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Comparative Genomic Analysis of Carnobacterium Maltaromaticum: Study of Diversity and Adaptation to Different Environments Christelle Iskandar

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Comparative genomic analysis of Carnobacterium maltaromaticum: Study of diversity and adaptation to different environments Christelle Iskandar To cite this version: Christelle Iskandar. Comparative genomic analysis of Carnobacterium maltaromaticum: Study of diversity and adaptation to different environments. Food and Nutrition. Université de Lorraine, 2015. English. NNT : 2015LORR0245. tel-01754646 HAL Id: tel-01754646 https://hal.univ-lorraine.fr/tel-01754646 Submitted on 30 Mar 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Université de Lorraine École Nationale Supérieure d’Agronomie et des Industries Alimentaires Ecole Doctorale Sciences et Ingénierie des Ressources, Procédés, Produits, Environnement (RP2E) Laboratoire d’Ingénierie des Biomolécules (LIBio) THESE présentée devant L’Université de Lorraine pour obtenir le grade de Docteur de l’Université de Lorraine Spécialité : Procédés Biotechnologiques et Alimentaires Par Christelle ISKANDAR Analyse par génomique comparée de Carnobacterium maltaromaticum : Etude de la diversité et de l’adaptation à différents environnements Comparative genomic analysis of Carnobacterium maltaromaticum: Study of diversity and adaptation to different environments Prof. Xavier DOUSSET UMR INRA-SECALIM - ONIRIS Nantes Rapporteur Dr. Marie-Christine UMR 1319 MICALIS – INRA Jouy en Josas Rapporteur CHAMPOMIER-VERGES Dr. Veronique FARAH - Fundamental and Applied Research Examinateur DELCENSERIE for Animals & Health - University of Liege Dr. Fréderic BORGES LIBIO Laboratoire d'Ingénierie des Examinateur Biomolécules ENSAIA - Université de Lorraine Prof. Anne-Marie REVOL- LIBIO Laboratoire d'Ingénierie des Directrice de thèse JUNELLES Biomolécules ENSAIA - Université de Lorraine Dr. Catherine CAILLIEZ- LIBIO Laboratoire d'Ingénierie des Co-directrice de thèse GRIMAL Biomolécules ENSAIA - Université de Lorraine Dédicace Je dédie ce travail A mes parents, qui ont tout sacrifié pour me voir réussir. Vous êtes la source de mes efforts et la flamme de mon cœur. A mes frères lumière de mes jours, mon soutien moral, source de joie et de bonheur. Vous m’avez toujours aidée et encouragée durant tout le chemin. Christelle II Remerciements Ce travail de thèse a été réalisé au sein du Laboratoire d’Ingénierie des Biomolécules LIBio. La réalisation de ce mémoire a été possible grâce au concours de plusieurs personnes à qui je voudrais témoigner toute ma reconnaissance. Je remercie tout d’abord les membres du jury, Monsieur Xavier DOUSSET Professeur à ONIRIS Nantes et Madame Marie-Christine CHAMPOMIER-VERGES, Directrice de recherche à l’INRA, rapporteurs de thèse et Madame Veronique DELCENSERIE, assistant- professeur à l’université de Liège, examinatrice des travaux de thèse, pour avoir accepté de juger ce travail.. J’exprime ensuite toute ma reconnaissance à mes encadrants, Madame Anne-Marie REVOL- JUNELLES, directrice de thèse, Madame Catherine CAILLIEZ-GRIMAL co-directrice et Monsieur Fréderic BORGES pour avoir accepté de diriger ce travail. Merci pour votre aide, votre soutien et spécialement pour votre confiance en moi. Je tiens à remercier aussi tout le personnel du LIBio, Monsieur Michel LINDER, directeur du LIBio, enseignant-chercheurs, doctorants, techniciens et stagiaires. C’était un grand plaisir de vous connaitre. Un grand merci à tous les membres de l’équipe de microbiologie, Myriam, Sylvie et Arnaud, pour leur soutien et leur bonne humeur. Je suis tout aussi redevable à Monsieur Emmanuel RONDAGS, Monsieur Fabrice BLANCHARD et Monsieur Cédric PARIS pour leur disponibilité et leurs judicieux conseils, qui ont contribué à alimenter ma réflexion. Je voudrais adresser un merci à ERASMUS MUNDUS qui m’a donné la chance de réaliser ce parcours en me procurant le financement nécessaire durant mes deux ans en France. Un grand merci à Madame Delphine LAURANT pour sa patience. Je voudrais exprimer ma reconnaissance envers les amis, spécialement Georges et Elie, qui m’ont apporté leur support moral et intellectuel malgré la distance. Un très grand merci à Christelle SALAMEH pour sa confiance et son support inestimable. Tu es plus qu’une amie, tu es une sœur, un compagnon de route dans les moments agréables, et un soutien dans les moments pénibles. Une pensée particulière à mon cher ami Ibrahim. Ta présence m’a donnée la force et le courage pour pouvoir toujours avancer. Enfin, un vif remerciement s’adresse à mes parents, mes frères et ma tante Roula, pour leur encouragement, leur confiance et l’entraide dans les moments difficiles. III Résumé Carnobacterium est un genre bactérien ubiquiste appartenant au groupe des bactéries lactiques (LAB). Les souches de Carnobacterium maltaromaticum sont présentes dans une grande diversité d’environnements et de produits alimentaires. Elles présentent de nombreuses propriétés, dont un effet positif en fabrication fromagère et des potentialités probiotiques qui en font un microorganisme à forte potentialité industrielle. L’objectif de ce travail de thèse est d’approfondir les connaissances sur C. maltaromaticum par une étude génomique. Neuf génomes de bactéries du genre Carnobacterium, dont 5 de C. maltaromaticum, disponibles sur la plateforme MicroScope ont été analysés et comparés. Carnobacterium maltaromaticum DSM20342 MX5 possède un génome de 3,85 Mbp, le plus grand génome parmi les LAB connus, de 1 Mbp de plus que celui des autres Carnobacterium n’appartenant pas à l’espèce C. maltaromaticum. L’analyse génomique détaillée indique la présence de quelques voies métaboliques spécifiques et suggère que les souches de C. maltaromaticum et C. divergens présenteraient une surface cellulaire caractérisée par une grande diversité moléculaire.Les trois autres souches de Carnobacterium présenteraient une surface fortement dépourvue en molécules de surfaces dont les protéines. Les propriétés de surface qui en découlent seraient à relier à la capacité de ces deux espèces à coloniser différents habitats. Par ailleurs, les souches de C. maltaromaticum isolées de différents produits laitiers se caractérisent par une grande diversité génomique. Afin de caractériser le niveau de diversité, les gènes impliqués dans les voies métaboliques d’utilisation du lactose (voie du Tagatose-6Phosphate, gènes lac) et du galactose (voie de Leloir, gènes gal) ont été caractérisés par analyse génomique au sein du genre Carnobacterium. De plus, ces gènes ont été recherchés par PCR chez 42 souches de C. maltaromaticum. Les deux voies sont présentes et organisées différemment chez les différentes souches de C. maltaromaticum d’origine laitière et non laitière L’analyse de ces gènes au niveau de la population révèle une dissémination des deux voies au sein des 4 lignées de cette population. La voie de Leloir est présente dans les lignées I, II et III et la voie du Tagatose- 6Phosphate dans les lignées I, II et IV. Ces résultats suggèrent que les gènes lac et gal ont évolué selon un schéma complexe, qui est le reflet du haut niveau de diversité génétique de la population. La recherche de ces gènes au sein des 237 génomes de LAB disponibles sur la plateforme MicroScope Mage indique que les gènes lac et gal présentent un niveau de diversité élevé parmi les différents genres bactériens constituant le groupe des LAB, avec une dominance de la présence de la voie de Leloir. Ce niveau de diversité génétique n’est retrouvé qu’à l’échelle du genre chez les LAB et non de l’espèce, comme c’est le cas de C. maltaromaticum. Mots-clés : Carnobacterium maltaromaticum, diversité, adaptation, comparaison génomique, lactose. Summary Carnobacterium bacteria belong to the lactic acid bacteria (LAB) and are ubiquitous. Carnobacterium maltaromaticum strains are present in a wide variety of environments and foods. They have many positive properties in cheese manufacturing that make them microorganisms of industrial interest. The objective of this thesis is to deepen the knowledge on C. maltaromaticum by a comparative genomic approach. Nine Carnobacterium genomes, including 5 C. maltaromaticum, available on the platform MicroScope were analyzed and compared. Carnobacterium maltaromaticum DSM20342 MX5 is the largest genome among LAB, 1Mbp more than other Carnobacterium species. Detailed analysis indicates the presence of some specific metabolic pathways, and the presence of a high molecular diversity of cell surface proteins in C. maltaromaticum
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  • High Variability of Levels of Aliivibrio and Lactic Acid Bacteria in the Intestinal Microbiota of Farmed Atlantic Salmon Salmo Salar L

    High Variability of Levels of Aliivibrio and Lactic Acid Bacteria in the Intestinal Microbiota of Farmed Atlantic Salmon Salmo Salar L

    Ann Microbiol (2015) 65:2343–2353 DOI 10.1007/s13213-015-1076-3 ORIGINAL ARTICLE High variability of levels of Aliivibrio and lactic acid bacteria in the intestinal microbiota of farmed Atlantic salmon Salmo salar L. Félix A. Godoy1 & Claudio D. Miranda2,3 & Geraldine D. Wittwer1 & Carlos P. Aranda1 & Raúl Calderón4 Received: 10 November 2014 /Accepted: 11 March 2015 /Published online: 16 April 2015 # Springer-Verlag Berlin Heidelberg and the University of Milan 2015 Abstract In the present study, the structure of the intestinal structure of the intestinal microbiota of farmed Atlantic salm- microbiota of Atlantic salmon (Salmo salar L.) was studied on enabling detection of a minority of taxa not previously using culture and culture-independent methods. Three adult reported as part of the intestinal microbiota of salmonids, in- specimens of S. salar were collected from a commercial salm- cluding the genera Hydrogenophilus, Propionibacterium, on farm in Chile, and their intestinal microbiota were studied Cronobacter, Enhydrobacter, Veillonella, Prevotella,and by partial sequencing of the 16S rRNA gene of pure cultures Atopostipes, as well as to evaluate the health status of farmed as well as of clone libraries. Out of the 74 bacterial isolates, fish when evaluating the dominance of potential pathogenic Pseudomonas was the most predominant genus among cul- species and the incidence of lactic acid bacteria. tured microbiota. In clone libraries, 325 clones were obtained from three adult fish, and a total of 36 operational taxonomic Keywords Aquaculture . Intestinal microbiota . Aliivibrio . units (OTUs) were identified. This indicated that lactic acid Salmon farming . Salmo salar bacteria (Weissella, Leuconostoc, and Lactococcus genera) comprised more than 50 % of identified clones in two fishes.
  • Primate Vaginal Microbiomes Exhibit Species Specificity Without Universal Lactobacillus Dominance

    Primate Vaginal Microbiomes Exhibit Species Specificity Without Universal Lactobacillus Dominance

    The ISME Journal (2014) 8, 2431–2444 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance Suleyman Yildirim1,6, Carl J Yeoman1,7, Sarath Chandra Janga1,8, Susan M Thomas1, Mengfei Ho1,2, Steven R Leigh1,3,9, Primate Microbiome Consortium5, Bryan A White1,4, Brenda A Wilson1,2 and Rebecca M Stumpf1,3 1The Institute for Genomic Biology, University of Illinois, Urbana, IL, USA; 2Department of Microbiology, University of Illinois, Urbana, IL, USA; 3Department of Anthropology, University of Illinois, Urbana, IL, USA and 4Department of Animal Sciences, University of Illinois, Urbana, IL, USA Bacterial communities colonizing the reproductive tracts of primates (including humans) impact the health, survival and fitness of the host, and thereby the evolution of the host species. Despite their importance, we currently have a poor understanding of primate microbiomes. The composition and structure of microbial communities vary considerably depending on the host and environmental factors. We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. The nine primate species included: humans (Homo sapiens), yellow baboons (Papio cynocephalus), olive baboons (Papio anubis), lemurs (Propithecus diadema), howler monkeys (Alouatta pigra), red colobus (Pilioco- lobus rufomitratus), vervets (Chlorocebus aethiops), mangabeys (Cercocebus atys) and chim- panzees (Pan troglodytes). Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and diversity.