Étude De La Diversité Archéenne Dans Les Salaisons, Les Fromages Et Les Aliments À Saumure Présenté Par Anthony Bernard Présenté Par Lucie Dubois

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Étude De La Diversité Archéenne Dans Les Salaisons, Les Fromages Et Les Aliments À Saumure Présenté Par Anthony Bernard Présenté Par Lucie Dubois Faculté des Bioingénieurs Étude de la diversité archéenne dans les salaisons, les fromages et les aliments à saumure Présenté par Anthony Bernard Promoteur : Prof. Jacques Mahillon (UCL/ELI/MIAE) Lecteurs : Prof. Véronique Delcenserie (ULg/DDA) Prof. Claude Bragard (UCL/ELI/ELIM) Mémoire de fin d’études présenté en vue de l’obtention du diplôme de Bioingénieur : sciences agronomiques Année académique 2017-2018 Pour commencer, je voudrais remercier mon promoteur, le Professeur Jacques Mahillon, pour avoir proposé un tel sujet. Ses précieux conseils combinés à sa gestion conviviale du labo MIAE ont rendu mon mémoire des plus agréable. Je tiens à exprimer ma reconnaissance toute particulière à Carole Michaux qui a suivi mon travail de A à Z. Sa rigueur, ses connaissances et sa disponibilité ont grandement contribués à la réussite de ce mémoire. Je la remercie aussi pour la lecture et la correction approfondie du travail. Pour avoir répondu à mes nombreuses questions mais aussi pour avoir organisé d’innombrables goûters, je remercie tous les membres du laboratoire MIAE. Je remercie aussi tous les mémorants avec qui j’ai partagé cette expérience. Je remercie également Véronique Delcenserie et Claude Bragard d’être lecteurs et jury de ce mémoire. Enfin, je remercie ma famille, mes amis et toutes les personnes qui, de près ou de loin, ont ajouté leur grain de sel dans ce mémoire et m’ont soutenu au cours de ces cinq dernières années. Je remercie en particulier Julien pour sa relecture soignée du travail. Bonne lecture. Table des matières Table des matières Table des matières ............................................................................................................ i Liste des abréviations ..................................................................................................... iii 1 Introduction ......................................................................................................... - 1 - 1.1 Les archées ............................................................................................................. - 1 - 1.1.1 Historique des découvertes et phylogénie ........................................................... - 1 - 1.1.2 Diversité et écologie ............................................................................................ - 3 - 1.1.3 Caractéristiques principales................................................................................. - 4 - 1.1.4 Métabolisme ....................................................................................................... - 7 - 1.1.5 Applications ........................................................................................................ - 7 - 1.2 Les haloarchées .................................................................................................... - 10 - 1.2.1 Introduction sur les organismes halophiles ........................................................ - 10 - 1.2.2 Classification des archées halophiles et diversité ............................................... - 11 - 1.2.3 Écologie ............................................................................................................ - 14 - 1.2.4 Caractéristiques principales............................................................................... - 15 - 1.2.5 Métabolisme ..................................................................................................... - 17 - 1.2.6 Adaptations osmotiques aux milieux salins........................................................ - 18 - 1.3 Les archées dans l’alimentation ............................................................................ - 20 - 2 Objectifs ............................................................................................................. - 24 - 3 Matériel et méthodes......................................................................................... - 25 - 3.1 Échantillons .......................................................................................................... - 25 - 3.1.1 Charcuteries ...................................................................................................... - 25 - 3.1.2 Fromages .......................................................................................................... - 25 - 3.1.3 Sels de salage .................................................................................................... - 26 - 3.2 Milieux de culture ................................................................................................. - 26 - 3.2.1 CDM (Chemically DeFined Medium) ................................................................... - 27 - 3.2.2 Hv-YPC (Yeast-Peptone-Casamino acids) ........................................................... - 29 - 3.2.3 MGM (ModiFied Growth Medium) .................................................................... - 30 - 3.2.4 DBCM2 .............................................................................................................. - 31 - 3.3 Mise en culture ..................................................................................................... - 32 - 3.3.1 Charcuteries et Fromages .................................................................................. - 32 - 3.3.2 Sels ................................................................................................................... - 33 - 3.4 Prélèvement des colonies ..................................................................................... - 34 - 3.5 PCR (Polymerase Chain Reaction) ......................................................................... - 34 - 3.6 Électrophorèse...................................................................................................... - 36 - i Table des matières 3.7 Séquençage .......................................................................................................... - 36 - 3.8 Nomenclature des isolats ..................................................................................... - 37 - 3.9 Conservation longue durée des souches ............................................................... - 37 - 3.10 Microbiologie alimentaire .................................................................................... - 37 - 3.10.1 Préparation des échantillons ......................................................................... - 38 - 3.10.2 Mise en culture et normes respectées........................................................... - 38 - 3.11 Extraction d’ADN total des sels et des aliments .................................................... - 40 - 3.11.1 Extraction d’ADN à partir des sels ................................................................. - 40 - 3.11.2 Extraction d’ADN à partir d’aliments : DNeasy® PowerFood® Microbial Kit .... - 40 - 3.11.3 Extraction d’ADN à partir d’aliments : NucleoSpin® Food .............................. - 41 - 3.12 Nested-PCR pour la métagénomique .................................................................... - 41 - 4 Résultats............................................................................................................. - 42 - 4.1 Microbiologie culture-dépendante ....................................................................... - 42 - 4.1.1 Culture sur milieux spécifiques pour les sels de salage....................................... - 42 - 4.1.2 Culture sur milieux spécifiques pour les matrices alimentaires .......................... - 51 - 4.1.3 Microbiologie alimentaire ................................................................................. - 56 - 4.2 Microbiologie culture-indépendante .................................................................... - 58 - 5 Discussion ........................................................................................................... - 60 - 5.1 Le choix des matrices alimentaires ....................................................................... - 60 - 5.2 Le choix des milieux et des conditions de culture ................................................. - 66 - 5.3 Le protocole de la méthode culture-indépendante .............................................. - 68 - 6 Conclusion et perspectives ................................................................................. - 70 - Bibliographie .............................................................................................................. - 72 - Annexes ..................................................................................................................... - 83 - Annexe 1 : Gels d’électrophorèse ...................................................................................... - 83 - Annexe 2 : Colonies isolées ............................................................................................... - 89 - ii Liste des abréviations Liste des abréviations Abréviation Signification °C Degré Celsius β Béta µm Micromètre µl Microlitre al. Alii ADN Acide désoxyribonucléique ARNr Acide ribonucléique ribosomial ADP Adénosine diphosphate ATP Adénosine triphosphate Aw Activité de l’eau BeT Bromure d’Ethidium BLAST Basic Local Alignment Search Tool CDM Chemically Defined Medium CFU Colony Forming Unit CTAB Cetyl trimethylammonium bromide DPANN Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota et Nanohaloarchaeota EDTA Éthylène diaminetétra-acétique EPT Eau Peptonée Tamponnée F Forward FBA Fromage « Œillet de Bouillon » bergerie d’Acremont FC Fromage de Chimay FH Fromage de Herve doux FM Fromage Morbier FMAT Flore Mésophile Aérobie Totale FS
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