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
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 GeoÂ]origin of Food 8
1.5 GeoÂ] origin Determination … Evolution of Molecular Techniques 13
1.6 Pros and Cons of Molecular Techniques Used as GeoÂ]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 OTAÂ]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 CultureÂ] 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 RoselloÂ]Soto, Sonia BarbaÂ]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 NonÂ] 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 SeafoodÂ]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 AcidÂ]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 RoselloÂ]Soto, Sonia BarbaÂ]Orellana, Francisco J. Barba, Francisco Quilez, Shahin Roohinejad, and Mohamed Koubaa
13.1 Introduction 309
13.2 Polymerase Chain Reaction (PCR)Â]based Methods 310
13.3 Fluorescent In Situ Hybridization 316
13.4 ImmunoÂ]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 BiosensorÂ]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 BiosensorÂ]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 ReactionÂ]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 15216Â]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
