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Microbial Diversity Analyses in a Changing Landscape

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Microbial Diversity Analyses in a Changing Landscape FACULTY OF SCIENCES Microbial diversity analyses in a changing landscape Lactic acid bacteria in food fermentations as a test case MSc. Isabel Snauwaert Doctor (Ph.D.) in Sciences, Biochemistry and Biotechnology (Ghent University) Dissertation submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) in Bioengineering Sciences (Vrije Universiteit Brussel) Promotors: Prof. dr. Peter Vandamme (Ghent University) Prof. dr. ir. Luc De Vuyst (Vrije Universiteit Brussel) Prof. dr. Anita Van Landschoot (Ghent University) I feel more microbe than man Snauwaert, I. | Microbial diversity analyses in a changing landscape: Lactic acid bacteria in food fermentations as a test case ©2014, Isabel Snauwaert ISBN-number: 978-9-4619724-0-8 All rights reserved. No part of this thesis protected by this copyright notice may be reproduced or utilised in any form or by any means, electronic or mechanical, including photocopying, recordinghttp://www.universitypress.be or by any information storage or retrieval system without written permission of the author. Printed by University Press | Joint Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium th Publicly defended in Ghent, Belgium, November 25 , 2014 Author’sThis Ph.D. email work address: was supported by FWO-Flanders, BOF project, and the Vrije Universiteit Brussel (SRP, IRP, and IOF projects). [email protected] ExaminationProf. dr. Savvas SAVVIDES Committee (Chairman) L-Probe: Laboratory for Protein Biochemistry and Biomolecular Engineering FacultyProf. of Sciences, dr. Peter Ghent VANDAMME University, Ghent, Belgium (Promotor UGent) LM-UGent: Laboratory of Microbiology Faculty ofProf. Sciences, dr. ir. Ghent Luc DE University, VUYST Ghent, Belgium (Promotor VUB) IMDO: Research Group of Industrial Microbiology and Food Biotechnology Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Prof. dr. Anita VAN LANDSCHOOT Brussels, Belgium (Promotor UGent) Laboratory of Biochemistry and Brewing Faculty of BioscienceProf. Engineering, dr. Edilbert Ghent VAN University, DRIESSCHE Ghent, Belgium (Secretary) SPRO: Research Group of Protein Chemistry Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Prof. dr.Brussels, Tom COENYE Belgium LPM: Laboratory of Pharmaceutical Microbiology Faculty of Pharmaceutical Sciences, Ghent University,Prof. dr. Anne Ghent, WILLEMS Belgium LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Ghent, Belgium ii Prof. dr. ir. Ronnie WILLAERT SBB: Research Group of Structural Biology Brussels Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Prof. dr.Brussels, Tom LENAERTS Belgium MLG: Machine Learning Group Faculty of Sciences, Université Libre de Bruxelles, Brussels, Belgium AI lab: Artificial Intelligence lab Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Prof. dr. SebastiaanBrussels, EELTINK Belgium Research Group of Chemical Engineering Faculty of Engineering, Vrije Universiteit Brussel,Prof. Brussels, dr. Rudi BelgiumVOGEL Lehrstuhl für Technische Mikrobiologie Center of Life and Food Sciences Weihenstephan, Technische Universität München, München, Germany Dankwoord Vijf jaar heb ik als een ’Bezig Bijtje’ in de gangen van het laboratorium voor Microbiologie rondgecrosst. Al die jaren heb ik mezelf kunnen zijn en me zo maximaal kunnen ontplooien. Mijn dankbaarheid uitdrukken op papier is dus geen Professoreenvoudige Vandamme opdracht en is sowieso ontoereikend. Maar ik doe hier toch een poging. , Peter, allereerst wil ik u bedanken omdat u me de kans hebt gegeven om dit onderzoek uit te voeren. Bedankt om vertrouwen te hebben in mijn kunnen,Professor om mij De vrijheid Vuyst te geven in de invulling van het project en om mij naar vele workshops en congressen te laten gaan. Dankzij u heb ik veel kunnen bijleren. , bedankt om mij als één van uw doctoraatstudentenProfessor Van teLandschoot behandelen. Zo nodigde u me uit om samen te lunchen met het IMDO-team en zelfs bij het kerstetentje, waardoor ik me bijzonder welkom voelde. , dankzij uw connecties met de brouwerijen konden we de nodige stalen Lieveverzamelen. buurvrouwtjes Simpelweg onmisbaar voor mijn onderzoek. , jullie waren mijn warme thuisbasis binnen het labo. Onze bureau was een plaatsje waar ik veel gelachen heb,Charlie waar ik raad kon vragen, waar ik iedere morgen goed gezind werd en waar ik ook even triest mocht zijn. Jullie zijn stuk voor stuk top-collega’s en vriendinnen. : mijn partner in crime én mijn tweede brain. Nooit gedacht dat iemand mijn gek idee ook effectief mee ging uitvoeren: op een workshop in Detroit om 4 uur in de ochtend opstaan om nog voor de start te kunnen fitnessen, ontbijten én scriptjes schrijven. En dan s’ avonds vroeg in bed, want er was toch niets te doen in Detroit. Gelukkig wel in Liverpool: de cafeetjes waren er zo gezellig en het bier zeer drinkbaar. Maar nog belangrijker: brainstormen met jou was pure synergie, we brachten elkaar steeds tot een hoger niveau. Dankzij jou was er geen probleem dat niet tot een oplossing kon komen. Anne,iv Timo, Jindrich, Freek, Jessy, Anneleen, Bram V. Helen , en , mijn maatjes, veel meerGwen, dan Sofie, alleen Joke collega’s.Jonas Samen gaan eten, op café gaan en kletsen kon alle dipjes doen overwaaien en gaf mij weer moed. HeerlijkGwen om jullie te leren kennen! , en : wat deed het pijn om jullie één voor één te zien vertrekken na het beëindigen van jullie doctoraat. , zonder jou was ik zelfs nooit doctorandus geworden. Je hebt als mijn stagebegeleisterSofie je enthousiasme, gedrevenheid en relativeringsvermogen op mij geprojecteerd.Joke Door jouJonas kreeg ik definitief de microbiologie-microbe teKim pakken. , jij was en bent nog steeds een onuitputtelijke bron van ideeën voor leuke activiteiten. En en , ook jullie bleef ik tot op vandaag missen. , bij de start van mijn doctoraat had ik het gevoel had dat je niet volledig geloofde in mijn capaciteiten. Maar achteraf ben ik daar blij om. Want zo heb je me assertiever en sterker gemaakt, want ik wilde bewijzen dat ik het wel kon. Een waardevolle attitude die ik nu meeneem naar het bedrijfsleven. En ook je lieve en dankbare tips voor de combinatie werk én zorg voor een pittige dochter, zullen mij altijd bij blijven. Het schrijven van ditJeannine, dankwoord Evie, toont Bart aan H., dat Liesbeth, er zoveel Maarten, warme persoonlijkheden Leilei, Bart V., bijen LM-UgentJoke werken. Zoals al eerder gezegd: dit dankwoord is sowieso ontoereikend. Zo denk ik nog aan en alle andere collega’s van LM-Ugent. Bedankt voor de warme en hartelijke sfeer in het labo, ik was er elke dag opnieuw welkom. Lieve IMDO collega’s, als bezoeker in een ’vreemd’ laboratorium komen is niet evident.Tom, Audrey, Ik was Maria, plots David, weer de Henning, leek die Moens niets wistKoen liggen en iedereen lastig viel met mijn vragen. Maar ik kon steeds bij jullie terecht. Expliciet een merci aan en . Na twee uur treinen van Brugge naar Etterbeek voelde ik me vaak suf (zelfs koffie hielp dan niet). Maar na aankomst, kregen jullie mij altijd weer vrolijk. Lindseys Het doctoraat mocht dan wel boeiend zijn, maar gelukkig is er in mijn levenIlse ook nog meer. Lieve , het is altijd heerlijk om samen met mijn vriendinnen wijntjes te drinken en te kletsen. Jullie zijn stuk voor stuk topwijven. , mijn capaciteitmevrouw Mitchell om te plannen en efficiënt te werken was even zoek geraakt de laatste twee maanden. Merci om mij toen weer op de rails te zetten. En ook jij bedankt, , omdat je gewoon dé meest attente persoon bent die ik ken. Mama en papa v , bedankt voor alle kansen die jullie mij gaven. Jullie bleven mij onvoorwaardelijk steunen en geloofden in mijn capaciteiten.Papa Door jullie kon ik studeren wat ik maar wilde en kan ik nu terugkijken op een heerlijke studententijd. Kortom, zonder jullie liefdeMama en vertrouwen kan ik niet. , ooit lachte ik met je als academische ’nerd’ en ’pietje precies’, maar ik vrees dat ik deze eigenschappen zeker van je meekreeg. , ik hoop dat ik van jou het ’mama-zijn’ heb geërfd en voor mijn dochter Helena nu net zo’n supermama zal zijn zoals jij altijd voor mij bentEvelien geweest (en nog altijd bent).Filip Sanne OokMathilde (mijn ideale zus), (de eeuwige enthousiasteling),Jan (R en latexHilde kenner: heerlijk om iemand met dezeLeens vaardighedenBert inPieter de familie te hebben), (altijd paraat als babysit) en mijn schoonfamilie: - (English Expert), (de onmisbare SOS oma), de gekke , en - : dikke merci! Het zijn vijf leerrijke jaren geweest, maar toch ben ikBram enorm opgeluchtHelena dat ik eindelijkBram een punt achter dit werk mag zetten. Het is nu tijd om mij te focussen op de belangrijke dingen in het leven en dat zijn jullie - en kleine -. , jij hebt gevoeld hoe zwaar het afwerken van het doctoraat op mijn schouders woog na de geboorte van ons klein spook. Ik heb je de voorbije maandenLieve meer dochter dan ooit nodig gehad en jij bent er steeds voor mij geweest. Jouw onvoorwaardelijke liefde is het mooiste dat ik heb mogen tegengekomen in mijn leven. , mijn klein pittig vrouwtje, ik kijk ernaar uit om je te zien opgroeien en je heel erg veel liefde te geven. Gent, 17 november 2014 Isabel Snauwaert Table of Contents Examination Committee i Dankwoord iii Table of Contents vii List of Figures xi List of Tables xiii Nederlandstalige Samenvatting xxiii English Summary xxv I Introduction 1 Background & Objectives 3 Outline 5 II Literature Overview 7 1 Microbial Diversity Analyses of Food Fermentations 9 1.1 Traditional Methods . 10 1.1.1 Plate Culturing . 11 1.1.2 Cultivation-Independent Molecular Techniques . 12 1.2 Microbial Diversity Analyses in the HT Sequencing Era . 14 1.2.1 Platforms . 15 1.2.2 (Meta)genomics . 17 2viii Importance of LAB in Food Fermentations 23 3 LAB Taxonomy 27 3.1 Phylogenetics . 28 3.2 Polyphasic Taxonomy . 31 3.3 Genomic Taxonomy . 32 III Experimental Work 35 4 Traditional Workflow in Microbial Diversity Analyses 37 Weissella fabalis Fruc- tobacillus tropaeoli 4.1 Characterization of Strains of sp.
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