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Moroccan Camel Milk Microbiota, a Source of New Lactic Acid Bacteria

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Moroccan camel milk microbiota, a source of new lactic acid bacteria Zaina Kadri Promoter: Prof. Dr. Peter Vandamme Co-promoter: Prof. Dr. Mohamed Amar Co-promoter: Prof. Dr. Omar El Farricha Year: 2016 EXAMINATION COMMITTEE Prof. Dr. Saad Ibnsouda Koraichi (Chairman) Faculty of Sciences and Technology Sidi Mohamed Ben Abdellah University, Fez, Morocco Prof. Dr. Mohamed Amar (Promotor) National Center for Scientific and Technical Research, CNRST Laboratory of Microbiology and Molecular Biology, LMBM Rabat, Morocco Prof. Dr. Peter Vandamme (Promotor) Faculty of Sciences Ghent University, Ghent, Belgium Prof. Dr. Omar El Farricha (Promotor) Faculty of Sciences and Technology Sidi Mohamed Ben Abdellah University, Fez, Morocco Prof. Dr. Ir. Jean Swings Faculty of Sciences Ghent University, Ghent, Belgium Prof. Dr. Khalid Sendide Al Akhawayn University, Ifrane, Morocco Prof. Dr. Kurt Houf Faculty of Veterinary Medicine Ghent University, Ghent, Belgium Prof. Dr. Guissi Sanae Faculty of Sciences and Technology Sidi Mohamed Ben Abdellah University, Fez, Morocco Prof. Dr. Ibijbijen Jamal Faculty of Sciences Moulay Ismail University, Meknes, Morocco i ACKNOWLEDGEMENTS I would like to express my sincere gratitude and appreciation to the person who made all this possible, Prof. Dr. Mohamed Amar. You always dedicated me your time, expertise, and good proposal. I would like to express my special thanks for giving me the opportunity to do this work at the Laboratory of Microbiology and Molecular Biol- ogy of the National Center for Scientific and Technical Research. This study was only possible thanks to you. My genuine gratitude and gratefulness are extended to Prof. Peter Vandamme. Your tremendous guidance, your expertise, thoughtful insights into microbiology, un- derstanding, kindness and helpfulness would be the unforgettable blessing of this stage. I am highly indebted to you for giving me the opportunity to carry out my Ph.D study at the Laboratory of Microbiology of the University of Gent. I also would like to thank Prof. Dr. Omar El Farricha for his enthusiastic guid- ance and for his support and assistance during my Ph.D study in the Faculty of Sciences and Technology of the University Sidi Mohamed Ben Abdellah. Sincere thanks and gratitude are extended to my friends and colleagues from the Laboratory of Microbiology and Molecular Biology, Dr. Tarik Aaanniz, Prof. Mouna Ouadghiri, Mr. Lahcen Ouchari, Mr. Mohamed Chenaoui, Mrs. Bahia Rached, Mrs. Sanae Karmouna, Mr. Azzedine Badouri and Mrs. Leila Bouchane for their collabora- tion in different parts of this work. Your support and assistance would be the unforget- table blessing of this Ph. D study. I would like to give my special thanks to Margo Cnockaert, from the Laboratory of Microbiology of the University of Gent, who has always shared everything with me and encouraged me all the time. She helped me both with knowledge in researching and everyday living. She has been a very good friend and colleague. I would also like to thank Dr. Freek Spitaels from the Laboratory of Microbiol- ogy of the University of Gent, for his enthusiastic guidance. I appreciate your willing- ness to help me. I am thankful to all the staff of the Laboratory of Microbiology and of LMG Bacteria Collection for all collaboration to this project. Their research experience and thoughtful explanations are highly appreciated. ii I would like to thank the members of the examination committee (Prof. Dr. Peter Vandamme, Prof. Dr. Mohamed Amar, Prof. Dr. Omar El Farricha, Prof. Dr. Ir. Jean Swings, Prof. Dr. Saad Ibnsouda Koraichi, Prof. Dr. Khalid Sendide, Prof. Dr. Guissi Sanae, Prof. Dr. Jamal Ibijbijen and Prof. Dr. Kurt Houf) for their evaluation and com- ments on the thesis. I thank my parents, Mr. Mohamed Kadri and Mrs. Sanae Kettani, my brother Ahmed, my sister Nada, my aunt Oumama Kadri, and all members of family for their continued support and inspiration throughout this project. Lastly, thanks to my friends O.C, I.B, T.L and Z.B for trusting me and for their friendship and assistance. iii TABLE OF CONTENTS LIST OF FIGURES ............................................................................................... vii LIST OF TABLES ................................................................................................... x LIST OF ABBREVIATIONS ................................................................................ xi PART I ............................................................................................................................ INTRODUCTION & OBJECTIVES ......................................................................... 1 GENERAL INTRODUCTION ............................................................................... 2 OBJECTIVES .......................................................................................................... 2 General objectives .................................................................................................. 4 Specific objectives ................................................................................................. 6 OUTLINE OF THE THESIS .................................................................................. 8 PART II........................................................................................................................... LITERATURE ........................................................................................................... 11 CHAPTER 1: THE DROMEDARY CAMEL AND CAMEL MILK ............... 12 1.1 The dromedary camel .................................................................................... 12 1.2 Dromedaries as milking animals .................................................................... 12 1.2.1 Taxonomy and breeds ............................................................................. 12 1.2.2 The reproduction in dromedary camels .................................................. 12 1.2.3 Camel population in the world ................................................................ 13 1.3 Characteristics of lactation and camel milk ................................................... 13 1.3.1 Characteristics of camel milk.................................................................. 13 1.3.2 Lactation and milk yield ......................................................................... 13 1.3.3 Milk contents and pH .............................................................................. 14 1.3.4 Camel milk: a remedy for medical problems .......................................... 16 1.4 Microbiological quality of camel milk .......................................................... 16 1.4.1 Introduction ............................................................................................. 16 1.4.2 Total bacterial content (TBC) ................................................................. 17 1.4.3 Enterobacteriaceae ................................................................................. 17 1.4.4 Pathogens in camel milk ......................................................................... 18 1.4.5 Bifidobacteria .......................................................................................... 19 1.4.6 Lactic acid bacteria ................................................................................. 19 1.4.7 Camelimonas........................................................................................... 20 1.4.8 Fungi in camel milk ................................................................................ 20 CHAPTER 2: LACTIC ACID BACTERIA ........................................................ 21 2.1. General characteristics .................................................................................. 21 2.2. Taxonomy and phylogeny of lactic acid bacteria ......................................... 22 iv 2.2.1. Bacterial taxonomy and the polyphasic species definition .................... 22 2.2.2. Taxonomy and phylogeny of lactic acid bacteria .................................. 23 2.3. Classification and identification methods for lactic acid bacteria ................ 28 2.3.1. Phenotypic methods ............................................................................... 28 2.3.2. Genotypic methods ................................................................................ 30 2.4. Fingerprinting methods as tools for dereplication ........................................ 34 CHAPTER 3: THE GENERA STREPTOCOCCUS, LACTOCOCCUS AND ENTEROCOCCUS. ................................................................................................ 35 3.1. The genus Streptococcus............................................................................... 35 3.1.1. Taxonomy of the genus Streptococcus .................................................. 35 3.1.2. Identification methods of the genus Streptococcus ............................... 36 3.2. The genus Lactococcus ................................................................................. 37 3.2.1. Taxonomy of the genus Lactococcus ..................................................... 37 3.2.2. Identification methods of the genus Lactococcus .................................. 38 3.3. The genus Enterococcus ............................................................................... 39 3.3.1. Taxonomy of the genus Enterococcus ................................................... 39 3.3.2. Identification methods of the genus Enterococcus ................................ 40 CHAPTER 4. THE IDENTIFICATION OF
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