Molecular Techniques in Food Biology

Aly Farag El Sheikha, PhD is a Researcher at Department of Biology, McMaster University, Hamilton, Ontario, Canada Robert Levin, PhD is a Professor Emeritus at Department of Food Science at the University of Massachusetts, Amherst, MA, USA Jianping Xu, PhD is a Professor at Department of Biology at McMaster University, Hamilton, Ontario, Canada

• List of Contributors xiiiPreface xviiAcknowledgments xixSection I General Topics 11 How to Determine the Geographical Origin of Food by Molecular Techniques 3Aly Farag El Sheikha1.1 Linkage Between Food and Its Geographical Origin: Historical View 31.2 Scope and Approach 41.3 Definitions Related to Tracking of Food Origins 41.4 Driving Forces for Determining the Geo]origin of Food 81.5 Geo] origin Determination … Evolution of Molecular Techniques 131.6 Pros and Cons of Molecular Techniques Used as Geo]Discriminative Tools of Food 161.7 Conclusions 17References 182 Unraveling Pathogenic Behavior of Phytopathogens through Advanced Molecular Techniques 27Avantina S. Bhandari and Neeta Sharma2.1 Introduction 272.2 Plant Pathogens: A Menace to Agricultural Productivity 282.3 Future Directions 38References 393 Molecular Characterization of Ochratoxigenic Fungal Flora as an Innovative Tool to Certify Coffee Origin 47Aly Farag El Sheikha and Nadege Donkeng Nganou3.1 Introduction: Coffee Factsheet 473.2 The Microflora of Coffee 503.3 Detection of Ochratoxigenic Fungi in Coffee by Molecular Techniques 553.4 Using Molecular Detection of OTA]producing Fungi to Certify Coffee Origin: Is it Possible? 573.5 Conclusions and Future Perspectives 63References 634 Molecular and “Omics” Techniques for Studying Gut Microbiota Relevant to Food Animal Production 71Joshua Gong, Chengbo Yang, and Ehsan Khafipour4.1 Introduction 714.2 Methods for Studying Gut Microbiota Composition 724.3 Culture] independent Techniques 724.4 Tools for Functional Studies of Gut Microbiota 754.5 “Omics” 764.6 Animal Models 784.7 Bioinformatics 794.8 Application in Poultry and Swine Research 804.9 Integrated Approaches for Studying Gut Microbiome 834.10 Conclusions and Future Directions 84Acknowledgments 85References 855 Molecular Techniques for Making Recombinant Enzymes Used in Food Processing 95Wenjing Hua, Aly Farag El Sheikha, and Jianping Xu5.1 Introduction 955.2 Molecular Strategies to Produce Recombinant Enzymes Used in the Food Industry 965.3 Applications and Safety Issues of Enzymes in the Food Industry 1065.4 Conclusions and Future Perspectives 109References 110Section II Fruits and Vegetables 1156 Molecular Identification and Distribution of Yeasts in Fruits 117Justine Ting, Rui Xu, and Jianping Xu6.1 Introduction 1176.2 Molecular Methods for Distinguishing Yeast Species and Strains 1186.3 Yeast Diversity in Wild/fresh Fruits 1206.4 Yeast Diversity in Processed Fruits 1346.5 Conclusions and Future Perspectives 141Acknowledgments 142References 1427 Current and New Insights on Molecular Methods to Identify Microbial Growth in Fruit Juices 145Elena Rosello]Soto, Sonia Barba]Orellana, Mohamed Koubaa, Shahin Roohinejad, Francisco Quilez, and Francisco J. Barba7.1 Introduction 1457.2 Microorganisms in Fruit Juices 1467.3 Conventional Identification Techniques 1487.4 Non] conventional Identification Techniques 1507.5 Molecular Techniques 1517.6 Conclusions and Future Perspectives 154References 154Section III Fish and Meat Products (Non-Fermented) 1618 Molecular Techniques Related to the Identification of the Bacterial Flora of Seafood 163Robert E. Levin8.1 Introduction 1638.2 Major Seafood Spoilage Bacteria 1648.3 Seafood]borne Bacterial Pathogens 1838.4 Conclusions and Future Perspectives 201References 2019 Assessment of the Microbial Ecology of Meat and Meat Products at the Molecular Level: Current Status and Future Perspectives 215Spiros Paramithiotis, Agni Hadjilouka, and Eleftherios H. Drosinos9.1 Introduction 2159.2 Extraction of Nucleic Acids 2169.3 Microbial Communities Assessment 2169.4 Detection of Selected Bacterial Target 2209.5 Biodiversity Assessment 2259.6 Conclusion and Future Perspectives 226References 227Section IV Fermented Foods and Beverages 23910 Revolution in Fermented Foods: From Artisan Household Technology to the Era of Biotechnology 241Aly Farag El Sheikha10.1 Introduction 24110.2 Historical View: Where and When Did Fermentation Start? 24210.3 Fermented Foods: From the Past to the Current Era 24310.4 Fermented Foods and Health Effects 24610.5 Is it Possible to Trace the Geographical Origin of Fermented Foods? 24910.6 Conclusions and Future Perspectives 252References 25411 Molecular Techniques for the Identification of LAB in Fermented Cereal and Meat Products 261Malik Altaf Hussain11.1 Introduction 26111.2 Fermented Food Products 26211.3 Lactic Acid Bacteria and Fermented Foods 26511.4 Molecular Approaches Used to Study Fermenting Microflora 26811.5 Identification of Lab in Fermented Cereal and Meat Products 26911.6 Advantages of Molecular Techniques 27511.7 Concluding Remarks 275Acknowledgment 277References 27712 Molecular Techniques and Lactic Acid]Fermented Fruits and Vegetables 285Aly Farag El Sheikha12.1 Introduction 28512.2 Fermented Fruits and Vegetables: Between the Past and the Present 28612.3 Benefits of Fermented Fruits and Vegetables 28612.4 Techniques of Lab Analysis Used in Fermented Fruits and Vegetables 28812.5 Future Applications 30012.6 Conclusions 300References 30013 New Trends in Molecular Techniques to Identify Microorganisms in Dairy Products 309Elena Rosello]Soto, Sonia Barba]Orellana, Francisco J. Barba, Francisco Quilez, Shahin Roohinejad, and Mohamed Koubaa13.1 Introduction 30913.2 Polymerase Chain Reaction (PCR)]based Methods 31013.3 Fluorescent In Situ Hybridization 31613.4 Immuno]based Methodologies, Biochips, and Nanosensors 31713.5 Benefits and Limitations of Molecular Techniques 31813.6 Conclusions and Future Perspectives 318References 31814 Molecular Techniques for the Detection and Identification of Yeasts in Wine 323Cecilia Diaz, Grigori Badalyan, and Mark Bucking14.1 Introduction 32314.2 Methods of Identification and Detection of Biodiversity 32714.3 Enumeration of Wine Yeasts 33014.4 Diversity of Wine Yeasts 33214.5 Conclusions and Future Perspectives 334References 334Section V Foodborne Pathogens and Food Safety 34115 Rapid Detection of Food Pathogens Using Molecular Methods 343R.M.U.S.K. Rathnayaka, Rakshit K. Devappa, and Sudip Kumar Rakshit15.1 Introduction 34315.2 Methods Used to Detect Foodborne Pathogens 34415.3 Conclusions 355References 35516 Biosensor]Based Techniques: A Reliable and Primary Tool for Detection of Foodborne Pathogens 361Moni Gupta, Baby Summuna, Sachin Gupta, and Deepika Sharma16.1 Introduction 36116.2 Ideal Requirements for Biosensor]Based Microbial Detection Assay 36616.3 Need for Rapid Method 36716.4 Classification of Biosensors 36716.5 Conclusions and Future Perspectives 378References 37917 Molecular Identification and Detection of Foodborne and Feedborne Mycotoxigenic Fungi 385Glaucia E.O. Midorikawa, Robert N.G. Miller, and Daniela M. de C. Bittencourt17.1 Mycotoxigenic Fungi 38517.2 Polymerase Chain Reaction]based Characterization of Mycotoxigenic Fungi 38617.3 Genomics of Mycotoxigenic Fungi 39417.4 Functional Genomics of Mycotoxigenic Fungi 39617.5 Conclusions and Future Perspectives 398References 39818 Molecular Identification of Enteric Viruses in Fresh Produce 409Martin D’Agostino and Nigel Cook18.1 Introduction 40918.2 Sample Treatment 41018.3 Sample Receipt 41018.4 Removal of Viruses from the Food Surfaces 41018.5 Removal of Food Substances 41118.6 Concentration of Viruses 41118.7 Nucleic Acid Extraction 41118.8 Detection Assay 41218.9 ISO 15216]1/2:2013: The Future “Gold Standard” 41318.10 Quantitation 41518.11 What is a Positive? 41518.12 Future Developments and Requirements 41618.13 Conclusions and Future Perspectives 416References 417Section VI Future Perspectives 42119 Molecular Techniques and Foodstuffs: Innovative Fingerprints, Then What? 423Aly Farag El Sheikha and Jianping Xu19.1 Introduction 42319.2 Emerging Fingerprinting Technologies 42419.3 DNA Fingerprints 42619.4 Conclusions and Future Perspectives 428References 431Index 435