming bacteria without killing them, representing a selective strategy to suppress a potentially critical trigger of intestinal inflammation, without disturbing the intestinal microbiota. Results We analyzed the metagenomic composition of the gut microbiome of 358 patients with CD from two different cohorts and characterized the presence of FimH-expressing bacteria. To assess the pathogenic role of FimH, we used human intestinal explants and tested a specific FimH blocker to prevent bacterial adhesion and associated inflammation. We observed a significant and disease activity-dependent enrichment of Enterobacteriaceae in the gut microbiome of patients with CD. Bacterial FimH expression was functionally confirmed in ileal biopsies from 65% of the patients with CD. Using human intestinal explants, we further show that FimH is essential for adhesion and to trigger inflammation. Finally, a specific FimH-blocker, TAK-018, inhibits bacterial adhesion to the intestinal epithelium and prevents inflammation, thus preserving mucosal integrity. Conclusions We propose that TAK-018, which is safe and well tolerated in humans, is a promising candidate for the treatment of CD and in particular in preventing its recurrence.

ano.nymous@ccsd.cnrs.fr.invalid (Grégoire Chevalier) 23 Sep 2021

https://hal.sorbonne-universite.fr/hal-03352896v1

[hal-03594297] Evidence for constitutive microbiota-dependent short-term control of food intake in mice: Is there a link with inflammation, oxidative stress, endotoxemia, and Glp-1?

AIMS: Although prebiotics, probiotics, and fecal transplantation can alter the sensation of hunger and/or feeding behavior, the role of the constitutive gut microbiota in the short-term regulation of food intake during normal physiology is still unclear. RESULTS: An antibiotic-induced microbiota depletion study was designed to compare feeding behavior in conventional and microbiota-depleted mice. Tissues were sampled to characterize the time profile of microbiota-derived signals in mice during consumption of either standard or high-fat food for 1 hour. Pharmacological and genetic tools were used to evaluate the contribution of postprandial endotoxemia and inflammatory responses in the short-term regulation of food intake. We observed constitutive microbial and macronutrient-dependent control of food intake at the time scale of a meal, i.e., within 1 hour of food introduction. Specifically, microbiota depletion increased food intake and the microbiota-derived anorectic effect became significant during the consumption of high-fat but not standard food. This anorectic effect correlated with a specific postprandial microbial metabolic signature and did not require postprandial endotoxemia or an NLRP3 (NOD-, LRR- and Pyrin domain-containing protein 3)-inflammasome mediated inflammatory response. Innovation and Conclusion: These findings show that the gut microbiota controls host appetite at the time scale of a meal under normal physiology. Interestingly, a microbiota-derived anorectic effect develops specifically with a high-fat meal, indicating that gut microbiota activity is involved in the satietogenic properties of foods.

ano.nymous@ccsd.cnrs.fr.invalid (Selma Ben Fradj) 12 Sep 2024

https://hal.science/hal-03594297v1

[hal-04145276] Transinteractome analysis reveals distinct niche requirements for isotype‐based plasma cell subsets in the bone marrow

Bone marrow (BM) long-lived plasma cells (PCs) are essential for long-term protection against infection, and their persistence within this organ relies on interactions with Cxcl12-expressing stromal cells that are still not clearly identified. Here, using single cell RNAseq and in silico transinteractome analyses, we identified Leptin receptor positive (LepR +) mesenchymal cells as the stromal cell subset most likely to interact with PCs within the BM. Moreover, we demonstrated that depending on the isotype they express, PCs may use different sets of integrins and adhesion molecules to interact with these stromal cells. Altogether, our results constitute an unprecedented characterization of PC subset stromal niches and open new avenues for the specific targeting of BM PCs based on their isotype.

ano.nymous@ccsd.cnrs.fr.invalid (Amélie Bonaud) 29 Jun 2023

https://hal.sorbonne-universite.fr/hal-04145276v1

[hal-04386368] Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption

The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium's gene expression strategies. Here, we investigated the effect of acetate on temporal changes in the transcriptome of F. duncaniae A2-165 cultures using RNA sequencing. We compared gene expression patterns between two growth phases (early stationary vs. late exponential) and two acetate levels (low: 3 mM vs. high: 23 mM). Only in low-acetate conditions, a general stress response was activated. In high-acetate conditions, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. Specifically, expression was strongly activated in the case of the feoAABC operon, which encodes a FeoB ferrous iron transporter, but not in the case of the feoAB gene, which encodes a second putative FeoAB transporter. Moreover, excess ferrous iron repressed feoB expression but not feoAB. Lastly, FeoB but not FeoAB peptides from strain A2-165 were found in abundance in a healthy human fecal metaproteome. In conclusion, we characterized two early-stationary transcriptomes based on acetate consumption and this work highlights the regulation of feoB expression in F. duncaniae A2-165.

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Verstraeten) 10 Jan 2024

https://hal.inrae.fr/hal-04386368v1

[hal-04321685] Integration of bacterial RNA-Seq & human gut microbiota metaproteomic datasets highlights Faecalibacterium duncaniae A2-165’s import systems

Abstract text (incl. references): Faecalibacterium are among the main bacteria responsible for the consumption of acetate and the production of butyrate, which has anti-inflammatory properties beneficial to intestinal health (1). Yet, little is known about how acetate availability affects this bacterium’s gene expression strategies either in a pure culture or in a complex environnement. Here, we show that, in the early stationary phase, F. duncaniae strain A2-165 can strongly regulate the expression of metabolic, transport and stress-response genes based on acetate availability in a pure culture model. Using RNA-seq, we compared gene expression patterns between two growth phases (late exponential vs. early stationary) and two acetate levels (low: 3 mM vs. high: 23 mM). At low-acetate levels, a general stress response was activated, and protein synthesis expression was down-regulated. At high- acetate levels, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. We analyzed a metaproteomic dataset obtained from eight healthy individuals (2), dedicated to the envelope fraction of the gut microbiota. Among the 42 transporter genes upregulated in high-acetate conditions, we found 236 peptides that matched with 10 transporter genes. The second highest degree of protein coverage (43.6%, 51 peptides) was found for the FeoB transporter. Of those 51 peptides, 9 were specific to a single protein in the metaproteomic dataset. Through multiomics and targeted approaches, this work highlights the crucial role that the feoAABC operon might play in iron homeostasis in F. duncaniae strain A2-165’s physiology (3). 1. R. Martin, D. Rios-Covian, E.Huillet, et al.. Faecalibacterium: a genus with expanding potential as a live biotherapeutic product in humans revue soumise à FEMS Microbiol Rev. 2. Henry C, Bassignani A, Berland M, Langella O, Sokol H, Juste C. (2022) Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups. Cells, 8 (11) 1340 3. S. Verstraeten, S. Layec, S. Auger, C. Juste, C.Henry, S. Charif, Y. Jaszczyszyn, H. Sokol, L.Beney, P. Langella, M. Thomas, E. Huillet. Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous irouptake, and stress-response genes based on acetate level in early-stationary cultures. https://doi.org/10.21203/rs.3.rs-2481125/v1 preprint en révision

ano.nymous@ccsd.cnrs.fr.invalid (Eugénie Huillet) 04 Dec 2023

https://hal.inrae.fr/hal-04321685v1

[hal-03880814] Genome Sequence and Assessment of Safety and Potential Probiotic Traits of Lactobacillus johnsonii CNCM I-4884

The probiotic strain Lactobacillus johnsonii CNCM I-4884 exhibits anti-Giardia activity in vitro and in vivo in a murine model of giardiasis. The aim of this study was the identification and characterization of the probiotic potential of L. johnsonii CNCM I-4884, as well as its safety assessment. This strain was originally classified as Lactobacillus gasseri based on 16S gene sequence analysis. Whole genome sequencing led to a reclassification as L. johnsonii. A genome-wide search for biosynthetic pathways revealed a high degree of auxotrophy, balanced by large transport and catabolic systems. The strain also exhibits tolerance to low pH and bile salts and shows strong bile salt hydrolase (BSH) activity. Sequencing results revealed the absence of antimicrobial resistance genes and other virulence factors. Phenotypic tests confirm that the strain is susceptible to a panel of 8 antibiotics of both human and animal relevance. Altogether, the in silico and in vitro results confirm that L. johnsonii CNCM I-4884 is well adapted to the gastrointestinal environment and could be safely used in probiotic formulations.

ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Boucard) 28 Jun 2024

https://hal.science/hal-03880814v1

[hal-04522926] Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast

The genetic engineering of genome fragments larger than 100 kbp is challenging and requires both specific methods and cloning hosts. The yeast Saccharomyces cerevisiae is considered as a host of choice for cloning and engineering whole or partial genomes from viruses, bacteria, and algae. Several methods are now available to perform these manipulations, each with its own limitations. In order to extend the range of yeast cloning strategies, a new approach combining two already described methods, Fusion cloning and CReasPy-Cloning, was developed. The CReasPy-Fusion method allows the simultaneous cloning and engineering of megabase-sized genomes in yeast by the fusion of bacterial cells with yeast spheroplasts carrying the CRISPR-Cas9 system. With this new approach, we demonstrate the feasibility of cloning and editing whole genomes from several Mycoplasma species belonging to different phylogenetic groups. We also show that CReasPy-Fusion allows the capture of large genome fragments with high efficacy, resulting in the successful cloning of selected loci in yeast. We finally identify bacterial nuclease encoding genes as barriers for CReasPy-Fusion by showing that their removal from the donor genome improves the cloning efficacy.

ano.nymous@ccsd.cnrs.fr.invalid (Gabrielle Guesdon) 06 Nov 2024

https://hal.inrae.fr/hal-04522926v1

[anses-04372908] Exploring the relationship between Faecalibacterium duncaniae and Escherichia coli in inflammatory bowel disease (IBD): Insights and implications

Inflammatory bowel disease (IBD) is a group of disorders characterized by an inflammation of the gastrointestinal tract (GIT) and represents a major social and economic burden. Despite ongoing research into the etiology and pathophysiology of this multifactorial disease, treatment options remain limited. From this perspective, the gut microbiota has emerged as a potential player in the pathogenesis of IBD, and animal and human studies support this hypothesis. Indeed, the human gut is one of the most complex ecological communities (composed of 1013-1014 microorganisms) that plays a critical role in human health by influencing normal physiology and disease susceptibility through its collective metabolic activities and host interactions. In addition, live probiotic bacteria present in some food products (which transit through the GIT) have been shown to interact with the host immune system and confer several health benefits. The aim of this review is to provide an overview of the link between Faecalibacterium duncaniae and Escherichia coli and IBD, highlighting the main areas of research in this field. An ecological perspective on the gut microbiota may offer new insights for the development of clinical therapies targeting this bacterial community to improve human health.

ano.nymous@ccsd.cnrs.fr.invalid (Alejandro Cabezas-Cruz) 08 Feb 2024

https://anses.hal.science/anses-04372908v1

[hal-03794189] A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica

Yarrowia lipolytica , a non conventional oleaginous yeast species, has attracted attention due to its high lipid degradation and accumulation capacities. Y. lipolytica is used as a chassis for the production of usual and unusual lipids and lipid derivatives. While the genes involved in the intracellular transport and activation of fatty acids in different cellular compartments have been characterized, no genes involved in fatty acid transport from the extracellular medium into the cell have been identified thus far. In this study, we identified secreted proteins involved in extracellular fatty acid binding. Recent analysis of the Y. lipolytica secretome led to the identification of a multigene family that encodes four secreted proteins, preliminarily named UP1 to UP4. These proteins were efficiently overexpressed individually in wild-type and multideletant strain (Q4: Δup1Δup2Δup3Δup4 ) backgrounds. Phenotypic analysis demonstrated the involvement of these proteins in the binding of extracellular fatty acids. Additionally, gene deletion and overexpression prevented and promoted sensitivity to octanoic acid (C8) toxicity, respectively. The results suggested binding is dependent on aliphatic chain length and fatty acid concentration. 3D structure modeling supports the proteins’ role in fatty acid assimilation at the molecular level. We discovered a family of extracellular-fatty-acid-binding proteins in Y. lipolytica and have proposed to name its members eFbp1 to eFbp4. The exact mode of eFbps action remains to be deciphered individually and synergistically; nevertheless, it is expected that the proteins will have applications in lipid biotechnology, such as improving fatty acid production and/or bioconversion.

ano.nymous@ccsd.cnrs.fr.invalid (Djamila Onésime) 15 Jan 2024

https://hal.inrae.fr/hal-03794189v1

[hal-04281314] Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates

ABSTRACT Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum -related diseases.

ano.nymous@ccsd.cnrs.fr.invalid (Jeanne Laurentie) 12 Nov 2023

https://hal.science/hal-04281314v1

[hal-04251786] Unveiling the Secrets of Long-Term Staphylococcus aureus Infections: Insights into Inflammation, Metabolism, and Epigenetic Changes from Non-Immune Cells Transcriptomes

Staphylococcus aureus, an opportunistic pathogen, is responsible for a spectrum of severe chronic diseases such as chronic osteomyelitis and chronic mastitis in humans and in cows, respectively. Although traditionally regarded as an extracellular pathogen, S. aureus has been identified within non-immune cells such as osteoblasts (associated with osteomyelitis) or mammary gland epithelial cells (linked to cow mastitis), potentially influencing the infection outcome. The detection of signals specific from infected bacteria-bearing cells is complicated by dilution and confounding signals by bystander effects in uninfected cells. To address this, we developed a novel long-term infection model for non-immune cells using a flow cytometric approach, enabling the isolation of cells containing internalized S. aureus from mixed populations. This model facilitates a detailed analysis of the impact of prolonged S. aureus infection on the transcriptional program of human non-immune (osteoblast-like) cells. RNA-seq, KEGG, and Reactome pathway enrichment analyses revealed a remodeled transcriptomic profile marked by heightened immune and inflammatory responses, metabolic dysregulations influencing bacterial intracellular life, and downregulation of genes encoding epigenetic regulators, including those involved in chromatin-repressive complexes (e.g., NuRD, BAHD1, and PRC1) and epifactors associated with DNA methylation. Additionally, sets of genes related to cell adhesion or neurotransmission were deregulated. Our findings suggest a long-term impact of intracellular S. aureus infection through epigenetic modifications in host cells, potentially leading to pathophysiological dysfunctions alongside the defense response during infection. These results not only enhance our understanding of biological processes in long-term S. aureus infections of non-immune cells but also provide an atlas of deregulated host genes and biological pathways, identifying potential markers and candidates for prophylactic and therapeutic approaches. Moreover, building on this in vitro work, we have initiated a collaboration with the NuMeCan Institute to validate these observations in vivo in a mini-pig model of S. aureus infection. This animal study will be complemented by an exploration of the serum metabolome and the intestinal microbiota in the chronicity of S. aureus infection. Furthermore, these investigations will be extended to the context of S. aureus mastitis in cows through collaboration with Canadian colleagues.

ano.nymous@ccsd.cnrs.fr.invalid (Aurélie Nicolas) 20 Oct 2023

https://hal.inrae.fr/hal-04251786v1

[hal-04823328] Dual RNA-seq study of the dynamics of coding and non-coding RNA expression during Clostridioides difficile infection in a mouse model

Clostridioides difficile is the leading cause of healthcare-associated diarrhea in industrialized countries. Many questions remain to be answered about the mechanisms governing its interaction with the host during infection. Non-coding RNAs (ncRNAs) contribute to shape virulence in many pathogens and modulate host responses; however, their role in C. difficile infection (CDI) has not been explored. To better understand the dynamics of ncRNA expression contributing to C. difficile infectious cycle and host response, we used a dual RNA-seq approach in a conventional murine model. From the pathogen side, this transcriptomic analysis revealed the upregulation of virulence factors, metabolism, and sporulation genes, as well as the identification of 61 ncRNAs differentially expressed during infection that correlated with the analysis of available raw RNA-seq data sets from two independent studies. From these data, we identified 118 potential new transcripts in C. difficile , including 106 new ncRNA genes. From the host side, we observed the induction of several pro-inflammatory pathways, and among the 185 differentially expressed ncRNAs, the overexpression of microRNAs (miRNAs) previously associated to inflammatory responses or unknown long ncRNAs and miRNAs. A particular host gene expression profile could be associated to the symptomatic infection. In accordance, the metatranscriptomic analysis revealed specific microbiota changes accompanying CDI and specific species associated with symptomatic infection in mice. This first adaptation of in vivo dual RNA-seq to C. difficile contributes to unravelling the regulatory networks involved in C. difficile infectious cycle and host response and provides valuable resources for further studies of RNA-based mechanisms during CDI. IMPORTANCE Clostridioides difficile is a major cause of nosocomial infections associated with antibiotic therapy classified as an urgent antibiotic resistance threat. This pathogen interacts with host and gut microbial communities during infection, but the mechanisms of these interactions remain largely to be uncovered. Noncoding RNAs contribute to bacterial virulence and host responses, but their expression has not been explored during C. difficile infection. We took advantage of the conventional mouse model of C. difficile infection to look simultaneously to the dynamics of gene expression in pathogen, its host, and gut microbiota composition, providing valuable resources for future studies. We identified a number of ncRNAs that could mediate the adaptation of C. difficile inside the host and the crosstalk with the host immune response. Promising inflammation markers and potential therapeutic targets emerged from this work open new directions for RNA-based and microbiota-modulatory strategies to improve the efficiency of C. difficile infection treatments.

ano.nymous@ccsd.cnrs.fr.invalid (Victor Kreis) 06 Dec 2024

https://hal.science/hal-04823328v1

[hal-04170846] Characterization and quantification of antibiotic resistance gene variants in gut microbiota.

The world is reaching a point where effectiveness of antibiotics could be completely com- promised in the near future, if antimicrobial resistance (AMR) continues to spread globally. The intestinal microbiota of human and domestic animals is suspected to be the main reser- voir of AMR organisms and therefore of antibiotic resistance genes (ARGs). Advances in DNA sequencing technology and more specially metagenomic approaches have shown that several ARGs are prevalent and shared between most gut microbiota. Although nucleotide diversity is documented for many ARGs, each variant following independent spread, the dis- tribution of theses variants in gut resistomes is still completely unknown. This study aims to understand if ARGs described as identical in different microbiomes are actually the same variants. We adapted DESMAN, an algorithm developed to reconstruct strains from metagenomic data, to characterize different variants from a pool of ARGs. The tool was applied to ARGs detected in metagenomic cecal samples from chicken raised under different condi- tions. Among 22 genes analyzed, 15 have at least 2 stable variants, 7 (ant(6), blaTEM-1 , erm(B), erm(F), tet(Q), tet(L) and tet(32)) showing variants with important differences in proportions between samples depending on rearing condition and age of animals. Sequence comparison between variants reconstructed by DESMAN and those identified from bacterial isolates revealed a perfect match. These results attest the reliability of the tool to recon- struct different variants of the same ARG directly from metagenomic data and to infer their relative proportion in different samples. It opens the way for futher analysis to understand their relative abondance, persistence and transmission between microbiomes.

ano.nymous@ccsd.cnrs.fr.invalid (Ouléye Sidibe) 25 Jul 2023

https://hal.inrae.fr/hal-04170846v1

[hal-04862942] L,D-transpeptidases and peptidoglycan cross-linking in Clostridioides difficile

<div><p>Although resistance of C. difficile to β-lactams is a leading contributor to the development of C. difficile infection, the underlying mechanisms of resistance are still largely unknown. Thus, the contribution of β-lactamases to β-lactam resistance was recently shown to be very modest in C. difficile. C. difficile has an original peptidoglycan (PG) structure with mainly 3-3 cross-links to the detriment of the widespread 4-3 cross-links. The 3-3 cross-links are synthesized by non-classical transpeptidases, namely the L,Dtranspeptidases (LDTs). All LDTs identified so far share the conserved YkuD catalytic domain and are not efficiently inhibited by most β-lactams. This suggests that LDTs could contribute to β-lactams resistance in C. difficile. C. difficile encodes three putative LDT, Ldt1, Ldt2 and Ldt3, with the YkuD domain. In this study, we generated a combination of single, double and triple deletion mutants of the corresponding genes and the triple mutant was confirmed via whole genome sequencing. Vegetative cells PG was purified from the different C. difficile strains grown in TY, digested with mutanolysin and the muropeptides analyzed by RP-UHPLC. Surprisingly, 3-3 cross-link formation was not abolished in vegetative cells of the triple mutant and only mutation of ldt1 affected their abundance. Structure of the spore PG was also determined. The spore PG is loosely cross-linked but 3-3 cross-links could still be identified. However, spore PG cross-linking remained unchanged in the triple mutant. These results suggest the presence of at least a fourth LDT containing a novel catalytic domain. Work is underway to tentatively identify this enzyme.</p></div>

ano.nymous@ccsd.cnrs.fr.invalid (Ana Oliveira Paiva) 03 Jan 2025

https://hal.science/hal-04862942v1

[hal-04535964] Biofilm formation of the food spoiler Brochothrix thermosphacta on different industrial surface materials using a biofilm reactor

Brochothrix thermosphacta is considered as a major food spoiler bacteria. This study evaluates biofilm formation by B. thermosphacta CD337(2) - a strong biofilm producer strain - on three food industry materials (polycarbonate (PC), polystyrene (PS), and stainless steel (SS)). Biofilms were continuously grown under flow at 25 degrees C in BHI broth in a modified CDC biofilm reactor. Bacterial cells were enumerated by plate counting, and biofilm spatial organization was deciphered by combining confocal laser scanning microscopy and image analysis. The biofilms had the same growth kinetics on all three materials and reach 8log CFU/cm2 as maximal concentration. Highly structured biofilms were observed on PC and PS, but less structured ones on SS. This difference was confirmed by structural quantification analysis using the image analysis software tool BiofilmQ. Biofilm on SS show less roughness, density, thickness and volume. The biofilm 3D structure seemed to be related to the coupon topography and roughness. The materials used in this study do not affect biofilm growth. However, their roughness and topography affect the biofilm architecture, which could influence biofilm behaviour.

ano.nymous@ccsd.cnrs.fr.invalid (Antoine Gaillac) 07 Apr 2024

https://hal.inrae.fr/hal-04535964v1

[hal-04318017] Diving into bacterial dormancy: emergence of osmotically stable wall-less forms in an aquatic environment

Bacteria can respond to environmental stresses by entering a dormant state, called viable but non-culturable (VBNC) state, in which they no longer grow in routine culture media. VBNC pathogens pose thus a significant risk for human and animal health as they are not detected by standard growth-based techniques and can “wake up” back into a vegetative and virulent state. Although hundreds of species were reported to become VBNC in response to different stresses, the molecular mechanisms governing this phenotypic switch remain largely elusive. Here, we characterized the VBNC state transition process in the Gram-positive pathogen Listeria monocytogenes in response to nutritional deprivation. By combining fluorescence microscopy, cryo-electron tomography and analytical biochemistry, we found that starvation in mineral water drives L. monocytogenes into a VBNC state via a mechanism of cell wall (CW) shedding that generates osmotically stable CW-deficient (CWD) coccoid forms. This phenomenon occurs in multiple L. monocytogenes strains and in other Listeria species, suggesting it may be a stress-adapting process transversal to the Listeria genus. Transcriptomic and gene-targeted approaches revealed the stress response regulator SigB and the autolysin NamA as major moderators of CW loss and VBNC state transition. Finally, we show that this CWD dormant state is transient as VBNC Listeria revert back to a walled, vegetative and virulent state after passage in embryonated eggs. Our findings provide unprecedented detail on the mechanisms governing the transition to a VBNC state, and reveal that dormant CWD bacterial forms can naturally arise in aquatic environments without osmotic stabilization. This may represent an alternative strategy for bacterial survival in oligotrophic conditions, which can potentially generate public health-threatening reservoirs of undetectable pathogens.

ano.nymous@ccsd.cnrs.fr.invalid (Filipe Carvalho) 25 Jan 2024

https://hal.inrae.fr/hal-04318017v1

[hal-04742896] Aquatic environment drives the emergence of cell wall-deficient dormant forms in Listeria

Stressed bacteria can enter a dormant viable but non-culturable (VBNC) state. VBNC pathogens pose an increased health risk as they are undetectable by growth-based techniques and can wake up back into a virulent state. Although widespread in bacteria, the mechanisms governing this phenotypic switch remain elusive. Here, we investigate the VBNC state transition in the human pathogen Listeria monocytogenes. We show that bacteria starved in mineral water become VBNC by converting into osmotically stable cell wall-deficient coccoid forms, a phenomenon that occurs in other Listeria species. We reveal the bacterial stress response regulator SigB and the autolysin NamA as major actors of VBNC state transition. We lastly show that VBNC Listeria revert to a walled and virulent state after passage in chicken embryos. Our study provides more detail on the VBNC state transition mechanisms, revealing wall-free bacteria naturally arising in aquatic environments as a potential survival strategy in hypoosmotic and oligotrophic conditions.

ano.nymous@ccsd.cnrs.fr.invalid (Filipe Carvalho) 18 Oct 2024

https://hal.inrae.fr/hal-04742896v1

[hal-04541065] Probiotics against Giardia, which therapeutic future?

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Florent) 10 Apr 2024

https://enva.hal.science/hal-04541065v1

[hal-04106612] Neonatal necrotizing enterocolitis: Clostridium butyricum and Clostridium neonatale fermentation metabolism and enteropathogenicity

Bacterial colonization in the gut plays a pivotal role in neonatal necrotizing enterocolitis (NEC) development, but the relationship between bacteria and NEC remains unclear. In this study, we aimed to elucidate whether bacterial butyrate end-fermentation metabolites participate in the development of NEC lesions and confirm the enteropathogenicity of Clostridium butyricum and Clostridium neonatale in NEC. First, we produced C.butyricum and C.neonatale strains impaired in butyrate production by genetically inactivating the hbd gene encoding β-hydroxybutyryl-CoA dehydrogenase that produces end-fermentation metabolites. Second, we evaluated the enteropathogenicty of the hbd-knockout strains in a gnotobiotic quail model of NEC. The analyses showed that animals harboring these strains had significantly fewer and less intense intestinal lesions than those harboring the respective wild-type strains. In the absence of specific biological markers of NEC, the data provide original and new mechanistic insights into the disease pathophysiology, a necessary step for developing potential novel therapies.

ano.nymous@ccsd.cnrs.fr.invalid (Laurent Ferraris) 25 May 2023

https://hal.inrae.fr/hal-04106612v1

[hal-04581779] A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle

Abstract Background Nine male and eight female calves born to a Normande artificial insemination bull named “Ly” were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality. Results Using Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G &gt; A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes. Conclusions In conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.

ano.nymous@ccsd.cnrs.fr.invalid (Julien Corbeau) 21 May 2024

https://hal.inrae.fr/hal-04581779v1

[hal-04516979] Molecular mechanisms underlying the structural diversity of rhamnose-rich cell wall polysaccharides in lactococci

In Gram-positive bacteria, cell wall polysaccharides (CWPS) play critical roles in bacterial cell wall homeostasis and bacterial interactions with their immediate surroundings. In lactococci, CWPS consist of two components: a conserved rhamnan embedded in the peptidoglycan layer and a surface-exposed polysaccharide pellicle (PSP), which are linked together to form a large rhamnose-rich CWPS (Rha-CWPS). PSP, whose structure varies from strain to strain, is a receptor for many bacteriophages infecting lactococci. Here, we examined the first two steps of PSP biosynthesis, using in vitro enzymatic tests with lipid acceptor substrates combined with LC-MS analysis, AlfaFold2 modeling of protein 3D-structure, complementation experiments, and phage assays. We show that the PSP repeat unit is assembled on an undecaprenyl-monophosphate (C55P) lipid intermediate. Synthesis is initiated by the WpsA/WpsB complex with GlcNAc-P-C55 synthase activity and the PSP precursor GlcNAc-P-C55 is then elongated by specific glycosyltransferases that vary among lactococcal strains, resulting in PSPs with diverse structures. Also, we engineered the PSP biosynthesis pathway in lactococci to obtain a chimeric PSP structure, confirming the predicted glycosyltransferase specificities. This enabled us to highlight the importance of a single sugar residue of the PSP repeat unit in phage recognition. In conclusion, our results support a novel pathway for PSP biosynthesis on a lipid-monophosphate intermediate as an extracellular modification of rhamnan, unveiling an assembly machinery for complex Rha-CWPS with structural diversity in lactococci.

ano.nymous@ccsd.cnrs.fr.invalid (Hugo Guérin) 28 Mar 2024

https://hal.inrae.fr/hal-04516979v1

[hal-03812187] Chronic dietary exposure to a glyphosate-based herbicide results in total or partial reversibility of plasma oxidative stress, cecal microbiota abundance and short-chain fatty acid composition in broiler hens

Glyphosate-based herbicides (GBHs) are massively used in agriculture. However, few studies have investigated the effects of glyphosate-based herbicides on avian species although they are largely exposed via their food. Here, we investigated the potential reversibility of the effects of chronic dietary exposure to glyphosate-based herbicides in broiler hens. For 42 days, we exposed 32-week-old hens to glyphosate-based herbicides via their food (47 mg/kg/day glyphosate equivalent, glyphosate-based herbicides, n = 75) corresponding to half glyphosate’s no-observed-adverse-effect-level in birds. We compared their performance to that of 75 control animals (CT). Both groups (glyphosate-based herbicides and control animals) were then fed for 28 additional days without glyphosate-based herbicides exposure (Ex-glyphosate-based herbicides and Ex-control animals). Glyphosate-based herbicides temporarily increased the plasma glyphosate and AMPA (aminomethylphosphonic acid) concentrations. Glyphosate and aminomethylphosphonic acid mostly accumulated in the liver and to a lesser extent in the leg muscle and abdominal adipose tissue. Glyphosate-based herbicides also temporarily increased the gizzard weight and plasma oxidative stress monitored by TBARS (thiobarbituric acid reactive substances). Glyphosate-based herbicides temporarily decreased the cecal concentrations of propionate, isobutyrate and propionate but acetate and valerate were durably reduced. The cecal microbiome was also durably affected since glyphosate-based herbicides inhibited Barnesiella and favored Alloprevotella . Body weight, fattening, food intake and feeding behavior as well as plasma lipid and uric acid were unaffected by glyphosate-based herbicides. Taken together, our results show possible disturbances of the cecal microbiota associated with plasma oxidative stress and accumulation of glyphosate in metabolic tissues in response to dietary glyphosate-based herbicides exposure in broiler hens. Luckily, glyphosate-based herbicides at this concentration does not hamper growth and most of the effects on the phenotypes are reversible.

ano.nymous@ccsd.cnrs.fr.invalid (Mathias Fréville) 31 Oct 2022

https://hal.inrae.fr/hal-03812187v1

[hal-04064962] Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections

The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the bla CTX-M gene in seven BC, including one for which no extended-spectrum b-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18 mecA/ C genes detected by the BCID2 were not confirmed. No carbapenemase, mecA/C, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections. IMPORTANCE Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 Editor

ano.nymous@ccsd.cnrs.fr.invalid (François Caméléna) 11 Apr 2023

https://hal.inrae.fr/hal-04064962v1

[hal-04116782] A cross-circulatory platform for monitoring innate allo-responses in lung grafts

Lung transplantation is the only curative option for end-stage chronic respiratory diseases. However the survival rate is only about 50% at 5 years. Although experimental evidences have shown that innate allo-responses impact on the clinical outcome, the knowledge of the involved mechanisms involved is limited. We established a cross-circulatory platform to monitor the early recruitment and activation of immune cells in an extracorporeal donor lung by coupling blood perfusion to cell mapping with a fluorescent marker in the pig, a commonly-used species for lung transplantation. The perfusing pig cells were easily detectable in lung cell suspensions, in broncho-alveolar lavages and in different areas of lung sections, indicating infiltration of the organ. Myeloid cells (granulocytes and monocytic cells) were the dominant recruited subsets. Between 6 and 10 h of perfusion, recruited monocytic cells presented a strong upregulation of MHC class II and CD80/86 expression, whereas alveolar macrophages and donor monocytic cells showed no significant modulation of expression. This cross-circulation model allowed us to monitor the initial encounter between perfusing cells and the lung graft, in an easy, rapid, and controllable manner, to generate robust information on innate response and test targeted therapies for improvement of lung transplantation outcome.

ano.nymous@ccsd.cnrs.fr.invalid (Matthieu Glorion) 05 Jun 2023

https://hal.inrae.fr/hal-04116782v1

[hal-04619907] Recueil de projets d'expertise internationale à INRAE. Tome 2

Ce document dit "Recueil de projets d’expertise internationale" complète un premier volume édité en 2021 sur le même type d’activité (https://hal.inrae.fr/hal-04037409). Depuis la création en 2020 de la Direction Générale Déléguée à l’Expertise et l’Appui aux Politiques Publiques (DGDEAPP) il est souligné dans les échanges internes l’importance de mieux connaître, comprendre et "donner à voir" ce que recouvrent ces activités et les produits qui les caractérisent. L’Expertise-projet internationale (EPI) a été définie à travers une note de cadrage élaborée via un groupe d’experts référents. Cette note est accessible sur l’intranet de la DAPP. Au-delà de ce cadrage institutionnel, il semble important et opportun de partager les expériences concrètes, ainsi que la diversité des projets menés par les chercheurs sur cette activité. C’est le but de ce recueil que d’illustrer cette multitude de situations et d’expériences. Ainsi ce document rassemble une quarantaine de projets menés dans plus de 30 pays à travers le monde. On découvre à travers ce recueil un grand nombre d’organisations internationales commanditaires (bailleurs de l’expertise) allant de l’AFD, la FAO, le FIDA, La Banque Mondiale, l’Union Européenne (AEE, JRC), plusieurs agences onusiennes (OMS, PNUD, OMM, UNEP, GEF), l’OCDE, mais aussi des cabinets privés qui font appel à l’expertise scientifique des chercheurs de l’établissement. On y découvre également une grande diversité thématique qu’il est impossible de décrire sans en oublier mais qui vont de la sécurité sanitaire des aliments, des innovations institutionnelles pour une agriculture durable, des dispositifs d’alerte précoce pour prévenir les inondations (CREWS), la valorisation des eaux usées (REUSE), l’économie de la déforestation, les méthodes pour limiter l’impact de l’élevage (MRV), la robotique agricole, des méthodes et outils pour reconsidérer les inégalités, la pauvreté, les structures familiales etc. Si INRAE est aujourd’hui un acteur mondialement reconnu pour la réalisation de projets de recherche dimensionnant et de haut niveau, la montée en puissance des projets d’Expertise Internationale représente un nouveau vecteur de valorisation de ses savoir-faire en renforçant sa visibilité et sa notoriété.

ano.nymous@ccsd.cnrs.fr.invalid (Olga Chekhurska) 21 Jun 2024

https://hal.inrae.fr/hal-04619907v1

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

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

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

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

[cea-04065971] A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation

Protein aggregation in biotherapeutics can reduce their activity and effectiveness. It may also promote immune reactions responsible for severe adverse effects. The impact of plastic materials on protein destabilization is not totally understood. Here, we propose to deconvolve the effects of material surface, air/liquid interface, and agitation to decipher their respective role in protein destabilization and aggregation. We analyzed the effect of polypropylene, TEFLON, glass and LOBIND surfaces on the stability of purified proteins (bovine serum albumin, hemoglobin and α-synuclein) and on a cell extract composed of 6000 soluble proteins during agitation ( P = 0.1–1.2 W/kg). Proteomic analysis revealed that chaperonins, intrinsically disordered proteins and ribosomes were more sensitive to the combined effects of material surfaces and agitation while small metabolic oligomers could be protected in the same conditions. Protein loss observations coupled to Raman microscopy, dynamic light scattering and proteomic allowed us to propose a mechanistic model of protein destabilization by plastics. Our results suggest that protein loss is not primarily due to the nucleation of small aggregates in solution, but to the destabilization of proteins exposed to material surfaces and their subsequent aggregation at the sheared air/liquid interface, an effect that cannot be prevented by using LOBIND tubes. A guidance can be established on how to minimize these adverse effects. Remove one of the components of this combined stress - material, air (even partially), or agitation - and proteins will be preserved.

ano.nymous@ccsd.cnrs.fr.invalid (Marion Schvartz) 12 Sep 2023

https://cea.hal.science/cea-04065971v1

[hal-03762047] Two functionally distinct heme/iron transport systems are virulence determinants of the fish pathogen Flavobacterium psychrophilum

Bacterial pathogens have a critical impact on aquaculture, a sector that accounts for half of the human fish consumption. Flavobacterium psychrophilum (phylum Bacteroidetes) is responsible for bacterial cold-water disease in salmonids worldwide. The molecular factors involved in host invasion, colonization and haemorrhagic septicaemia are mostly unknown. In this study, we identified two new TonB-dependent receptors, HfpR and BfpR, that are required for adaptation to iron conditions encountered during infection and for virulence in rainbow trout. Transcriptional analyses revealed that their expression is tightly controlled and upregulated under specific iron sources and concentrations. Characterization of deletion mutants showed that they act without redundancy: BfpR is required for optimal growth in the presence of high haemoglobin level, while HfpR confers the capacity to acquire nutrient iron from haem or haemoglobin under iron scarcity. The gene hfpY, co-transcribed with hfpR, encodes a protein related to the HmuY family. We demonstrated that HfpY binds haem and contributes significantly to host colonization and disease severity. Overall, these results are consistent with a model in which both BfpR and Hfp systems promote haem uptake and respond to distinct signals to adapt iron acquisition to the different stages of pathogenesis. Our findings give insight into the molecular basis of pathogenicity of a serious pathogen belonging to the understudied family Flavobacteriaceae and point to the newly identified haem receptors as promising targets for antibacterial development.

ano.nymous@ccsd.cnrs.fr.invalid (Yueying Zhu) 26 Aug 2022

https://hal.science/hal-03762047v1

[hal-04344510] Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery

Background Most interactions between the host and its microbiota occur at the gut barrier, and primary colonizers are essential in the gut barrier maturation in the early life. The mother–offspring transmission of microorganisms is the most important factor influencing microbial colonization in mammals, and C-section delivery (CSD) is an important disruptive factor of this transfer. Recently, the deregulation of symbiotic host-microbe interactions in early life has been shown to alter the maturation of the immune system, predisposing the host to gut barrier dysfunction and inflammation. The main goal of this study is to decipher the role of the early-life gut microbiota-barrier alterations and its links with later-life risks of intestinal inflammation in a murine model of CSD. Results The higher sensitivity to chemically induced inflammation in CSD mice is related to excessive exposure to a too diverse microbiota too early in life. This early microbial stimulus has short-term consequences on the host homeostasis. It switches the pup’s immune response to an inflammatory context and alters the epithelium structure and the mucus-producing cells, disrupting gut homeostasis. This presence of a too diverse microbiota in the very early life involves a disproportionate short-chain fatty acids ratio and an excessive antigen exposure across the vulnerable gut barrier in the first days of life, before the gut closure. Besides, as shown by microbiota transfer experiments, the microbiota is causal in the high sensitivity of CSD mice to chemical-induced colitis and in most of the phenotypical parameters found altered in early life. Finally, supplementation with lactobacilli, the main bacterial group impacted by CSD in mice, reverts the higher sensitivity to inflammation in ex-germ-free mice colonized by CSD pups’ microbiota. Conclusions Early-life gut microbiota-host crosstalk alterations related to CSD could be the linchpin behind the phenotypic effects that lead to increased susceptibility to an induced inflammation later in life in mice.

ano.nymous@ccsd.cnrs.fr.invalid (M. Barone) 30 May 2024

https://hal.inrae.fr/hal-04344510v1

[hal-04324709] Molecular mechanisms underlying the structural diversity of complex rhamnose-rich cell wall polysaccharides in lactococci

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Pierre Chapot-Chartier) 05 Dec 2023

https://hal.inrae.fr/hal-04324709v1

[hal-04208434] La muqueuse pulmonaire en période périnatale : un monde à comprendre pour lutter contre la sensibilité du jeune à la bronchiolite

La bronchiolite est la principale maladie respiratoire du nourrisson contre laquelle il n’existe pas de traitements efficaces. C’est une infection due au virus respiratoire syncytial (VRS). La période périnatale est une phase importante dans la maturation de la muqueuse pulmonaire exerçant un déterminisme sur la réactivité des poumons de l’hôte exposés à des pathogènes. Comprendre les caractéristiques physiologiques, immunologiques et microbiologiques des poumons au début de la vie peut conduire à de nouvelles stratégies innovantes contre les agents infectieux. Nous faisons l’hypothèse que le microbiote pulmonaire est un acteur déterminant de la santé des jeunes.

ano.nymous@ccsd.cnrs.fr.invalid (Claire Chottin) 22 Jul 2024

https://hal.inrae.fr/hal-04208434v1

[hal-04287124] Polymerization cycle of actin homolog MreB from a Gram-positive bacterium

In most rod-shaped bacteria, the actin homologue MreB is an essential component of the protein complex effecting cell wall elongation. The polymerization cycle and filament properties of eukaryotic actin have studied for decades and are well characterized. However, purification and in vitro work on MreB proteins have proven very difficult. Current knowledge of MreB biochemical and polymerization properties remains limited and is based on MreB proteins from Gram-negative species. In this study, we report the first observation of organized filaments and the first 3D-structure of MreB from a Gram-positive bacterium. We have purified MreB from the thermophilic Geobacillus stearothermophilus and shown that it forms straight pairs of protofilaments in vitro, and that polymerization depends on the presence of both lipids and nucleotide triphosphate. Two spatially close short hydrophobic sequences mediate membrane anchoring. Importantly, we demonstrate that unlike eukaryotic actin, nucleotide hydrolysis is a prerequisite for MreB interaction with the membrane, and that binding to lipids then triggers polymerization. Based on our results, we propose a molecular model for the mechanism of MreB polymerization.

ano.nymous@ccsd.cnrs.fr.invalid (Wei Mao) 15 Nov 2023

https://hal.inrae.fr/hal-04287124v1

[hal-04541448] Probiotics against Giardia: a future therapeutic alternative?

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Boucard) 10 Apr 2024

https://enva.hal.science/hal-04541448v1

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PUBLICATIONS

> Click here to access the recent publication list from Micalis

HAL : Dernières publications

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

[hal-04739209] Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease

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

[hal-04009559] Polysaccharide II Surface Anchoring, the Achilles’ Heel of Clostridioides difficile

[hal-04764203] Outcomes of Enterococcus faecalis infective endocarditis according to MIC of amoxicillin: a multicentric study

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

[inserm-03962400] Evaluation of ceftolozane-tazobactam susceptibility on a French nationwide collection of Enterobacterales

[hal-03216705] Temocillin susceptibility among Enterobacterales strains recovered from blood culture in France

[hal-04833227] Alteration of Cardiolipin-Dependent Mitochondrial Coupling in Muscle Protects against Obesity

[hal-03105418] Cardiolipin content controls mitochondrial coupling and energetic efficiency in muscle

[hal-01594853] One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

[hal-02914082] Détermination de la souplesse hors plan d’un assemblage de composites boulonnés à l’aide d’une démarche d’homogénéisation

[hal-04918234] Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs

[hal-03153762] IBISBA-FR : Une infrastructure en soutien au développement de la biotechnologie industrielle comme technologie clef pour l’industrie du futur et pour accompagner la bioéconomie et l’économie circulaire

[hal-03973514] MATERNAL MICROBIOTAS TRANSFER IMPACTS MICROBIOTA-GUT-BRAIN AXIS IN OFFSPRING

[hal-03981886] Impact d'un transfert de microbiotes maternels et de leurs métabolites sur l'expression de marqueurs entéroendocrines chez le raton

[hal-02180624] Enzymes Required for Maltodextrin Catabolism in Enterococcus faecalis Exhibit Novel Activities

[hal-03352896] Blockage of bacterial FimH prevents mucosal inflammation associated with Crohn’s disease

[hal-03594297] Evidence for constitutive microbiota-dependent short-term control of food intake in mice: Is there a link with inflammation, oxidative stress, endotoxemia, and Glp-1?

[hal-04145276] Transinteractome analysis reveals distinct niche requirements for isotype‐based plasma cell subsets in the bone marrow

[hal-04386368] Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption

[hal-04321685] Integration of bacterial RNA-Seq & human gut microbiota metaproteomic datasets highlights Faecalibacterium duncaniae A2-165’s import systems

[hal-03880814] Genome Sequence and Assessment of Safety and Potential Probiotic Traits of Lactobacillus johnsonii CNCM I-4884

[hal-04522926] Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast

[anses-04372908] Exploring the relationship between Faecalibacterium duncaniae and Escherichia coli in inflammatory bowel disease (IBD): Insights and implications

[hal-03794189] A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica

[hal-04281314] Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates

[hal-04251786] Unveiling the Secrets of Long-Term Staphylococcus aureus Infections: Insights into Inflammation, Metabolism, and Epigenetic Changes from Non-Immune Cells Transcriptomes

[hal-04823328] Dual RNA-seq study of the dynamics of coding and non-coding RNA expression during Clostridioides difficile infection in a mouse model

[hal-04170846] Characterization and quantification of antibiotic resistance gene variants in gut microbiota.

[hal-04862942] L,D-transpeptidases and peptidoglycan cross-linking in Clostridioides difficile

[hal-04535964] Biofilm formation of the food spoiler Brochothrix thermosphacta on different industrial surface materials using a biofilm reactor

[hal-04318017] Diving into bacterial dormancy: emergence of osmotically stable wall-less forms in an aquatic environment

[hal-04742896] Aquatic environment drives the emergence of cell wall-deficient dormant forms in Listeria

[hal-04541065] Probiotics against Giardia, which therapeutic future?

[hal-04106612] Neonatal necrotizing enterocolitis: Clostridium butyricum and Clostridium neonatale fermentation metabolism and enteropathogenicity

[hal-04581779] A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle

[hal-04516979] Molecular mechanisms underlying the structural diversity of rhamnose-rich cell wall polysaccharides in lactococci

[hal-03812187] Chronic dietary exposure to a glyphosate-based herbicide results in total or partial reversibility of plasma oxidative stress, cecal microbiota abundance and short-chain fatty acid composition in broiler hens

[hal-04064962] Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections

[hal-04116782] A cross-circulatory platform for monitoring innate allo-responses in lung grafts

[hal-04619907] Recueil de projets d'expertise internationale à INRAE. Tome 2

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

[cea-04065971] A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation

[hal-03762047] Two functionally distinct heme/iron transport systems are virulence determinants of the fish pathogen Flavobacterium psychrophilum

[hal-04344510] Gut barrier-microbiota imbalances in early life lead to higher sensitivity to inflammation in a murine model of C-section delivery

[hal-04324709] Molecular mechanisms underlying the structural diversity of complex rhamnose-rich cell wall polysaccharides in lactococci

[hal-04208434] La muqueuse pulmonaire en période périnatale : un monde à comprendre pour lutter contre la sensibilité du jeune à la bronchiolite

[hal-04287124] Polymerization cycle of actin homolog MreB from a Gram-positive bacterium

[hal-04541448] Probiotics against Giardia: a future therapeutic alternative?

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