-
[hal-01201920] Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi– yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Morel) 18 Sep 2015
https://amu.hal.science/hal-01201920
-
[hal-01204245] Complete genome sequence of the probiotic Lactobacillus casei strain BL23
The entire genome of Lactobacillus casei BL23, a strain with probiotic properties, has been sequenced. The genomes of BL23 and the industrially used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar.
ano.nymous@ccsd.cnrs.fr.invalid (Alain Mazé) 23 Sep 2015
https://hal.science/hal-01204245
-
[hal-01867036] Exploring multiple effects of Zn0.15Mg0.85O nanoparticles on Bacillus subtilis and macrophages
Exploring multiple effects of Zn0.15Mg0.85O nanoparticles on Bacillus subtilis and macrophages
ano.nymous@ccsd.cnrs.fr.invalid (Sandrine Auger) 03 Sep 2018
https://hal.science/hal-01867036
-
[hal-03353101] Targeting the Respiratory Syncytial Virus N 0 -P Complex with Constrained α-Helical Peptides in Cells and Mice
Respiratory syncytial virus (RSV) is the main cause of severe respiratory infection in young children worldwide, and no therapies have been approved for the treatment of RSV infection. Data from recent clinical trials of fusion or L polymerase inhibitors for the treatment of RSV-infected patients revealed the emergence of escape mutants, highlighting the need for the discovery of inhibitors with novel mechanisms of action. Here we describe stapled peptides derived from the N terminus of the phosphoprotein (P) that act as replication inhibitors.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Galloux) 23 Sep 2021
https://hal.inrae.fr/hal-03353101
-
[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-04535964
-
[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-04106612
-
[hal-03287046] Prebiotic Supplementation During Pregnancy Modifies the Gut Microbiota and Increases Metabolites in Amniotic Fluid, Driving a Tolerogenic Environment In Utero
The gut microbiota is influenced by environmental factors such as food. Maternal diet during pregnancy modifies the gut microbiota composition and function, leading to the production of specific compounds that are transferred to the fetus and enhance the ontogeny and maturation of the immune system. Prebiotics are fermented by gut bacteria, leading to the release of short-chain fatty acids that can specifically interact with the immune system, inducing a switch toward tolerogenic populations and therefore conferring health benefits. In this study, pregnant BALB/cJRj mice were fed either a control diet or a diet enriched in prebiotics (Galacto-oligosaccharides/Inulin). We hypothesized that galacto-oligosaccharides/inulin supplementation during gestation could modify the maternal microbiota, favoring healthy immune imprinting in the fetus. Galacto-oligosaccharides/inulin supplementation during gestation increases the abundance of Bacteroidetes and decreases that of Firmicutes in the gut microbiota, leading to increased production of fecal acetate, which was found for the first time in amniotic fluid. Prebiotic supplementation increased the abundance of regulatory B and T cells in gestational tissues and in the fetus. Interestingly, these regulatory cells remained later in life. In conclusion, prebiotic supplementation during pregnancy leads to the transmission of specific microbial and immune factors from mother to child, allowing the establishment of tolerogenic immune imprinting in the fetus that may be beneficial for infant health outcomes.
ano.nymous@ccsd.cnrs.fr.invalid (Carole Brosseau) 15 Jul 2021
https://hal.inrae.fr/hal-03287046
-
[hal-02941413] Determinants of activity in glutaredoxins: an in vitro evolved Grx1-like variant of Escherichia coli Grx3
The Escherichia coli glutaredox ins 1 and 3 (Grx 1 and Grx3) are structurally similar (37 % sequence identity), yet have different activities in vivo. Unlike Grx3, Grx 1 efficiently reduces protein disulfides in proteins such as RR (ribonucleotide reductase), whereas it is poor at reducing S-glutathionylated proteins. An E. coli strain lacking genes encoding thioredoxins 1 and 2 and Grx 1 is not viable on either rich or minimal medium; however, a M43V mutation in Grx3 restores growth under these conditions and results in a Grx1-like protein [Ortenberg, Con, Porat and Beckwith (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 7439-7944]. To uncover the structural basis of this change in activity, we have compared wild-type and mutant Grx3 using CD and NMR spectroscopy. Ligand-induced stability measurements demonstrate that the Grx3(M43V/C65Y) mutant has acquired affinity for RR. Far-UV CD spectra reveal no significant differences, but differences are observed in the near-UV region indicative of tertiary structural changes. NMR H-1-N-15 HSQC (heteronuclear single quantum coherence) spectra show that approximately half of the 82 residues experience significant (Delta delta > 0.03 p.p.m.) chemical shift deviations in the mutant, including nine residues experiencing extensive (Delta delta >= 0.15 p.p.m.) deviations. To test whether the M43V mutation alters dynamic properties of Grx3, H/D (hydrogen/deuterium) exchange experiments were performed demonstrating that the rate at which backbone amides exchange protons with the solvent is dramatically enhanced in the mutant, particularly in the core of the protein. These data suggest that the Grx1-like activity of the Grx3(M43V/C65Y) mutant may be explained by enhanced intrinsic motion allowing for increased specificity towards larger substrates such as RR.
ano.nymous@ccsd.cnrs.fr.invalid (Tobias h. Elgán) 17 Sep 2020
https://hal.inrae.fr/hal-02941413
-
[inserm-00622573] Small variable segments constitute a major type of diversity of bacterial genomes at the species level.
BACKGROUND: Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. RESULTS: We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. CONCLUSIONS: This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes.
ano.nymous@ccsd.cnrs.fr.invalid (Fabrice Touzain) 12 Sep 2011
https://inserm.hal.science/inserm-00622573
-
[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) 02 Mar 2022
https://hal.science/hal-03594297
-
[hal-04436033] Plasticité gliale dans le complexe dorso-vagal en réponse à des régimes « gras-sucrés » de type occidental
Introduction et but de l’étude Le surpoids et l’obésité sont en partie causées par des altérations du contrôle neurophysiologique de la prise alimentaire. Dans l’hypothalamus les plasticités gliale (activations astrocytaire et microgliale) et neuronale (renouvellement neuronal) jouent un rôle dans la régulation de la prise alimentaire en fonction des besoins de l’organisme (régulation de la sensation de faim et de satiété en fonction des apports énergétiques) et notamment dans l’adaptation aux régimes riches en énergie. Pour mieux comprendre ces mécanismes, il est important de caractériser les modifications plastiques de la glie dans des structures cérébrales participant à la régulation de la prise alimentaire autres que l’hypothalamus, comme le complexe dorso-vagal dans le tronc cérébral. Nous avons plus spécifiquement ciblé l’area postrema (AP), dont les neurones reçoivent les informations en provenance du système digestif par la voie nerveuse (nerf vague et projections du noyau du tractus solitaire [NTS]) et par la voie sanguine (hormones et métabolites circulants). L’objectif de cette étude était de caractériser les modifications plastiques de la glie dans l’AP et le NTS, chez le rongeur, en réponse à l’exposition à un régime gras et sucré de type occidental, administré de façon chronique ou lors d’épisodes répétés. Matériel et méthodes Nous avons analysé, sur des coupes de tronc cérébral dans l’AP et le NTS, la plasticité morphologique des astrocytes (déploiement des prolongements astrocytaires) par immunomarquage de la GFAP, et la plasticité phénotypique de la microglie (activation microgliale caractérisée par des modifications morphologiques) par immunomarquage de Iba1 sur deux modèles de rongeurs : – des rats soumis pendant 1 mois à un régime pro-inflammatoire, riche en lipides et sucres, et pauvre en fibres ; – des souris soumises à des épisodes courts et répétés d’un régime riche en lipides et sucres, modèle de souris « yoyo », en régime standard au moment du sacrifice, permettant de caractériser la persistance des effets de l’exposition à ces régimes. Résultats et analyse statistique Nous avons montré une augmentation du déploiement astrocytaire et un épaississement de la barrière astrocytaire entre l’AP et le NTS après 1 mois de régime gras-sucré chez le rat ainsi qu’après une exposition répétée à un régime gras-sucré chez la souris. En revanche nous n’avons pas observé de modification du nombre ou de la morphologie des cellules microgliales, chez les rats et souris soumis au régime gras-sucré, ce qui suggère l’absence d’activation microgliale dans ces régions. Conclusion Ces résultats mettent en évidence un phénomène de plasticité astrocytaire renforçant la barrière entre l’AP et le NTS (deux régions mitoyennes du tronc cérébral impliquées dans la satiété) en réponse à des régimes de type occidental (gras-sucrés). Cet effet est observé après une exposition chronique chez le rat ou après des expositions répétées chez la souris, ce qui suggère la persistance de l’impact du régime sur la barrière astrocytaire. Cette modification astrocytaire dans le complexe dorso-vagal pourrait ainsi jouer un rôle dans l’adaptation de la prise alimentaire aux besoins énergétiques de l’organisme.
ano.nymous@ccsd.cnrs.fr.invalid (Gaëlle Champeil-Potokar) 03 Feb 2024
https://agroparistech.hal.science/hal-04436033
-
[hal-03287943] Glial plasticity in the dorsal vagal complex in response to western diet in rodents
Growing evidence indicates that glial plasticity plays a role in feeding control, by adapting neuronal transmission to metabolic needs. Astroglial morphological changes and microglial activation occurs in response to feeding, in the hypothalamus and in other brain area involved in feeding regulation such as the olfactory bulb. Glial plasticity seems to evolve to glial activation in response to high-fat-high-sugar western diets (WD) consumption generating pro-inflammatory/obesogenic states. There is an abundant glial population in the dorsal vagal complex (DVC), a brainstem area involved in the integration of digestive signals. A thick border of astrocytes delineates the area postrema (AP), a circumventricular organ with permeable blood barrier, from the nucleus of the tractus solitarius (NTS) homing neuronal species involved in satiety, and astrocytes. Microglia are also abundant in the AP and NTS, where pro-inflammatory signals may arrive from the gut in response to dietary load and digestion. However, little is known about the involvement of these glial populations in the satietogenic signals from the DVC. Our aim was to evaluate astrocytes and microglial changes in response to chronic or repeated episodes of western diet in the DVC of rats or mice. We have analysed the extent of the astrocyte spreading and the number and morphological phenotype of microglia in the AP and NTS by immunohistochemistry, on two rodent models: rats submitted to a high-fat/high-sugar diet (WD), and mice submitted to several 1-week-episodes of WD. Brainstems were taken after killing, fixed in formalin, and cryostat-cut coronal sections were labelled and analysed for astrocytes (GFAP) and microglia (Iba1). We found an increase in the astrocyte spreading (GFAP labelled area and thickness) between the AP and the NTS (but not in the astrocytes within the NTS) after one month of WD in rats as well as in mice after the repeated episodes of WD, as compared to control animals. We did not observe any increase in the microglial number or morphology within the AP in WD fed animals whereas we found an increased number of microglial cells in the NTS of WD fed rats as compared to controls. These glial changes were associated with several digestive markers alteration.These results show morphological changes enlarging the astroglial barrier between the AP and NTS in the DVC of rodents receiving a western diet. This was observed after a chronic exposition in rats or repeated expositions in mice, suggesting a persistence of the influence of the diet on the size of the astroglial barrier. Such an astroglial morphological plasticity in the DVC, between the AP and the NTS, may play a role in the adaptation of the satietogenic activity of the neurons to the type of diet.
ano.nymous@ccsd.cnrs.fr.invalid (G. Champeil-Potokar) 16 Jul 2021
https://hal.inrae.fr/hal-03287943
-
[hal-04542203] Influence du régime sur la plasticité gliale dans le complexe dorso-vagal
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Gaëlle Champeil-Potokar) 11 Apr 2024
https://hal.science/hal-04542203
-
[hal-03171983] Dietary switch to Western diet induces hypothalamic adaptation associated with gut microbiota dysbiosis in rats
Background: Early hyperphagia and hypothalamic inflammation encountered after Western diet (WD) are linked to rodent propensity to obesity. Inflammation in several brain structures has been associated with gut dysbiosis. Since gut microbiota is highly sensitive to dietary changes, we hypothesised that immediate gut microbiota adaptation to WD in rats is involved in inflammation-related hypothalamic modifications. Methods: We evaluated short-term impact of WD consumption (2 h, 1, 2 and 4 days) on hypothalamic metabolome and caecal microbiota composition and metabolome. Data integration analyses were performed to uncover potential relationships among these three datasets. Finally, changes in hypothalamic gene expression in absence of gut microbiota were evaluated in germ-free rats fed WD for 2 days. Results: WD quickly and profoundly affected the levels of several hypothalamic metabolites, especially oxidative stress markers. In parallel, WD consumption reduced caecal microbiota diversity, modified its composition towards pro-inflammatory profile and changed caecal metabolome. Data integration identified strong correlations between gut microbiota sub-networks, unidentified caecal metabolites and hypothalamic oxidative stress metabolites. Germ-free rats displayed reduced energy intake and no changes in redox homoeostasis machinery expression or pro-inflammatory cytokines after 2 days of WD, in contrast to conventional rats, which exhibited increased SOD2, GLRX and IL-6 mRNA levels. Conclusion: A potentially pro-inflammatory gut microbiota and an early hypothalamic oxidative stress appear shortly after WD introduction. Tripartite data integration highlighted putative links between gut microbiota sub-networks and hypothalamic oxidative stress. Together with the absence of hypothalamic modifications in germ-free rats, this strongly suggests the involvement of the microbiota-hypothalamus axis in rat adaptation to WD introduction and in energy homoeostasis regulation.
ano.nymous@ccsd.cnrs.fr.invalid (Mélanie Fouesnard) 07 Sep 2021
https://hal.science/hal-03171983
-
[hal-04320445] Recurrent Western dieting alters brain homeostasis and regulation of food intake via persistent changes in the gut microbiota-host symbiosis
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Mélanie Fouesnard) 04 Dec 2023
https://hal.inrae.fr/hal-04320445
-
[hal-03371052] para-Sulphonato-calix[n]arenes as selective activators for the passage of molecules across the Caco-2 model intestinal membrane
The passage of Lucifer Yellow across the Caco-2 intestinal model membrane has been studied for the para-sulphonato-calix[n]arenes, the results show that para-sulphonato-calix[4]arene and para-sulphonato-calix[8]arene activate membrane passage when used simultaneously with a transport probe, Lucifer Yellow, whereas para-sulphonato-calix[6]arene has no effect.
ano.nymous@ccsd.cnrs.fr.invalid (Eszter Roka) 08 Oct 2021
https://hal.inrae.fr/hal-03371052
-
[hal-01960692] Thioether bond formation by SPASM domain radical SAM enzymes: C α H-atom abstraction in subtilosin A biosynthesis
AlbA is a radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by radical SAM enzymes.
ano.nymous@ccsd.cnrs.fr.invalid (Alhosna Benjdia) 31 May 2022
https://normandie-univ.hal.science/hal-01960692
-
[hal-03371041] Large negatively charged organic host molecules as inhibitors of endonuclease enzymes
Three large negatively charged organic host molecules; β-cyclodextrin sulphate, para-sulphonato-calix[6]arene and para-sulphonato-calix[8]arene have been shown to be effective inhibitors of endonuclease in the low micromolar range, additionally para-sulphonato-calix[8]arene is a partial inhibitor of rhDNase I.
ano.nymous@ccsd.cnrs.fr.invalid (Yannick Tauran) 08 Oct 2021
https://hal.inrae.fr/hal-03371041
-
[hal-01597154] Discriminatory antibacterial effects of calix[n]arene capped silver nanoparticles with regard to Gram positive and Gram negative bacteria
Silver nanoparticles capped with nine different sulphonated calix[n] arenes were tested for their anti-bacterial effects against B. subtilis and E. coli at an apparent concentration of 100 nM in calix[n] arene. The results show the para-sulphonato-calix[n] arenes are active against Gram positive bacteria and the derivatives having sulphonate groups at both para and alkyl terminal positions are active against Gram negative bacteria. The calix[6] arene derivative with only O-alkyl sulphonate groups shows bactericidal activity.
ano.nymous@ccsd.cnrs.fr.invalid (Samira Boudebbouze) 28 Sep 2017
https://hal.science/hal-01597154
-
[hal-01204487] para-Sulphonato-calix[n]arenes as selective activators for the passage of molecules across the Caco-2 model intestinal membrane
The passage of Lucifer Yellow across the Caco-2 intestinal model membrane has been studied for the para-sulphonato-calix[n]arenes, the results show that para-sulphonato-calix[4]arene and para-sulphonato-calix[8]arene activate membrane passage when used simultaneously with a transport probe, Lucifer Yellow, whereas para-sulphonato-calix[6]arene has no effect.
ano.nymous@ccsd.cnrs.fr.invalid (Eszter Roka) 23 Sep 2015
https://hal.science/hal-01204487
-
[hal-01204429] Large negatively charged organic host molecules as inhibitors of endonuclease enzymes
Three large negatively charged organic host molecules; beta-cyclodextrin sulphate, para-sulphonato-calix[6] arene and para-sulphonato-calix[8]-arene have been shown to be effective inhibitors of endonuclease in the low micromolar range, additionally para-sulphonato-calix[8]arene is a partial inhibitor of rhDNase I.
ano.nymous@ccsd.cnrs.fr.invalid (Yannick Tauran) 23 Sep 2015
https://hal.science/hal-01204429
-
[hal-04396015] para -Sulphonato-calix[ n ]arene capped silver nanoparticles challenge the catalytic efficiency and the stability of a novel human gut serine protease inhibitor
Eubacterium saburreum serpin from human gut microbiota inhibits the pancreatic elastase associated with pancreatitis, inhibition is strongly increased by para -sulphonato-calix[8]arene silver nanoparticles.
ano.nymous@ccsd.cnrs.fr.invalid (Nizar Akermi) 15 Jan 2024
https://hal.science/hal-04396015
-
[hal-02618271] Para-Sulphonato-calix[n]arene capped silver nanoparticles challenge the catalytic efficiency and the stability of a novel human gut serine protease inhibitor.
The Eubacterium saburreum serine protease inhibitor from the human gut microbiota inhibits the eukaryotic pancreatic elastase associated with acute pancreatitis. Interestingly, the inhibition efficiency and stability are markedly increased by the para-sulphonato-calix[8]arene capped silver nanoparticles. Moreover, this enzyme is distinguishable by its high inhibitory effect at broad pH range between 2-10 and temperatures from 10 to 40 °C, in the presence of para-sulphonato-calix[8]arene capped silver nanoparticles the enzyme remains active even at 70 °C.
ano.nymous@ccsd.cnrs.fr.invalid (Nizar Akermi) 25 May 2020
https://hal.inrae.fr/hal-02618271
-
[hal-02622192] Turning off <em>Bacillus cereus</em> quorum sensing system with peptidic analogs
We explored quenching of the PlcR-PapR quorum-sensing system in<em> Bacillus cereus</em>. We generated PapR(7)-peptidic derivatives that inhibit this system and thus the production of virulence factors, reflected by a loss in hemolytic activity, without affecting bacterial growth. To our knowledge, these peptides represent the first potent synthetic inhibitors of quorum-sensing in <em>B. cereus</em>.
ano.nymous@ccsd.cnrs.fr.invalid (Avishag Yehuda) 26 May 2020
https://hal.inrae.fr/hal-02622192
-
[hal-01190507] Supramolecular stabilization of acid tolerant L-arabinose isomerase from Lactobacillus sakei
L-Arabinose isomerase stability is a crucial criterion for the industrial application of this biocatalyst. Noria and NoriaPG are capable of increasing the L-arabinose isomerase stability not only at high temperatures but also at low pH. Such results highlight, for the first time, the use of the Noria series of molecules for protein stabilization and activation.
ano.nymous@ccsd.cnrs.fr.invalid (Said Jebors) 01 Sep 2015
https://hal.science/hal-01190507
-
[hal-02618848] Biopréservation et hautes pressions: des outils pour la maîtrise des dangers microbiologiques dans les aliments.
L'utilisation d’additifs conservateurs est souvent nécessaire pour assurer la sécurité microbiologique des produits carnés réfrigérés faiblement acides. Le projet ANR BLac HP (2014-2019) a étudié une nouvelle stratégie de stabilisation des produits carnés réfrigérés pour assurer le contrôle des flores indésirables à la fois végétatives et sporulées. Grâce à une approche pluridisciplinaire, les travaux ont montré que la combinaison de la biopréservation par des bactéries lactiques et d’un traitement hautes pressions permettait d’assurer la qualité microbiologique de dés de jambon cuits à teneur réduite en nitrite pendant toute leur durée de vie. Le traitement permet de plus une qualité sensorielle optimale sans impact environnemental supplémentaire par rapport au procédé conventionnel. Mots-clés: spores, jambon, nitrites.
ano.nymous@ccsd.cnrs.fr.invalid (Hélène Simonin) 25 May 2020
https://hal.inrae.fr/hal-02618848
-
[hal-01204375] Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage
The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.
ano.nymous@ccsd.cnrs.fr.invalid (Stephane Chaillou) 23 Sep 2015
https://hal.science/hal-01204375
-
[hal-02933270] Interactions entre Staphylococcus xylosus et Lactobacillus sakei dans une matrice «saucisson» modèle
[...]
ano.nymous@ccsd.cnrs.fr.invalid (C. Zuliani) 08 Sep 2020
https://hal.inrae.fr/hal-02933270
-
[hal-03685819] The project INSECT4CITY: assessment of benefits and risks of insect-based bioconversion for recycling bio-waste from urban and peri-urban areas
In urban and peri-urban areas, where waste management is more than ever a major issue, insect farming may be an ecological way to recycle bio-waste in a circular bioeconomy approach. Indeed, someinsect species such as Hermetia illucens can grow on many types of organic substrates and can convert them into valuable byproducts(1). There may be a wide variety of insect bioconversion products since larvae are a natural source of micronutrients, amino acids and antimicrobial compounds. They are also rich in proteins which can be used for animal feed, in fats used for the production of biodiesel, in chitin used in various industries, and they produce a type of manure called frass that can be used as biofertilizer(2). However, besides its ecological and nutritional benefits, risks of insectbased bioconversion should be identified and monitored. Indeed, some chemical contaminants may be found in insect farming environment, in their feeding substrates or can be produced during processing methods(3). Moreover, microbiological contaminants may be found in the farming insect chain(4). Therefore, it is necessary to assess the impact of these contaminants on insect survival and to determine their fate in the insect. It is also important to assess the environmental, social and economic impact of insect-based bioconversion and to determine the consumer acceptability of these new processes and products
ano.nymous@ccsd.cnrs.fr.invalid (Erwan Engel) 02 Jun 2022
https://hal.inrae.fr/hal-03685819
-
[hal-02921909] Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705
The nucleotide sequences of plasmids pRC12 (12,342 bp; GC 43.99%) and pRC18 (18,664 bp; GC 34.33%), harbored by the bacteriocin-producer Lactobacillus curvatus CRL 705, were determined and analyzed. Plasmids pRC12 and pRC18 share a region with high DNA identity (> 83% identity between RepA, a Type II toxin-antitoxin system and a tyrosine inte-grase genes) and are stably maintained in their natural host L. curvatus CRL 705. Both plas-mids are low copy number and belong to the theta-type replicating group. While pRC12 is a pUCL287-like plasmid that possesses iterons and the repA and repB genes for replication, pRC18 harbors a 168 amino acid replication protein affiliated to RepB, which was named RepB'. Plasmid pRC18 also possesses a pUCL287-like repA gene but it was disrupted by an 11 kb insertion element that contains RepB', several transposases/IS elements, and the lactocin Lac705 operon. An Escherichia coli / Lactobacillus shuttle vector, named plasmid p3B1, carrying the pRC18 replicon (i.e. repB' and replication origin), a chloramphenicol resistance gene and a pBluescript backbone, was constructed and used to define the host range of RepB'. Chloramphenicol-resistant transformants were obtained after electropora-tion of Lactobacillus plantarum CRL 691, Lactobacillus sakei 23K and a plasmid-cured derivative of L. curvatus CRL 705, but not of L. curvatus DSM 20019 or Lactococcus lactis NZ9000. Depending on the host, transformation efficiency ranged from 10 2 to 10 7 per μg of DNA; in the new hosts, the plasmid was relatively stable as 29-53% of recombinants kept it after cell growth for 100 generations in the absence of selective pressure. Plasmid p3B1 could therefore be used for cloning and functional studies in several Lactobacillus species.
ano.nymous@ccsd.cnrs.fr.invalid (Lucrecia Terán) 25 Aug 2020
https://hal.inrae.fr/hal-02921909
-
[hal-01204341] Dynamic evolution during storage of meat and seafood products towards the selection of core and variable components of microbial spoilage
absent
ano.nymous@ccsd.cnrs.fr.invalid (Stephane Chaillou) 23 Sep 2015
https://hal.science/hal-01204341
-
[hal-03904120] Exploring the Diversity of Biofilm Formation by the Food Spoiler Brochothrix thermosphacta
Brochothrix thermosphacta is considered as a major spoiler of meat and seafood products. This study explores the biofilm formation ability and the biofilm structural diversity of 30 multi-origin B. thermosphacta strains using a set of complementary biofilm assays (biofilm ring test, crystal violet staining, and confocal laser scanning microscopy). Two major groups corresponding to low and high biofilm producers were identified. High biofilm producers presented flat architectures characterized by high surface coverage, high cell biovolume, and high surface area.
ano.nymous@ccsd.cnrs.fr.invalid (Antoine Gaillac) 03 Jan 2023
https://hal.inrae.fr/hal-03904120
-
[hal-02914960] Testing markers to characterize microbial communities in food ecosystems using a metagenomics approach
While metabarcoding is commonly used to describe prokaryotes in the microbiome of many environments, methods for describing micro-eukaryote diversity is lacking and requires better methodology and standardisation. One reason is that the universal fungal barcode, the Internal Transcribed Spacer (ITS) region, displays considerable size variation among yeasts and other micro-eukaryotes. There are also several repeats leading to sequencing errors or termination. Additionally, the ITS databases are far from complete, especially for Ascomycota that are commonly found in food. Other rDNA barcodes have been used but often do not harbor enough polymorphism to identify taxa at the Species level. In food, microbiota are usually composed of a reduced number of species compared to wild environments. Identifying micro-eukaryotes at the Species level, and potentially strain level, is therefore necessary.
ano.nymous@ccsd.cnrs.fr.invalid (Claire Vincent) 13 Aug 2020
https://hal.science/hal-02914960
-
[hal-03376554] Positive effect of combining high pressure and biopreservation treatments on lowering the bacterial growth during storage of diced cooked ham with reduced nitrite salt
We investigated the combined effects of biopreservation and high pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of dice cooked ham from local supermarkets, sampled near the use-by-date, were characterised. The four ham microbiota showed a relative low diversity but harboured quite dissimilar communities. Two ham samples were dominated by different Proteobacteria (Pseudomonas, Serratia for one, Psychrobacter and Vibrio for the other one) while the two others were dominated by Firmicutes ( Latilactobacillus and Leuconostoc ). Second, sterile diced cooked ham, prepared with reduced level of nitrite was inoculated with the two Proteobacteria-rich microbiota collected from the aforementioned commercial samples together with a Lactococcus lactis protective strain. Dices were then treated at 500 MPa for 5 minutes and bacterial dynamics was monitored during storage at 8°C. Applied alone, none of the treatments stabilized durably the growth of hams microbiota. Nevertheless, the combination of biopreservation and high pressure treatment was efficient to reduce the growth of Proteobacteria spoilage species. However, this effect was dependent on the nature of the initial microbiota, showing that use of biopreservation and high pressure treatment as an alternative to nitrite reduction for ensuring cooked ham microbial safety merits attention but still requires improvement.
ano.nymous@ccsd.cnrs.fr.invalid (Stéphane Chaillou) 13 Oct 2021
https://hal.inrae.fr/hal-03376554
-
[hal-02914971] Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere
Data in this article provide detailed information on the diversity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were monitored throughout the refrigerated storage period to estimate the impact of packaging atmosphere and the use of potassium lactate as chemical preservative. The data include several types of analysis aiming at providing a comprehensive microbial ecology of spoilage during storage and how the process parameters do influence this phenomenon. The analysis includes: the gas content in packaging, pH, chromametric measurements, plate counts (total mesophilic aerobic flora and lactic acid bacteria), sensorial properties of the products, meta-metabolomic quantification of volatile organic compounds and bacterial community metagenetic analysis. Bacterial diversity was monitored using two types of amplicon sequencing (16S rRNA and GyrB encoding genes) at different time points for the different conditions (576 samples for gyrB and 436 samples for 16S rDNA). Sequencing data were generated by using Illumina MiSeq. The sequencing data have been deposited in the bioproject PRJNA522361. Samples accession numbers vary from SAMN10964863 to SAMN10965438 for gyrB amplicon and from SAMN10970131 to SAMN10970566 for 16S.
ano.nymous@ccsd.cnrs.fr.invalid (Simon Poirier) 13 Aug 2020
https://hal.inrae.fr/hal-02914971
-
[hal-04282392] Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios
Background The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics. Methods Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers. Results Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism. Conclusion We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.
ano.nymous@ccsd.cnrs.fr.invalid (Simon Poirier) 13 Nov 2023
https://hal.inrae.fr/hal-04282392
-
[hal-03751737] Contribution of omics to biopreservation: Toward food microbiome engineering
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
ano.nymous@ccsd.cnrs.fr.invalid (Frédéric Borges) 15 Aug 2022
https://hal.inrae.fr/hal-03751737
-
[hal-03798971] Combination of High-Pressure Treatment at 500 MPa and Biopreservation with a Lactococcus lactis Strain for Lowering the Bacterial Growth during Storage of Diced Cooked Ham with Reduced Nitrite Salt
We investigated the combined effects of biopreservation and high-pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of diced cooked ham from local supermarkets were characterized and stored frozen. Second, sterile diced cooked ham, prepared with reduced levels of nitrite, was inoculated with two different microbiota collected from the aforementioned commercial samples together with a nisin-producing Lactococcus lactis protective strain able to recover from a 500 MPa high-pressure treatment. Samples were then treated at 500 MPa for 5 min, and bacterial dynamics were monitored during storage at 8 °C. Depending on samples, the ham microbiota was dominated by different Proteobacteria (Pseudomonas, Serratia, Psychrobacter, or Vibrio) or by Firmicutes (Latilactobacillus and Leuconostoc). Applied alone, none of the treatments stabilized during the growth of the ham microbiota. Nevertheless, the combination of biopreservation and high-pressure treatment was efficient in reducing the growth of Proteobacteria spoilage species. However, this effect was dependent on the nature of the initial microbiota, showing that the use of biopreservation and high-pressure treatment, as an alternative to nitrite reduction for ensuring cooked ham microbial safety, merits attention but still requires improvement.
ano.nymous@ccsd.cnrs.fr.invalid (Stéphane Chaillou) 05 Oct 2022
https://hal.inrae.fr/hal-03798971
-
[hal-02960423] Utilisation des microbiotes comme modèles
L’étude microbiologique des aliments est limitée par la variabilité entre lots (diversité et abondance des espèces) et la présence possible de bactéries inconnues ou non encore cultivées. On peut contourner cette limite par deux approches. L’une reconstitue des cocktails de souches à partir de cultures pures dans des aliments modèles simplifiés et permet la construction de modèles mathématiques. L’autre récolte les microbiotes naturels des aliments sans culture préalable. Dans ce cas,la modélisation est plus difficile mais les microbiotes sont reproductibles et plus proches de la réalité. La complémentarité de ces approches est discutée
ano.nymous@ccsd.cnrs.fr.invalid (Monique Zagorec) 07 Oct 2020
https://hal.inrae.fr/hal-02960423
-
[hal-03210645] Application of a path-modelling approach for deciphering causality relationships between microbiota, volatile organic compounds and off-odour profiles during meat spoilage
Microbiological spoilage of meat is considered as a process which involves mainly bacterial metabolism leading to degradation of meat sensory qualities. Studying spoilage requires the collection of different types of experimental data encompassing microbiological, physicochemical and sensorial measurements. Within this framework, the objective herein was to carry out a multiblock path modelling workflow to decipher causality relationships between different types of spoilage-related responses: composition of microbiota, volatilome and off-odour profiles. Analyses were performed with the Path-ComDim approach on a large-scale dataset collected on fresh turkey sausages. This approach enabled to quantify the importance of causality relationships determined a priori between each type of responses as well as to identify important responses involved in spoilage, then to validate causality assumptions. Results were very promising: the data integration confirmed and quantified the causality between data blocks, exhibiting the dynamical nature of spoilage, mainly characterized by the evolution of off-odour profiles caused by the production of volatile organic compounds such as ethanol or ethyl acetate. This production was possibly associated with several bacterial species like Lactococcus piscium, Leuconostoc gelidum, Psychrobacter sp. or Latilactobacillus fuchuensis. Likewise, the production of acetoin and diacetyl in meat spoilage was highlighted. The Path-ComDim approach illustrated here with meat spoilage can be applied to other large-scale and heterogeneous datasets associated with pathway scenarios and represents a promising key tool for deciphering causality in complex biological phenomena.
ano.nymous@ccsd.cnrs.fr.invalid (Ngoc-Du Martin Luong) 28 Apr 2021
https://hal.science/hal-03210645
-
[hal-02960426] Biopréservation et hautes pressions : effet sur les communautés microbiennes
Les communautés bactériennes présentes sur le jambon cuit ont été caractérisées. Elles étaient dominées soit par des firmicutes soit par des protéobactéries, dont parfois des espèces jusque-là non cultivées. Leur dynamique après traitement haute pression et ajout d’une culture protectrice a été suivie. Si chaque communauté répond différemment au traitement haute pression et à la biopréservation, la combinaison des deux traitements permet bien de stabiliser le produit, avec un envahissement par la souche protectrice.
ano.nymous@ccsd.cnrs.fr.invalid (Monique Zagorec) 07 Oct 2020
https://hal.inrae.fr/hal-02960426
-
[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-03962400
-
[hal-02617680] Draft Genome sequence of <em>Lactobacillus curvatus</em> FLEC03, a meat-borne isolate from beef carpaccio packaged in a modified atmosphere
In this study, we present the draft genome sequence for Lactobacillus curvatus FLEC03. This strain was isolated from beef carpaccio packaged in a modified atmosphere. The draft genome will contribute to understanding the role of L. curvatus strains in food products (fermentation, biopreservation, or spoilage) through comparative genomics with other strains.
ano.nymous@ccsd.cnrs.fr.invalid (Lucrecia C. Terán) 25 May 2020
https://hal.inrae.fr/hal-02617680
-
[hal-04565234] MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice
Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Manghi) 01 May 2024
https://hal.inrae.fr/hal-04565234
-
[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-02941029
-
[hal-04460334] Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
ano.nymous@ccsd.cnrs.fr.invalid (Tim van den Bossche) 06 May 2024
https://hal.science/hal-04460334
-
[inserm-02501395] Gut Dysbiosis during Influenza Contributes to Pulmonary Pneumococcal Superinfection through Altered Short-Chain Fatty Acid Production
Secondary bacterial infections often complicate viral respiratory infections. We hypothesize that perturbation of the gut microbiota during influenza A virus (IAV) infection might favor respiratory bacterial superinfection. Sublethal infection with influenza transiently alters the composition and fermentative activity of the gut microbiota in mice. These changes are attributed in part to reduced food consumption. Fecal transfer experiments demonstrate that the IAV-conditioned microbiota compromises lung defenses against pneumococcal infection. In mechanistic terms, reduced production of the predominant short-chain fatty acid (SCFA) acetate affects the bactericidal activity of alveolar macrophages. Following treatment with acetate, mice colonized with the IAV-conditioned microbiota display reduced bacterial loads. In the context of influenza infection, acetate supplementation reduces, in a free fatty acid receptor 2 (FFAR2)-dependent manner, local and systemic bacterial loads. This translates into reduced lung pathology and improved survival rates of double-infected mice. Lastly, pharmacological activation of the SCFA receptor FFAR2 during influenza reduces bacterial superinfection.
ano.nymous@ccsd.cnrs.fr.invalid (Valentin Sencio) 06 Mar 2020
https://inserm.hal.science/inserm-02501395
-
[hal-01906028] Genetic deficiency of Indoleamine 2,3-dioxygenase promotes gut microbiota-mediated metabolic health
The association between altered gut microbiota, intestinal permeability, inflammation and cardiometabolic diseases is becoming increasingly clear but remains poorly understood1,2. Indoleamine 2,3-dioxygenase is an enzyme induced in many types of immune cells, including macrophages in response to inflammatory stimuli, and catalyzes the degradation of tryptophan along the kynurenine pathway. Indoleamine 2,3-dioxygenase activity is better known for its suppression of effector T cell immunity and its activation of regulatory T cells3,4. However, high indoleamine 2,3-dioxygenase activity predicts worse cardiovascular outcome5,6,7,8,9 and may promote atherosclerosis and vascular inflammation6, suggesting a more complex role in chronic inflammatory settings. Indoleamine 2,3-dioxygenase activity is also increased in obesity10,11,12,13, yet its role in metabolic disease is still unexplored. Here, we show that obesity is associated with an increase of intestinal indoleamine 2,3-dioxygenase activity, which shifts tryptophan metabolism from indole derivative and interleukin-22 production toward kynurenine production. Indoleamine 2,3-dioxygenase deletion or inhibition improves insulin sensitivity, preserves the gut mucosal barrier, decreases endotoxemia and chronic inflammation, and regulates lipid metabolism in liver and adipose tissues. These beneficial effects are due to rewiring of tryptophan metabolism toward a microbiota-dependent production of interleukin-22 and are abrogated after treatment with a neutralizing anti-interleukin-22 antibody. In summary, we identify an unexpected function of indoleamine 2,3-dioxygenase in the fine tuning of intestinal tryptophan metabolism with major consequences on microbiota-dependent control of metabolic disease, which suggests indoleamine 2,3-dioxygenase as a potential therapeutic target.
ano.nymous@ccsd.cnrs.fr.invalid (Ludivine Laurans) 26 Oct 2018
https://hal.sorbonne-universite.fr/hal-01906028
-
[hal-04543494] Arabidopsis seeds altered in the circadian clock protein TOC1 are characterized by higher level of linolenic acid
The circadian clock plays a critical role in regulating plant physiology and metabolism. However, the way in which the clock impacts the regulation of lipid biosynthesis in seeds is partially understood. In the present study, we characterized the seed fatty acid (FA) and glycerolipid (GL) compositions of pseudo-response regulator mutants. Among these mutants, toc1 (timing of cab expression 1) exhibited the most significant differences compared to control plants. These included an increase in total FA content, characterized by elevated levels of linolenic acid (18:3) along with a reduction in linoleic acid (18:2). Furthermore, our findings revealed that toc1 developing seeds showed increased expression of genes related to FA metabolism. Our results show a connection between TOC1 and lipid metabolism in Arabidopsis seeds.
ano.nymous@ccsd.cnrs.fr.invalid (Salim Makni) 12 Apr 2024
https://u-picardie.hal.science/hal-04543494
-
[hal-01604888] A metabolic engineering strategy for producing conjugated linoleic acids using the oleaginous yeast Yarrowia lipolytica
Conjugated linoleic acids (CLAs) have been found to have beneficial effects on human health when used as dietary supplements. However, their availability is limited because pure, chemistry-based production is expensive, and biology-based fermentation methods can only create small quantities. In an effort to enhance microbial production of CLAs, four genetically modified strains of the oleaginous yeast Yarrowia lipolytica were generated. These mutants presented various genetic modifications, including the elimination of beta-oxidation (pox1-6a dagger), the inability to store lipids as triglycerides (dga1a dagger dga2a dagger are1a dagger lro1a dagger), and the overexpression of the Y. lipolytica a dagger 12-desaturase gene (YlFAD2) under the control of the constitutive pTEF promoter. All strains received two copies of the pTEF-oPAI or pPOX-oPAI expression cassettes; PAI encodes linoleic acid isomerase in Propionibacterium acnes. The strains were cultured in neosynthesis or bioconversion medium in flasks or a bioreactor. The strain combining the three modifications mentioned above showed the best results: when it was grown in neosynthesis medium in a flask, CLAs represented 6.5% of total fatty acids and in bioconversion medium in a bioreactor, and CLA content reached 302 mg/L. In a previous study, a CLA degradation rate of 117 mg/L/h was observed in bioconversion medium. Here, by eliminating beta-oxidation, we achieved a much lower rate of 1.8 mg/L/h.
ano.nymous@ccsd.cnrs.fr.invalid (Nabila Imatoukene) 02 Oct 2017
https://hal.science/hal-01604888
