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Récepteur du goût sucré et diabète. 6. journée de l'innovation en diabétologie

Spore-forming bacteria are major players in life on Earth, and they are fascinating, as they adapt to many ecological niches. The spores are able to resist high temperatures, to dry out and to recover and germinate when outgrowth conditions become available. Spore-formers are mainly Gram-positive firmicute bacteria with low GC content; the Bacillus and Clostridia genera include prominent species. Bacillus subtilis is one of the most thoroughly studied bacteria, serving as a model to study sporulation and the regulatory networks controlling this differentiation system. B. subtilis is also a bacterium widely used for producing enzymes and metabolites of industrial importance. Among the spore-forming firmicutes, the Bacillus cereus group presents the most remarkable diversity. Frequently designated as “the Good, the Bad and the Ugly”, this bacterial group covers eight closely related species. They include the mammal pathogen Bacillus anthracis, responsible for anthrax disease, the insect pathogen Bacillus thuringiensis, used worldwide as a bioinsecticide to control pests of agricultural, forest and medical importance, and B. cereus senso stricto, an important food contaminant responsible for gastrointestinal disorders and, occasionally, more serious systemic diseases in immunecompromised individuals. The specific mammal toxicity of B. anthracis, the insecticidal activity of B. thuringiensis and the emetic activity of some B. cereus strains are due to plasmid genes. However, in addition to these specific traits, all these bacteria share chromosomal genes conferring the ability to colonize and to grow in abiotic and biotic environments. Interestingly, and in sharp contrast to these pathogens, a few B. cereus strains are used as probiotics in livestock animals and even, formerly, for humans, indicating the versatility of this group of bacteria. Among the pathogenic Clostridia, Clostridium botulinum and Clostridium perfringens are important sources of foodborne poisonings and infections, and the emergent opportunistic human pathogen Clostridium difficile is responsible for severe nosocomial intestinal infections. Due to the high resistance of the spores, to their adhesion properties and to their capacity to form biofilms, these anaerobic Clostridia and facultative anaerobic Bacilli are difficult to eliminate and have a direct economic impact upon the food industry and human health.This special issue of Research in Microbiology contains eight articles covering three main topics highlighted during the first BSPIT (Bactéries sporulantes pathogènes ou d'intérêt technologique) meeting which was held in France (Paris, July 6th and 7th, 2015) and hosted by the SFM (Société Française de Microbiologie), and which was mainly attended by French-speaking scientists.

Première source de gènes de la planète, les microorganismes représentent une ressource inestimable face aux challenges de durabilité qui sont les nôtres aujourd’hui. Tous les métabolismes y sont représentés et leur biodiversité encore largement sous- explorée est une source clé d’innovation et de valeur ajoutée. Une gestion appropriée des ressources est essentielle pour préserver cette biodiversité et favoriser son utilisation à des fins de développement durable. C'est la fonction première des Centre de Ressources Biologiques (CRB) qui ont pour mission de préserver la biodiversité ex-situ, toutes ressources biologiques confondues, et jouent de ce fait un rôle de conservatoire avec une fonction patrimoniale.On observe depuis plusieurs décennies une diminution drastique de la biodiversité, c'est vrai quelles que soient les ressources biologiques considérées, y compris les espèces microbiennes d'intérêt technologique impliquées dans la fabrication des aliments fermentés. Dès lors, il apparait essentiel de préserver cette diversité microbienne en grande partie responsable de la multiplicité et de la typicité des produits fermentés. C'est un enjeu de taille pour les CRB qui mettent aux services de ces ressources microbiennes une expertise et des outils de caractérisation adaptés. Complémentaire de la conservation in-situ, ils rendent visibles et accessibles ces ressources. Ils permettent en outre de tracer et de formaliser les échanges de matériel biologique et des données associées entre les différentes parties intéressées. Enfin, ils apportent un cadre normatif et règlementaire garant du respect de la propriété intellectuelle et du partage des avantages associé à l'utilisation de ces ressources

Nouveau regard sur les liens entre microorganismes du fromage et microbiote intestinal . 2 ème séminaire REPASTOL Apprivoiser le vivant invisible – Savoirs, usages, appropriations de la microbiodiversité fromagère

Séminaire Aliment-Microbiote 5 décembre 2016Retrouvez ici les présentations de la journée Aliment-Microbiote qui s'est déroulée à Agroparistech le 5 Décembre. Elle était organisée par les animateurs du programme du département CEPIA Modaltub – Devenir de l’aliment dans le tube digestif, en partenariat avec le département MICA.Comment nourrir notre microbiote intestinal ? quelle(s) part(s) (néoformés, xénobiotiques etc ..), quelle(s) structures de l’aliment issues du processus de digestion (à tous les étages) impactent notre microbiote et comment ? Comment aborder ces questions via une approche in vitro/digesteur ? Ces thèmes ont été abordés par des présentations de conférenciers invités et des communications courtes (10 min) de résultats illustrant la contribution de CEPIA à ces recherches.; Exploration des interactions fonctionnelles entre les bactéries de l'aliment fermenté et le microbiote. Séminaire Aliment-Microbiote

Microbial ecosystems of cheese can be explored at different scales, with a dynamic and/or spatial view, and for different purposes: functionalities, safety, nutrition. An incredible knowledge has been accumulated since Pasteur discoveries on the involvement of microorganisms in fermentation. However most of the work was dedicated to starter development and starter technological properties. By the way, the microbial ecology of cheese in the sense of “microorganisms real life within cheese” has been much less investigated. We know that key ripening phenomena like proteolysis, and lipolysis are due to close interactions between the cheese matrix and the bacterial enzymes provided by the bacterial colonies, but how does it work at a molecular level ? How diffuse substrates, enzymes, and products within and around the colony ? How colonies are communicating with each other, if they do? Which are the biochemical or biophysical properties of the cheese matrix that can significantly impact the microbial ecology ? Because the answers are largely missing, we are still not able to predict the behaviour of a strain in situ and its full impact on the curd ; a fortiori the behaviour of a complete ecosystem. This would probably require in the future multicriteria approaches. In this presentation, an overview of the main work dedicated to “real microbial life” in cheese will be summarized for discussion.

Dossier de Sciences Ouest : Les super-pouvoirs des microbes

Le lait est un aliment très riche (protéines, sucres) extrêmement favorable au développement de nombreuses espèces de microorganismes incluant les bactéries, les levures et les champignons filamenteux. Il est très vite contaminé à la sortie du trayon par une importante diversité microbienne (microorganismes pathogènes et d'altération mais aussi microorganismes "utiles"). Les microorganismes que l'on retrouve dans le lait proviennent majoritairement de l'environnement lié au lieu de collecte et de transformation. La diversité microbienne des laits est très grande : diversité de genres et d'espèces mais aussi des souches au sein d'une espèce donnée (diversité intra-spécifique). On observe, parallèlement à l'amélioration des pratiques d'hygiène au sein des lieux de collecte et de transformation des laits, une baisse globale de la diversité microbienne présente dans le lait. Cette baisse de diversité concerne l'ensemble des microorganismes, les pathogènes mais aussi les microorganismes utiles qui, dans le cas des produits laitiers fermentés, peuvent selon les technologies de transformation employées, jouer un rôle important dans la typicité et les caractéristiques final des produits fabriqués. La conservation de ces microorganismes d'intérêt au sein de structures dédiées, les Centres de Ressources Biologiques (CRB), présente dès lors un enjeu majeur. Sachant, qui plus est, que bon nombre des propriétés technologiques et pathogènes des souches, sinon toutes, sont souches dépendantes, la diversité-intra spécifique doit être prise en compte dans le choix des ressources microbiennes à préserver au sein de ces CRB. Les CRB microbiens ont pour rôle de conserver, identifier, diffuser et valoriser les ressources microbiennes. Ils ont un rôle patrimonial et doivent rendre ces ressources accessibles à l'ensemble des communautés scientifiques et industrielles à des fins de recherche et de valorisation. Ils doivent garantir la traçabilité et la fiabilité des données associées aux souches mais aussi garantir que la réglementation internationale liées à ces souches est respectée (Convention sur la Diversité Biologique et Protocole de Nagoya). L'existence de CRB thématiques, centrés sur une catégorie de ressources microbienne en lien avec une application potentielle, qui prennent en compte la diversité intra-spécifique, est essentielle. En permettant le criblage de la diversité microbienne ils sont des acteurs majeurs de l'innovation. Ils sont de ce fait complémentaires des grandes collections de microorganismes de renommée européenne ou internationales qui regroupent l'ensemble des souches type de microorganismes.

International audience; Bacillus cereus is a Gram-positive endospore forming bacterium known for its wide spectrum of phenotypic traits, enabling it to occupy diverse ecological niches. Although the population structure of B. cereus is highly dynamic and rather panmictic, production of the emetic B. cereus toxin cereulide is restricted to strains with specific genotypic traits, associated with distinct environmental habitats. Cereulide is an ionophoric dodecadepsipeptide that is produced non-ribosomally by an enzyme complex with an unusual modular structure, named cereulide synthetase (Ces non-ribosomal peptide synthetase). The ces gene locus is encoded on a mega virulence plasmid related to the B. anthracis toxin plasmid pXO1. Cereulide, a highly thermo- and pH- resistant molecule, is preformed in food, evokes vomiting a few hours after ingestion, and was shown to be the direct cause of gastroenteritis symptoms; occasionally it is implicated in severe clinical manifestations including acute liver failures. Control of toxin gene expression in emetic B. cereus involves central transcriptional regulators, such as CodY and AbrB, thereby inextricably linking toxin gene expression to life cycle phases and specific conditions, such as the nutrient supply encountered in food matrices. While in recent years considerable progress has been made in the molecular and biochemical characterization of cereulide toxin synthesis, far less is known about the embedment of toxin synthesis in the life cycle of B. cereus. Information about signals acting on toxin production in the food environment is lacking. We summarize the data available on the complex regulatory network controlling cereulide toxin synthesis, discuss the role of intrinsic and extrinsic factors acting on toxin biosynthesis in emetic B. cereus and stress how unraveling these processes can lead to the development of novel effective strategies to prevent toxin synthesis in the food production and processing chain.

Predictive models are mathematical expressions that describe the growth, survival, inactivation, or biochemical processes of foodborne bacteria. During processing of contaminated raw materials and food preparation, bacteria are entrapped into the food residues, potentially transferred to the equipment surfaces (abiotic or inert surfaces) or cross-contaminate other foods (biotic surfaces). Growth of bacterial cells can either occur planktonically in liquid or immobilized as colonies. Colonies are on the surface or confined in the interior (submerged colonies) of structured foods. For low initial levels of bacterial population leading to large colonies, the immobilized growth differs from planktonic growth due to physical constrains and to diffusion limitations within the structured foods. Indeed, cells in colonies experience substrate starvation and/or stresses from the accumulation of toxic metabolites such as lactic acid. Furthermore, the micro-architecture of foods also influences the rate and extent of growth. The micro-architecture is determined by (i) the non-aqueous phase with the distribution and size of oil particles and the pore size of the network when proteins or gelling agent are solidified, and by (ii) the available aqueous phase within which bacteria may swarm or swim. As a consequence, the micro-environment of bacterial cells when they grow in colonies might greatly differs from that when they grow planktonically. The broth-based data used for modeling (lag time and generation time, the growth rate, and population level) are poorly transferable to solid foods. It may lead to an over-estimation or under-estimation of the predicted population compared to the observed population in food. If the growth prediction concerns pathogen bacteria, it is a major importance for the safety of foods to improve the knowledge on immobilized growth. In this review, the different types of models are presented taking into account the stochastic behavior of single cells in the growth of a bacterial population. Finally, the recent advances in the rules controlling different modes of growth, as well as the methodological approaches for monitoring and modeling such growth are detailed.

Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. Methodology/Principal Findings We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event. Conclusions/Significance Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.

Background Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. Results We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Conclusions Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1101) contains supplementary material, which is available to authorized users.

During cheese ripening, micro-organisms grow as immobilised colonies, metabolising substrates present in the matrix which generate products triggered by enzymatic reactions. Local limitation rates of diffusion, either in the matrix or within the bacterial colonies, can be responsible for modulation in the metabolic and enzymatic activities of micro-organisms during ripening. How bacterial colonies immobilised in cheese are porous to these diffusing solutes has never been explored. The objective of this study was to determine if fluorescent dextrans of different sizes (4.4, 70 and 155 kDa) are able to penetrate through colonies of Lactococcus lactis LD61 immobilised in solid media, either agar or model cheese. Confocal microscopic observations showed that lactococcus colonies immobilised in these two media were porous to dextrans from 4 kDa to 155 kDa. However, the rate of diffusion of the solutes was faster inside the colonies immobilised in ultrafiltered-cheese than in agar when large dextrans were considered (≥70 kDa). The colonial shape of the lactococcus strain was also shown to be lenticular in agar and spherical in the model cheese, indicating that the physical pressure exerted on the colony by the surrounding casein network was probably isotropous in the UF-cheese but not in agar. In both cases, the fact that lactococcus colonies immobilised in solid media are porous to large dextran solutes suggests that substrates or enzymes are likely also to be able to migrate inside the colonies during cheese ripening.

Persistent bacteria in processing sites are of great concern in food industry, causing continuous recontamination and thus yielding compromised food quality and safety, lost productivity and environmental issues. The aim of this study was to develop a tool to reproduce bioadhesion under industrial conditions in order to investigate the impact of successive stress exposure on adhering microflora and further optimize food formulation, industrial process and surface sanitation.A pilot scale loop system was used to reproduce adhering flora after circulation of liquid egg in stainless steel pipeline at refrigerated temperature. Inoculation of the system was performed either by the circulation of non-pasteurized liquid egg or by the introduction of contaminated probe surface or insert. After 9 days of continuous flow, stainless steel inserts and sections were removed and analyzed with various conditions of incubation. The identification of culturable (ana)aerobe psychrotrophic and mesophilic isolates was performed by 16SrDNA sequencing. Moreover, the detection of Bacillus species was also performed using the PCR based GeneDisc® plateform.After loop circulation of non pasteurized liquid egg, bacterial isolates recovered from stainless steel surfaces were mainly composed of Gram-negative bacteria such as Pseudomonas, Myroides and Aeromonas. Enterobacteria and lactic acid bacteria were as well identified but with a lower extend, while Bacillus species were only detected by GeneDisc® plate. When the loop system was inoculated with an insert preliminary left for 2 months in an industrial pipeline, the proportion of recovered Gram-positive flora was higher. Indeed, Corynebacterium, Enterococcus and Staphylococcus were identified from industrial surfaces.Even though this system might favour fast growing colonizers, correlation was found between bacterial diversity recovered from pilot scale system and industrial pipeline surfaces. It is interesting to note a shift of diversity recovered from surfaces when industrial surfaces were used to inoculate the loop, suggesting the survival and persistence of given species after consecutive steps of production/sanitation. This system is promising to further study bacterial removal and inactivation upon exposure to acid or biocide taking into account protection due to embedded structure or food residues.

Procédé pour réduire la teneur bactérienne d'un milieu alimentaire et/ou biologique d'intérêt, contenant des gouttelettes lipides.

Préparation de matrices laitières contrôlées" : Distribution spatiale des colonies et interactions microbiennes in situ . Journée Thématique Plateforme LAIT

EMbaRC European Consortium of Microbial Resource Centres CIRM(INRA), CRBIP, DSMZ, CBS, CECT, MUM, BCCM, CABI The properties of microorganisms have been harnessed by man for thousands of years, particularly in brewing and baking but their uses continue to expand not just in food and healthcare but in almost all areas of industry and environmental maintenance. Their authentication, characterisation, stable storage and supply are a major contribution to the knowledge-based bioeconomy. The EMbaRC project is working to coordinate these microbial resources so that researchers in Europe and around the globe have better access and take full advantage of Europe’s microbial resource centres. EMbaRC will create a self-sustainable community of European Microbial Resource Centres. These centres will offer immense bio-diversity and a wide range of biological resources as well as expert services. Together this will encourage the development of new partnerships between public and private organisations which will not only generate revenue but also better microbial research. The project is further laying the foundation for a Global Biological Resource Centre Network giving Europe a lead role in on the global microbial scene. Part of this is setting up better access to biological resources and associated services. This benefits researchers as they will be able to take advantage of previous outcomes and other resources for their research. For EMbaRC to be a successful project, quality, standards and access need to be harmonised across all partner organisations. As such, an important element of the project is sharing best practices between all involved research institutes and ensuring the best operational standards are being used in all microbial research centres. EMbaRC researchers are also working on creating a code of conduct for biosecurity for European microbial biological resource collections. This will ensure that all specimens contained in any of the microbial resource centres will not, intentionally or unintentionally, be used in the creation of biological weapons. Furthermore, there are numerous microbial collections that have either been abandoned or are endangered that will receive support fromthe EMbaRC project. Their resources will be integrated into the larger EMbaRC community, adding immense value to the project and these smaller centres benefit from the resources and expertise of the larger centres.Over the long term, EMbaRC aims to bring together biological resource centres to find complementary sources of funding and ensure their continued existence. Moreover, joint research will improve strain and DNA storage and explore new microorganism identification methods. A greater number of users will have access to these resource centres, and their research through improved dissemination efforts, including the creation of an extensive web portal and information database as well as regular publication of results to the wider scientific community.Start date:1st February 2009 / Completion date: 31stJanuary 2012 Project webpage:www.embarc.eu

Biodiversité of Microorganisms Why create Biological Ressource Centers ?. Mahasarakham University

Identification des bactéries par spectrométrie de masse

Due to increasingly available bacterial genomes in databases, proteomic tools have recently been used to screen proteins expressed by micro-organisms in food in order to better understand their metabolism in situ. While the main objective is the systematic identification of proteins, the next step will be to bridge the gap between identification and quantification of these proteins. For that purpose, a new mass spectrometry-based approach was applied, using isobaric tagging reagent for quantitative proteomic analysis (iTRAQ), which are amine specific and yield labelled peptides identical in mass. Experimental Swiss-type cheeses were manufactured from microfiltered milk using Streptococcus thermophilus ITG ST20 and Lactobacillus helveticus ITG LH1 as lactic acid starters. At three ripening times (7, 20 and 69 days), cheese aqueous phases were extracted and enriched in bacterial proteins by fractionation. Each sample, standardised in protein amount prior to proteomic analyses, was: i) analysed by 2D-electrophoresis for qualitative analysis and ii) submitted to trypsinolysis, and labelled with specific iTRAQ tag, one per ripening time. The three labelled samples were mixed together and analysed by nano-LC coupled on-line with ESI-QTOF mass spectrometer. Thirty proteins, both from bacterial or bovine origin, were identified and efficiently quantified. The free bacterial proteins detected were enzymes from the central carbon metabolism as well as stress proteins. Depending on the protein considered, the quantity of these proteins in the cheese aqueous extract increased from 2.5 to 20 fold in concentration from day 7 to day 69 of ripening.

Food fermentation and biopreservation processes involve the use of various species and strains of bacteria and yeast. These strains are responsible for the targeted qualities of the food products that are sanitary, organoleptic (aroma and texture) and healthy qualities. The Florilege database project aims at (i) gathering bacterial and yeast phenotypes of food product of interest that are automatically extracted from PubMed-referenced full-text litterature by using a text mining approach (ii) managing the information in a relational database (iii) enabling multi-criteria requests via a Web user-friendly interface. To date 368 phenotypes, 260 synthetised or degraded molecules, 1076 medium or food products, 1181 bacterial taxons have been acquired by a combinaison of automatic and manual annotations of text, used for training the text-mining method.Food products are automatically categorized in Florilege according to the OntoBiotope ontology that we have extended with dairy and bakery products definitions. Taxa are categorized by the NCBI taxonomy. An ontology of microbial characteristics has been specifically enriched by the Florilege project. This ontology defines microbial phenotypes (Ontobiotope-Phenotype), including intracellular characteristics of cells (such as shape, antibiotic resistance...) and microbial uses (Ontobiotope-Use) that express the microbial alteration of the external environment, food or matrix, such as aroma, vitamin or other molecule production, degradation or food coloring.A preliminary Web interface is available for querying taxa, culture medium and food products at http://genome.jouy.inra.fr/Florilege/. The public availability of Florilege database is planned for the end of 2017 with a user-friendly interface for multi-criteria requests and access to various phenotypes.Florilege will be a highly valuable tool to (i) assess phenotypic biodiversity of food microbes (ii) assign biochemical functions to each strain/species from fermented or biopreserved food products (iii) help into the development of innovative food products in particular those that involve fermentation or biopreservation processes.