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Microbiota of spontaneously fermented game meat sausages Žgomba Maksimović, Ana Doctoral thesis / Disertacija 2019 Degree Grantor / Ustanova koja je dodijelila akademski / stručni stupanj: University of Zagreb, Faculty of Agriculture / Sveučilište u Zagrebu, Agronomski fakultet Permanent link / Trajna poveznica: https://urn.nsk.hr/urn:nbn:hr:204:465763 Rights / Prava: In copyright Download date / Datum preuzimanja: 2021-10-08 Repository / Repozitorij: Repository Faculty of Agriculture University of Zagreb University of Zagreb FACULTY OF AGRICULTURE Ana Žgomba Maksimović MICROBIOTA OF SPONTANEOUSLY FERMENTED GAME MEAT SAUSAGES DOCTORAL THESIS Zagreb, 2018 Sveučilište u Zagrebu AGRONOMSKI FAKULTET Ana Žgomba Maksimović MIKROBIOTA SPONTANO FERMENTIRANIH KOBASICA OD MESA DIVLJAČI DOKTORSKI RAD Zagreb, 2018 University of Zagreb FACULTY OF AGRICULTURE Ana Žgomba Maksimović MICROBIOTA OF SPONTANEOUSLY FERMENTED GAME MEAT SAUSAGES DOCTORAL THESIS Supervisor: Assoc. Prof. Mirna Mrkonjić Fuka, PhD. Zagreb, 2018 Sveučilište u Zagrebu AGRONOMSKI FAKULTET Ana Žgomba Maksimović MIKROBIOTA SPONTANO FERMENTIRANIH KOBASICA OD MESA DIVLJAČI DOKTORSKI RAD Mentorica: Izv. prof. dr.sc. Mirna Mrkonjić Fuka Zagreb, 2018 Bibliography data Scientific area: Biotechnical sciences Scientific field: Agriculture Branch of science: Production and processing of animal products Institution: University of Zagreb, Faculty of Agriculture, Department of Microbiology Supervisor: Assoc. Prof. Mirna Mrkonjić Fuka, PhD. Number of pages: 166 Number of images: 15 Number of tables: 36 Number of appendixes: 5 Number of references: 217 Date of oral examination: 01.03.2019. The members of the PhD defence committee: 1. Assist. Prof. Ivica Kos, PhD 2. Prof. Blaženka Kos, PhD 3. Prof. Danijel Karolyi, PhD The work will be deposit in: National and University Library of Zagreb, Street Hrvatske bratske zajednice 4 p.p. 550, 10000 Zagreb Central Agricultural Library, Faculty of Agriculture, Svetošimunska 25, 10000 Zagreb. The subject of the thesis was accepted at the session of the Faculty Council of the University of Zagreb Faculty of Agriculture, held on 8th November 2016, and approved at the session of the Senate of the University of Zagreb, held on 13th December 2016. UNIVERSITY OF ZAGREB FACULTY OF AGRICULTURE Statement of originality I, Ana Žgomba Maksimović, hereby declare that I have independently authored doctoral dissertation under the title: MICROBIOTA OF SPONTANEOUSLY FERMENTED GAME MEAT SAUSAGES With my signature I guarantee: - that I am the only author of this doctoral dissertation - that doctoral thesis is the original result of my work and that while writing it, I did not use any other sources except ones already cited - that I am familiar with the terms of the Ethic codex of the University of Zagreb (sec.19). Zagreb, _______________. ________________________ Signature of the PhD student Doctoral thesis grade: Date of oral examination: Members of the Doctoral PhD committee: Assist. Prof. Ivica Kos, PhD ______________________________ Prof. Blaženka Kos, PhD ______________________________ Prof. Danijel Karolyi, PhD ______________________________ Information about supervisor Mirna Mrkonjić Fuka was born in Zagreb in 1976. She graduated from the Faculty of Science and Mathematics in Zagreb in 2002 and received her PhD at Technical University Munich (TUM) in 2007 with the thesis on structural and functional diversity of proteolytic bacteria in soil. Since 2007 she has worked at the Department of Microbiology at the Faculty of Agriculture, University of Zagreb, where she was appointed Associate Professor in 2016. Her main scientific interests are the analysis of functional and structural diversity of bacterial communities in complex ecosystems, molecular-biological identification of lactic acid bacteria and selection of starter and bioprotective cultures. Mirna Mrkonjić Fuka teaches at the Faculty of Agriculture of the University of Zagreb, where she coordinates seven courses at undergraduate and graduate level. She was a mentor of seven bachelor and eighteen master theses and mentor of two student work rewarded with a Rector's Award. Mirna Mrkonjić Fuka has obtained several awards and acknowledgments (DAAD, FEMS, ERASMUS, CEEPUS, Society of University Teachers and Other Scientists in Zagreb) for her scientific and academic work. She has participated in several international (Tempus IV Program (2015-2017), See-Era. Net Plus (2010-2012), European Regional Development Fund (2006-2007), DFG-German Research Foundation (2002-2005)) and national projects (MZOS 2007-2013) of which she was the leader of two bilateral projects with Germany (2012-2013), one with Austria (2014-2015), one with Slovenia (2016- 2017) and one with China (2018-2019) as well as the leader of the project founded by Croatian Science Foundation (2014-2017). Since 2007 Mirna Mrkonjić Fuka has spent more than fifteen months at renowned foreign universities and scientific research institutions (BOKU, Austria; TUM, Germany; Helmholtz Zentrum Munich, Germany; Vitoria University, Wellington, New Zealand; Huazhong University, Wuhan, NR China). Mirna Mrkonjić Fuka is a member of the Croatian Microbiological Society, a member of the Board for the Use of GMOs at the Croatian Ministry of Health, and was a member of the Steering committee of the Institute for Agriculture and Tourism in Poreč. She has held more than 20 lectures at renowned foreign scientific research institutes and congresses and has published more than 30 scientific papers quoted 275 times according to WOS. Acknowledgements - Zahvala My genuine thanks to my mentor and supervisor, Assist. Prof. Mirna Mrkonjić Fuka, Ph.D., for giving me the opportunity to work on the project and to perform my PhD. I’m thankful for guiding me not only in these past 4 years, rather continuously guiding me back from the time I was an undergraduate student. I appreciate the time you took to teach me, direct my thesis and help me in all aspects of my work. Among other things, you encouraged me to be more proactive and to think critically, all of which helped to shape me into being a person I am today, both professionally and personally. I want to express my gratitude to my colleague and a friend Assist. Prof. Nataša Hulak, Ph.D. Since you joined our group as a postdoc, you were of immense help to me. Aldo often cut up in your own work, you always found time to help me in my moments of despair, figuring out why some of the analysis didn’t work. I could always count on your help in brainstorming ideas, theoretical planning of experiments and realising them. You were there when I needed motivation, support and a kind word from a friend. Working with you was never boring. I am thankful to Melita and Mateja, for your help in carrying out several experiments. Melita, your exceptional organisational skills made possible for everything to work out even when a large number of samples were processed in our lab, while Mateja, your contagious calmness and tranquillity provided a lovely working atmosphere even in the most stressful occasions. I am very grateful to both of you for always being there for me and supporting me in every way possible. I want to thank all the employees at the Faculty of Agriculture, Department of Microbiology. All of them, in one way or another, had a certain role in realising this thesis. Dragica and Sandra, you guided me since I was an undergraduate student and had the patience of repeatedly showing me some basic microbiological techniques and correcting me until I grasped them. At the duration of my Ph.D. studies, you continued to teach me new things. I owe so much to Sali, for motivating me, always having a kind word and for providing logistical support. Thanks to Darija, who managed to find a solution to every problem and with her contagious laughter made the working atmosphere more pleasant. I’m grateful to Prof. Sanja Sikora, Ph.D. giving me useful advices. Thanks to my colleagues Irina, Sanja and Ivana, who were supportive not only in the lab, but with working with students as well. I’m especially grateful to Irina for her work in analysing the data regarding next-generation sequencing and her help with the interpretation of results. I am grateful to all the other employees at the Faculty of Agriculture with whom I had the chance to work and to learn from them. I want to thank Prof. Michael Schloter, Ph.D. and the entire group of Research Unit for Comparative Microbiome Analysis at the Helmholtz Zentrum München for granting me an opportunity to be a part of their group. That was a very valuable experience for me. I want to thank Assist. Prof. Konrad Domig, Ph.D., and Marija Zunabovic-Pichler, Ph.D. for giving me the opportunity to perform my work at the Institute of Food Science, University of Natural Resources and Life Sciences, Vienna. I would particularly like to thank Marija Zunabovic-Pichler and Sigrid Mayrhofer, Ph.D., for their continuous support during my stay and helping me to settle into a new working environment, as well as for their valuable insights and advice regarding my work. I am grateful to all other employees at the Institute for a very warm welcome and a nice collaboration. I am grateful to Assist. Prof. Ivica Kos, Ph.D., Prof. Danijel Karolyi, Ph.D. and Prof. Blaženka Kos, Ph.D. on the time and effort they invested in improving this work, as members of the committee for evaluation of the dissertation. Without your input, this work wouldn’t be in its present form. In the end, I would like to thank my dear friends and family. Kristina, thank you for your down-to-earth view of life. You entered a dose of sanity in my life when I needed it most. Nikola, your recommendations on using certain programmes simplified and made easier writing this thesis. Thank you for always being honest and pragmatic, for being supportive as well as for giving me constructive criticism. Dino, thank you for motivating and helping me to enrol at the Faculty of Agriculture, now more than a decade ago, which determined my academic path.
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  • Development and Role of the Indigenous Gut Microbiota Of

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    Development and role of the indigenous gut microbiota of Spodoptera littoralis Dissertation To Fulfill the Requirements for the Degree of ,,doctor rerum naturalium“ (Dr. rer. nat.) Submitted to the Council of the Faculty of Biology and Pharmacy of the Friedrich Schiller University Jena by Beng-Soon Teh (M.Sc) born on 12.02.1985 in Penang, Malaysia Gutachter: 1. …. 2. …. 3. …. Tag der öffentlichen Verteidigung: Fluorescent GFP-tagged Enterococcus mundtii TABLE of CONTENTS Abbreviations and symbols 1. Introduction .......................................................................................................... 1 1.1 Host-microbiota symbiosis interactions ........................................................... 1 1.1.1 Insect-bacteria symbiosis interactions ........................................................ 2 1.2 Physiological conditions and stresses in the gut environment of insects ......... 3 1.3 Contributions of the gut microbiome ................................................................ 5 1.4 Diversity of the gut microbiota in insects ......................................................... 6 1.5 Model organism: Spodoptera littoralis ............................................................. 9 1.6 The physiology of lactic acid bacteria ............................................................ 10 1.6.1 General characteristics of enterococci ...................................................... 11 1.7 Colonization of enterococci in insects ............................................................ 14