Molecular Techniques in Food Biology: Safety, Biotechnology, Authenticity and Traceability

Molecular Techniques in Food Biology: Safety, Biotechnology, Authenticity & Traceability explores all aspects of microbe-food interactions, especially as they pertain to food safety. Traditional morphological, physiological, and biochemical techniques for the detection, differentiation, and identification of microorganisms have severe limitations. As an alternative, many of those responsible for monitoring food safety are turning to molecular tools for identifying foodborne microorganisms. This book reviews the latest molecular techniques for detecting, identifying, and tracing microorganisms in food, addressing both good foodborne microbes, such as those used for fermentation and in probiotics, and harmful ones responsible for foodborne illness and food quality control problems. Molecular Techniques in Food Biology: Safety, Biotechnology, Authenticity & Traceability brings together contributions by leading international authorities in food biology from academe, industry, and government. Chapters cover food microbiology, food mycology, biochemistry, microbial ecology, food biotechnology and bio-processing, food authenticity, food origin traceability, and food science and technology. Throughout, special emphasis is placed on novel molecular techniques relevant to food biology research and for monitoring and assessing food safety and quality. Brings together contributions from scientists at the leading edge of the revolution in molecular food biology Explores how molecular techniques can satisfy the dire need to deepen our understanding of how microbial communities develop in foods of all types and in all forms Covers all aspects of food safety and hygiene, microbial ecology, food biotechnology and bio-processing, food authenticity, food origin traceability, and more Fills a yawning gap in the world literature on food traceability using molecular techniques  This book is an important working resource for professionals in agricultural, food science, biomedicine, and government involved in food regulation and safety. It is also an excellent reference for advanced students in agriculture, food science and food technology, biochemistry, microbiology, and biotechnology, as well as academic researchers in those fields.

Table of Contents:
List of Contributors xiii Preface xvii Acknowledgments xix Section I General Topics 1 1 How to Determine the Geographical Origin of Food by Molecular Techniques 3 Aly Farag El Sheikha 1.1 Linkage Between Food and Its Geographical Origin: Historical View 3 1.2 Scope and Approach 4 1.3 Definitions Related to Tracking of Food Origins 4 1.4 Driving Forces for Determining the Geo]origin of Food 8 1.5 Geo] origin Determination … Evolution of Molecular Techniques 13 1.6 Pros and Cons of Molecular Techniques Used as Geo]Discriminative Tools of Food 16 1.7 Conclusions 17 References 18 2 Unraveling Pathogenic Behavior of Phytopathogens through Advanced Molecular Techniques 27 Avantina S. Bhandari and Neeta Sharma 2.1 Introduction 27 2.2 Plant Pathogens: A Menace to Agricultural Productivity 28 2.3 Future Directions 38 References 39 3 Molecular Characterization of Ochratoxigenic Fungal Flora as an Innovative Tool to Certify Coffee Origin 47 Aly Farag El Sheikha and Nadege Donkeng Nganou 3.1 Introduction: Coffee Factsheet 47 3.2 The Microflora of Coffee 50 3.3 Detection of Ochratoxigenic Fungi in Coffee by Molecular Techniques 55 3.4 Using Molecular Detection of OTA]producing Fungi to Certify Coffee Origin: Is it Possible? 57 3.5 Conclusions and Future Perspectives 63 References 63 4 Molecular and “Omics” Techniques for Studying Gut Microbiota Relevant to Food Animal Production 71 Joshua Gong, Chengbo Yang, and Ehsan Khafipour 4.1 Introduction 71 4.2 Methods for Studying Gut Microbiota Composition 72 4.3 Culture] independent Techniques 72 4.4 Tools for Functional Studies of Gut Microbiota 75 4.5 “Omics” 76 4.6 Animal Models 78 4.7 Bioinformatics 79 4.8 Application in Poultry and Swine Research 80 4.9 Integrated Approaches for Studying Gut Microbiome 83 4.10 Conclusions and Future Directions 84 Acknowledgments 85 References 85 5 Molecular Techniques for Making Recombinant Enzymes Used in Food Processing 95 Wenjing Hua, Aly Farag El Sheikha, and Jianping Xu 5.1 Introduction 95 5.2 Molecular Strategies to Produce Recombinant Enzymes Used in the Food Industry 96 5.3 Applications and Safety Issues of Enzymes in the Food Industry 106 5.4 Conclusions and Future Perspectives 109 References 110 Section II Fruits and Vegetables 115 6 Molecular Identification and Distribution of Yeasts in Fruits 117 Justine Ting, Rui Xu, and Jianping Xu 6.1 Introduction 117 6.2 Molecular Methods for Distinguishing Yeast Species and Strains 118 6.3 Yeast Diversity in Wild/fresh Fruits 120 6.4 Yeast Diversity in Processed Fruits 134 6.5 Conclusions and Future Perspectives 141 Acknowledgments 142 References 142 7 Current and New Insights on Molecular Methods to Identify Microbial Growth in Fruit Juices 145 Elena Rosello]Soto, Sonia Barba]Orellana, Mohamed Koubaa, Shahin Roohinejad, Francisco Quilez, and Francisco J. Barba 7.1 Introduction 145 7.2 Microorganisms in Fruit Juices 146 7.3 Conventional Identification Techniques 148 7.4 Non] conventional Identification Techniques 150 7.5 Molecular Techniques 151 7.6 Conclusions and Future Perspectives 154 References 154 Section III Fish and Meat Products (Non-Fermented) 161 8 Molecular Techniques Related to the Identification of the Bacterial Flora of Seafood 163 Robert E. Levin 8.1 Introduction 163 8.2 Major Seafood Spoilage Bacteria 164 8.3 Seafood]borne Bacterial Pathogens 183 8.4 Conclusions and Future Perspectives 201 References 201 9 Assessment of the Microbial Ecology of Meat and Meat Products at the Molecular Level: Current Status and Future Perspectives 215 Spiros Paramithiotis, Agni Hadjilouka, and Eleftherios H. Drosinos 9.1 Introduction 215 9.2 Extraction of Nucleic Acids 216 9.3 Microbial Communities Assessment 216 9.4 Detection of Selected Bacterial Target 220 9.5 Biodiversity Assessment 225 9.6 Conclusion and Future Perspectives 226 References 227 Section IV Fermented Foods and Beverages 239 10 Revolution in Fermented Foods: From Artisan Household Technology to the Era of Biotechnology 241 Aly Farag El Sheikha 10.1 Introduction 241 10.2 Historical View: Where and When Did Fermentation Start? 242 10.3 Fermented Foods: From the Past to the Current Era 243 10.4 Fermented Foods and Health Effects 246 10.5 Is it Possible to Trace the Geographical Origin of Fermented Foods? 249 10.6 Conclusions and Future Perspectives 252 References 254 11 Molecular Techniques for the Identification of LAB in Fermented Cereal and Meat Products 261 Malik Altaf Hussain 11.1 Introduction 261 11.2 Fermented Food Products 262 11.3 Lactic Acid Bacteria and Fermented Foods 265 11.4 Molecular Approaches Used to Study Fermenting Microflora 268 11.5 Identification of Lab in Fermented Cereal and Meat Products 269 11.6 Advantages of Molecular Techniques 275 11.7 Concluding Remarks 275 Acknowledgment 277 References 277 12 Molecular Techniques and Lactic Acid]Fermented Fruits and Vegetables 285 Aly Farag El Sheikha 12.1 Introduction 285 12.2 Fermented Fruits and Vegetables: Between the Past and the Present 286 12.3 Benefits of Fermented Fruits and Vegetables 286 12.4 Techniques of Lab Analysis Used in Fermented Fruits and Vegetables 288 12.5 Future Applications 300 12.6 Conclusions 300 References 300 13 New Trends in Molecular Techniques to Identify Microorganisms in Dairy Products 309 Elena Rosello]Soto, Sonia Barba]Orellana, Francisco J. Barba, Francisco Quilez, Shahin Roohinejad, and Mohamed Koubaa 13.1 Introduction 309 13.2 Polymerase Chain Reaction (PCR)]based Methods 310 13.3 Fluorescent In Situ Hybridization 316 13.4 Immuno]based Methodologies, Biochips, and Nanosensors 317 13.5 Benefits and Limitations of Molecular Techniques 318 13.6 Conclusions and Future Perspectives 318 References 318 14 Molecular Techniques for the Detection and Identification of Yeasts in Wine 323 Cecilia Diaz, Grigori Badalyan, and Mark Bucking 14.1 Introduction 323 14.2 Methods of Identification and Detection of Biodiversity 327 14.3 Enumeration of Wine Yeasts 330 14.4 Diversity of Wine Yeasts 332 14.5 Conclusions and Future Perspectives 334 References 334 Section V Foodborne Pathogens and Food Safety 341 15 Rapid Detection of Food Pathogens Using Molecular Methods 343 R.M.U.S.K. Rathnayaka, Rakshit K. Devappa, and Sudip Kumar Rakshit 15.1 Introduction 343 15.2 Methods Used to Detect Foodborne Pathogens 344 15.3 Conclusions 355 References 355 16 Biosensor]Based Techniques: A Reliable and Primary Tool for Detection of Foodborne Pathogens 361 Moni Gupta, Baby Summuna, Sachin Gupta, and Deepika Sharma 16.1 Introduction 361 16.2 Ideal Requirements for Biosensor]Based Microbial Detection Assay 366 16.3 Need for Rapid Method 367 16.4 Classification of Biosensors 367 16.5 Conclusions and Future Perspectives 378 References 379 17 Molecular Identification and Detection of Foodborne and Feedborne Mycotoxigenic Fungi 385 Glaucia E.O. Midorikawa, Robert N.G. Miller, and Daniela M. de C. Bittencourt 17.1 Mycotoxigenic Fungi 385 17.2 Polymerase Chain Reaction]based Characterization of Mycotoxigenic Fungi 386 17.3 Genomics of Mycotoxigenic Fungi 394 17.4 Functional Genomics of Mycotoxigenic Fungi 396 17.5 Conclusions and Future Perspectives 398 References 398 18 Molecular Identification of Enteric Viruses in Fresh Produce 409 Martin D’Agostino and Nigel Cook 18.1 Introduction 409 18.2 Sample Treatment 410 18.3 Sample Receipt 410 18.4 Removal of Viruses from the Food Surfaces 410 18.5 Removal of Food Substances 411 18.6 Concentration of Viruses 411 18.7 Nucleic Acid Extraction 411 18.8 Detection Assay 412 18.9 ISO 15216]1/2:2013: The Future “Gold Standard” 413 18.10 Quantitation 415 18.11 What is a Positive? 415 18.12 Future Developments and Requirements 416 18.13 Conclusions and Future Perspectives 416 References 417 Section VI Future Perspectives 421 19 Molecular Techniques and Foodstuffs: Innovative Fingerprints, Then What? 423 Aly Farag El Sheikha and Jianping Xu 19.1 Introduction 423 19.2 Emerging Fingerprinting Technologies 424 19.3 DNA Fingerprints 426 19.4 Conclusions and Future Perspectives 428 References 431 Index 435