Cover
Title Page
Copyright Page
Dedication Page
List of Contributors
Preface
Acknowledgments
Section I: General Topics
1. 1 How to Determine the Geographical Origin of Food by Molecular Techniques
  1. 1.1 Linkage Between Food and Its Geographical Origin: Historical View
  2. 1.2 Scope and Approach
  3. 1.3 Definitions Related to Tracking of Food Origins
  4. 1.4 Driving Forces for Determining the Geo‐origin of Food
  5. 1.5 Geo‐origin Determination … Evolution of Molecular Techniques
  6. 1.6 Pros and Cons of Molecular Techniques Used as Geo‐Discriminative Tools of Food
  7. 1.7 Conclusions
  8. References
2. 2 Unraveling Pathogenic Behavior of Phytopathogens through Advanced Molecular Techniques
  1. 2.1 Introduction
  2. 2.2 Plant Pathogens: A Menace to Agricultural Productivity
  3. 2.3 Future Directions
  4. References
3. 3 Molecular Characterization of Ochratoxigenic Fungal Flora as an Innovative Tool to Certify Coffee Origin
  1. 3.1 Introduction: Coffee Factsheet
  2. 3.2 The Microflora of Coffee
  3. 3.3 Detection of Ochratoxigenic Fungi in Coffee by Molecular Techniques
  4. 3.4 Using Molecular Detection of OTA‐producing Fungi to Certify Coffee Origin: Is it Possible?
  5. 3.5 Conclusions and Future Perspectives
  6. References
4. 4 Molecular and “Omics” Techniques for Studying Gut Microbiota Relevant to Food Animal Production
  1. 4.1 Introduction
  2. 4.2 Methods for Studying Gut Microbiota Composition
  3. 4.3 Culture‐independent Techniques
  4. 4.4 Tools for Functional Studies of Gut Microbiota
  5. 4.5 “Omics”
  6. 4.6 Animal Models
  7. 4.7 Bioinformatics
  8. 4.8 Application in Poultry and Swine Research
  9. 4.9 Integrated Approaches for Studying Gut Microbiome
  10. 4.10 Conclusions and Future Directions
  11. Acknowledgments
  12. References
5. 5 Molecular Techniques for Making Recombinant Enzymes Used in Food Processing
  1. 5.1 Introduction
  2. 5.2 Molecular Strategies to Produce Recombinant Enzymes Used in the Food Industry
  3. 5.3 Applications and Safety Issues of Enzymes in the Food Industry
  4. 5.4 Conclusions and Future Perspectives
  5. References
Section II: Fruits and Vegetables
1. 6 Molecular Identification and Distribution of Yeasts in Fruits
  1. 6.1 Introduction
  2. 6.2 Molecular Methods for Distinguishing Yeast Species and Strains
  3. 6.3 Yeast Diversity in Wild/fresh Fruits
  4. 6.4 Yeast Diversity in Processed Fruits
  5. 6.5 Conclusions and Future Perspectives
  6. Acknowledgments
  7. References
2. 7 Current and New Insights on Molecular Methods to Identify Microbial Growth in Fruit Juices
  1. 7.1 Introduction
  2. 7.2 Microorganisms in Fruit Juices
  3. 7.3 Conventional Identification Techniques
  4. 7.4 Non‐conventional Identification Techniques
  5. 7.5 Molecular Techniques
  6. 7.6 Conclusions and Future Perspectives
  7. References
Section III: Fish and Meat Products (Non‐Fermented)
1. 8 Molecular Techniques Related to the Identification of the Bacterial Flora of Seafood
  1. 8.1 Introduction
  2. 8.2 Major Seafood Spoilage Bacteria
  3. 8.3 Seafood‐borne Bacterial Pathogens
  4. 8.4 Conclusions and Future Perspectives
  5. References
2. 9 Assessment of the Microbial Ecology of Meat and Meat Products at the Molecular Level: Current Status and Future Perspectives
  1. 9.1 Introduction
  2. 9.2 Extraction of Nucleic Acids
  3. 9.3 Microbial Communities Assessment
  4. 9.4 Detection of Selected Bacterial Target
  5. 9.5 Biodiversity Assessment
  6. 9.6 Conclusion and Future Perspectives
  7. References
Section IV: Fermented Foods and Beverages
1. 10 Revolution in Fermented Foods
  1. 10.1 Introduction
  2. 10.2 Historical View: Where and When Did Fermentation Start?
  3. 10.3 Fermented Foods: From the Past to the Current Era
  4. 10.4 Fermented Foods and Health Effects
  5. 10.5 Is it Possible to Trace the Geographical Origin of Fermented Foods?
  6. 10.6 Conclusions and Future Perspectives
  7. References
2. 11 Molecular Techniques for the Identification of LAB in Fermented Cereal and Meat Products
  1. 11.1 Introduction
  2. 11.2 Fermented Food Products
  3. 11.3 Lactic Acid Bacteria and Fermented Foods
  4. 11.4 Molecular Approaches Used to Study Fermenting Microflora
  5. 11.5 Identification of Lab in Fermented Cereal and Meat Products
  6. 11.6 Advantages of Molecular Techniques
  7. 11.7 Concluding Remarks
  8. Acknowledgment
  9. References
3. 12 Molecular Techniques and Lactic Acid‐Fermented Fruits and Vegetables
  1. 12.1 Introduction
  2. 12.2 Fermented Fruits and Vegetables: Between the Past and the Present
  3. 12.3 Benefits of Fermented Fruits and Vegetables
  4. 12.4 Techniques of Lab Analysis Used in Fermented Fruits and Vegetables
  5. 12.5 Future Applications
  6. 12.6 Conclusions
  7. References
4. 13 New Trends in Molecular Techniques to Identify Microorganisms in Dairy Products
  1. 13.1 Introduction
  2. 13.2 Polymerase Chain Reaction (PCR)‐based Methods
  3. 13.3 Fluorescent In Situ Hybridization
  4. 13.4 Immuno‐based Methodologies, Biochips, and Nanosensors
  5. 13.5 Benefits and Limitations of Molecular Techniques
  6. 13.6 Conclusions and Future Perspectives
  7. References
5. 14 Molecular Techniques for the Detection and Identification of Yeasts in Wine
  1. 14.1 Introduction
  2. 14.2 Methods of Identification and Detection of Biodiversity
  3. 14.3 Enumeration of Wine Yeasts
  4. 14.4 Diversity of Wine Yeasts
  5. 14.5 Conclusions and Future Perspectives
  6. References
Section V: Foodborne Pathogens and Food Safety
1. 15 Rapid Detection of Food Pathogens Using Molecular Methods
  1. 15.1 Introduction
  2. 15.2 Methods Used to Detect Foodborne Pathogens
  3. 15.3 Conclusions
  4. References
2. 16 Biosensor‐Based Techniques
  1. 16.1 Introduction
  2. 16.2 Ideal Requirements for Biosensor‐based Microbial Detection Assay
  3. 16.3 Need for Rapid Method
  4. 16.4 Classification of Biosensors
  5. 16.5 Conclusions and Future Perspectives
  6. References
3. 17 Molecular Identification and Detection of Foodborne and Feedborne Mycotoxigenic Fungi
  1. 17.1 Mycotoxigenic Fungi
  2. 17.2 Polymerase Chain Reaction‐based Characterization of Mycotoxigenic Fungi
  3. 17.3 Genomics of Mycotoxigenic Fungi
  4. 17.4 Functional Genomics of Mycotoxigenic Fungi
  5. 17.5 Conclusions and Future Perspectives
  6. References
4. 18 Molecular Identification of Enteric Viruses in Fresh Produce
  1. 18.1 Introduction
  2. 18.2 Sample Treatment
  3. 18.3 Sample Receipt
  4. 18.4 Removal of Viruses from the Food Surfaces
  5. 18.5 Removal of Food Substances
  6. 18.6 Concentration of Viruses
  7. 18.7 Nucleic Acid Extraction
  8. 18.8 Detection Assay
  9. 18.9 ISO 15216‐1/2:2013: The Future “Gold Standard”
  10. 18.10 Quantitation
  11. 18.11 What is a Positive?
  12. 18.12 Future Developments and Requirements
  13. 18.13 Conclusions and Future Perspectives
  14. References
Section VI: Future Perspectives
1. 19 Molecular Techniques and Foodstuffs: Innovative Fingerprints, Then What?
  1. 19.1 Introduction
  2. 19.2 Emerging Fingerprinting Technologies
  3. 19.3 DNA Fingerprints
  4. 19.4 Conclusions and Future Perspectives
  5. References
Index
End User License Agreement

List of Tables

Chapter 01
1. Table 1.1 Pros and cons of the molecular techniques used for determination of the geo‐origin of food products.
Chapter 03
1. Table 3.1 The global production of coffee and top producers’ statistics.
2. Table 3.2 The global consumption of coffee.
3. Table 3.3 Characteristics of the samples used for analysis of fungal communities by PCR‐DGGE.
Chapter 04
1. Table 4.1 Comparison of the characteristics of common DNA sequencing technologies.
Chapter 05
1. Table 5.1 Food‐processing enzymes produced from microorganisms.
2. Table 5.2 Food industrial enzymes and technologies involved.
Chapter 06
1. Table 6.1 Yeast species diversity among isolates obtained from grape berry surfaces.
2. Table 6.2 Yeast species diversity in isolates obtained from apple fruit surfaces.
3. Table 6.3 Yeast species diversity in isolates obtained from various citrus fruits.
4. Table 6.4 Yeast species diversity in isolates obtained from a variety of other fruit.
5. Table 6.5 Yeast species diversity in isolates obtained from wine fermentations and musts.
6. Table 6.6 Yeast species diversity in isolates obtained from apple ciders and cider musts.
7. Table 6.7 Yeast species diversity in isolates obtained from processed olives.
8. Table 6.8 Yeast species diversity in isolates obtained from fruit juice processing.
9. Table 6.9 Yeast species diversity in isolates obtained from other processed fruits.
Chapter 07
1. Table 7.1 Most frequently identified yeasts in fruit juices.
Chapter 08
1. Table 8.1 PCR primers and DNA probes.*
Chapter 09
1. Table 9.1 Genomic regions and primers used in assessing the prokaryotic and eukaryotic content of the microecosystem of meat and meat products by PCR‐DGGE.
2. Table 9.2 Primer sequences, target genes, and amplicon sizes used in multiplex format for pathogen detection in meat and meat products.
3. Table 9.3 Sequences of primers and probes used for the simultaneous and quantitative detection of bacterial pathogens in meat and meat products.
Chapter 10
1. Table 10.1 Examples of fermented foods in various worldwide regions.
2. Table 10.2 Average consumption of fermented foods.
3. Table 10.3 Dominant bacteria species in Minas cheese identified by DGGE.
Chapter 11
1. Table 11.1 An overview of common and traditional fermented food products.
2. Table 11.2 Examples of different fermented foods categories and specific LAB strains.
3. Table 11.3 Examples of conventional and molecular techniques employed to identify LAB in fermented cereal products.
4. Table 11.4 Examples of conventional and molecular techniques used to identify lactic acid bacteria (LAB) in fermented meat products.
5. Table 11.5 Advantages and limitations of the different molecular techniques available to identify LAB.
Chapter 12
1. Table 12.1 Examples of fermented fruits and vegetables.
2. Table 12.2 The pros and cons of genotypic identification methods for lactic acid bacteria.
3. Table 12.3 Comparison between MALDI‐TOF MS and other identification methods.
Chapter 16
1. Table 16.1 Foodborne outbreaks caused by pathogenic microorganisms.
Chapter 19
1. Table 19.1 Advantages and limitations of different fingerprints.

List of Illustrations

Chapter 01
1. Figure 1.1 Developments in the history of geographical origin determination.
2. Figure 1.2 Analytic structure illustrating the scope of this chapter on determining the geo‐origin of food.
3. Figure 1.3 Interaction between consumers, food product, and origin.
4. Figure 1.4 What are the benefits of applying an effective traceability system on food chain components?
5. Figure 1.5 European food products with protected signature names.
6. Figure 1.6 Molecular techniques used for determining the geographical origin products. CE, capillary electrophoresis; ELISA, enzyme linked immunosorbent assay; GC‐MS, gas chromatography mass spectrometry; HPLC, high‐performance liquid chromatography; ICP‐MS, inductively coupled plasma mass spectrometry; IR, infrared spectroscopy; IRMS, isotope ratio mass spectrometry; NMR, nuclear magnetic resonance spectroscopy; PTR‐MS, proton transfer reaction mass spectrometry.
Chapter 02
1. Figure 2.1 Representation of the need for disease diagnosis.
2. Figure 2.2 Various methods of disease diagnosis. ELISA, enzyme‐linked immunosorbent assay; GC‐MS, gas chromatography mass spectrometry; PCR, polymerase chain reaction; RIA, radioimmunoassay.
Chapter 03
1. Figure 3.1 Map of coffee‐producing countries.
2. Figure 3.2 Photo of coffee flowers (Coffea arabica).
3. Figure 3.3 Photo of coffee fruit (Coffea arabica).
4. Figure 3.4 Liberica, robusta, and arabica: coffee bean differentiation.
5. Figure 3.5 Diagram showing stages of coffee production.
6. Figure 3.6 How PCR‐DGGE works with coffee samples as a traceability and detection tool.
7. Figure 3.7 PCR‐DGGE of 28S rDNA band profiles of both coffee varieties (arabica, robusta) from five regions of Cameroon. Samples were taken during two treatments (wet and dry). BAF, Bafang; BFSS, Bafoussam; DSCH, Dschang; M, Marker; MEL, Melong; SAN, Santchou. 1: A. carbonarius; 2: A. ochraceus; 3: A. niger.
8. Figure 3.8 Cluster analysis of of 28S rDNA band profiles of both coffee varieties (arabica, robusta) from five regions of Cameroon: Bafoussam, Dschang, Bafang, Santchou, and Melong.
Chapter 04
1. Figure 4.1 Molecular and “omics” approaches for studying the gut microbiome. The culture‐independent methods in combination with humanized animal models and bioinformatics provide a more comprehensive view of integrated approaches to study the gut microbiome, including composition, function, and host–microbe interaction. Animal models include gnotobiotic and transgenic/knock‐out animals. Human subjects refer to healthy humans or humans associated with acute or chronic diseases.
Chapter 05
1. Figure 5.1 Procedural flow sheets of directed evolution and rational design strategies.
2. Figure 5.2 Comparison of basic schemes of DNA shuffling, StEP, and RACHITT (Neylon 2004).
3. Figure 5.3 Schematic diagram of the RAISE method.
4. Figure 5.4 Schematic diagram of site‐directed mutagenesis by overlap extension. The dsDNA and synthetic oligonucleotides are represented by lines with arrows indicating the 5’‐to‐3’ orientation. The site of mutagenesis is indicated by the small black rectangle. Oligonucleotides are denoted by lower‐case letters and PCR products are denoted by pairs of upper‐case letters corresponding to the oligo primers used to generate that product. The boxed portion of the figure represents the proposed intermediate steps taking place during the course of reaction (3), where the denatured fragments anneal at the overlap and are extended 3’ by DNA polymerase (dotted line) to form the mutant fusion product. By adding additional primers “a” and “d” the mutant fusion product is further amplified by PCR.
5. Figure 5.5 An overview of food enzyme applications.
Chapter 06
1. Figure 6.1 Organization of the nuclear ribosomal RNA gene cluster in fungi. Common primers used for sequencing are also shown. IGS, intergenic spacer region; ITS, internal transcribed spacer region; LSU, large subunit; SSU, small subunit.
Chapter 08
1. Figure 8.1 A grouping of the Gram‐negative asporogenous rods, polar‐flagellate, oxidase positive and not sensitive to 2.5 i.u. of penicillin, on the results of four other tests. Redrawn from Shewan et al. (1960a) with permission.
2. Figure 8.2 Outline of the sequence of tests used in the screening of bacterial cultures from seafood. Redrawn from Shewan et al. (1960b) with permission. ^aAllocated to the genus Achromobacter in original figure.
3. Figure 8.3 Typical colonies with black centers of Shewanella putrefaciens on peptone iron agar.
4. Figure 8.4 Genetic transformation of Psychrobacter immobilis whereby growth of recipient A351‐Hyx‐7 is genetically transformed by DNA from a fishery isolate of P. immobilis, allowing growth on an M9A plate lacking hypoxanthine.
5. Figure 8.5 Relationship between the relative fluorescent intensity of DNA bands derived from PCR amplification and the number of DNA target sequences derived from CFU. Plotted values are the means and standard deviations derived from three independent assays. Inset: Image of PCR‐amplified product of mixed culture of bacterial fish flora with varying CFU/PCR: lanes 1–6, 5 × 10², 1 × 10³, 5 × 10³, 1 × 10⁴, 5 × 10⁴, and 1 × 10⁵ CFU respectively). Numbers above plotted points correspond to insert lanes.
6. Figure 8.6 Relationship between the relative fluorescent intensity of DNA bands and corresponding CFU derived from plate counts per gram of fish tissue. The dotted line corresponds to the extrapolated standard curve from Figure 8.5. The mean values from three independent assays for each fillet were plotted.
Chapter 10
1. Figure 10.1 The main developments of fermented foods through the history of mankind.
2. Figure 10.2 Locations of the regions traditionally producing Minas cheese.
3. Figure 10.3 PCR‐DGGE 16S rDNA profiles of Minas cheese bacteria from four regions (Araxá, Serro, Cerrado, and Canastra), Brazil.
4. Figure 10.4 Cluster analysis of 16S rDNA profiles of Minas cheese bacteria from four regions (Araxá, Serro, Cerrado, and Canastra), Brazil.
Chapter 11
1. Figure 11.1 Common molecular approaches available for the identification of LAB in fermented food products.
Chapter 12
1. Figure 12.1 How to ferment fruits and vegetables.
2. Figure 12.2 Some phenotypic techniques for identification of lactic acid bacteria.
3. Figure 12.3 Procedural flowcharts for some genotypic methods.
4. Figure 12.4 Procedural steps for the ribotyping technique.
5. Figure 12.5 Pulsed‐field gel electrophoresis (PFGE) methodology step by step.
6. Figure 12.6 Assessment of different microbial communities by DGGE. https://en.wikipedia.org/wiki/File:Step‐by‐step_procedure_of_using_DGGE_analysis_in_microbiology.pdf. Licensed under CC BY‐SA 3.0.
7. Figure 12.7 Matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF MS) workflow for bacterial identification.
Chapter 13
1. Figure 13.1 Main PCR‐based techniques used for identification and quantification of microbial growth in dairy products. DGGE, denaturing gradient gel electrophoresis; LH, length heterogeneity; RT, reverse transcription; SSCP, single‐strand conformation polymorphism; T‐RFLP, terminal restriction fragment length polymorphism; TTGE, temporal temperature gradient electrophoresis.
2. Figure 13.2 Steps of a T‐RFLP analysis.
3. Figure 13.3 Main steps of FISH analysis for bacterial in situ identification.
Chapter 14
1. Figure 14.1 Schematic representation of EMA‐PCR. Exclusion of EMA from live but not dead cells leads to cross‐linking of DNA in dead cells by EMA and then amplification of DNA sequences of live but not dead cells by PCR.
Chapter 15
1. Figure 15.1 Steps of nucleic acid hybridization process using reverse transcription for production of DNA fragments from RNA.
Chapter 16
1. Figure 16.1 Components of biosensor.
2. Figure 16.2 Biocomponents and transducers in a biosensor system. FET, field‐effect transistor.
3. Figure 16.3 Bacterial bioluminescence.
4. Figure 16.4 Electrochemical cell.
5. Figure 16.5 Electrochemical biosensor as screen‐printed electrode.
6. Figure 16.6 Diagrammatic illustration of the SPR principle (Quinn & Kennedy 1999) showing the Kretschmann (Kretschmann 1971) prism arrangement of the type used in BIA core instrumentation.
7. Figure 16.7 Piezoelectric biosensor.
8. Figure 16.8 Surface acoustic wave propagation sensor.
Chapter 19
1. Figure 19.1 A summary of food fingerprinting approaches. ELISA, enzyme‐linked immunosorbent assay; ESI‐MS, electrospray ionization mass spectrometry; GC, gas chromatography; HPLC, high‐performance liquid chromatography; HR‐MS, high‐resolution mass spectrometry; ICP‐MS, inductively coupled plasma‐mass spectrometry; IR, infrared spectroscopy; LC, liquid chromatography; MALDI‐TOF MS, matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry; MIR, mid‐infrared; NIR, near‐infrared; NMR, nuclear magnetic resonance spectroscopy; Q‐TOF‐MS, quadrupole‐time‐of‐flight mass spectrometry; SDS‐PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis; 2‐DE, two‐dimensional gel electrophoresis; UPLC, ultra‐performance liquid chromatography; UV, ultraviolet and visible spectroscopy.
2. Figure 19.2 Food fingerprinting: analytical approaches and foodstuffs.

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Library of Congress Cataloging‐in‐Publication Data
Names: El Sheikha, Aly F., (Researcher), 1978– editor. | Levin, Robert E., 1930– editor. | Xu, Jianping (Professor of Biology), 1965– editor.
Title: Molecular techniques in food biology : safety, biotechnology, authenticity and traceability / edited by Aly Farag El Sheikha, Robert Levin, Jianping Xu.
Description: First edition. | Hoboken, NJ : John Wiley & Sons, 2018. | Includes bibliographical references and index. |
Identifiers: LCCN 2017040685 (print) | LCCN 2017047614 (ebook) | ISBN 9781119374596 (pdf) | ISBN 9781119374619 (epub) | ISBN 9781119374602 (cloth)
Subjects: LCSH: Food–Biotechnology. | Food–Safety measures. | Food–Microbiology.
Classification: LCC TP248.65.F66 (ebook) | LCC TP248.65.F66 M655 2018 (print) | DDC 664/.024–dc23
LC record available at https://lccn.loc.gov/2017040685

Cover Design: Aly El Sheikha
Cover Images: (Background) © Max Krasnov/Shutterstock;(World map) © PASHA18/Gettyimages;(Fungus) © KATERYNA KON/SCIENCE PHOTO LIBRARY/Gettyimages;(Yeast cells) © Science Photo Library – STEVE GSCHMEISSNER/Gettyimages;(Bacteria) © David Marchal/iStockphoto; (Virus) © Antti‐Pekka Lehtinen/iStockphoto;(Food) © margouillat photo/Shutterstock; (DNA) © Tribalium/Shutterstock;(Metabolomic chromatogram, Genotyping example, and PCR‐DGGE) Courtesy of Aly El Sheikha

List of Contributors

Grigori Badalyan
Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) Schmallenberg
Germany

Francisco J. Barba
Faculty of Pharmacy
Preventive Medicine and Public Health
Food Sciences, Toxicology and Forensic Medicine Department
University of Valencia
Valencia
Spain

Sonia Barba‐Orellana
Centro Sanitario Integrado de Xirivella
Consorci Hospital General Universitari València
Valencia
Spain

Avantina S. Bhandari
Department of Nutrition
Isabella Thoburn College
Lucknow
India

Daniela M. de C. Bittencourt
Research & Development Department
Brazilian Agricultural Research Corporation – Embrapa
Parque Estação Biológica (PqEB)
Brasília
Brazil

Mark Bücking
Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)
Schmallenberg
Germany

Nigel Cook
Fera Science Ltd
Sand Hutton
York, UK

Martin D’Agostino
Fera Science Ltd
Sand Hutton
York, UK

Rakshit K. Devappa
Biorefining Research Institute
Lakehead University
Thunder Bay
Canada

Cecilia Díaz
Fraunhofer Institute for Molecular Biology and Applied Ecology (IME)
Schmallenberg
Germany

Eleftherios H. Drosinos
Laboratory of Food Quality Control and Hygiene
Department of Food Science and Human Nutrition
Agricultural University of Athens
Athens
Greece

Aly Farag El Sheikha
Department of Biology
McMaster University
Hamilton, Ontario, Canada

Faculty of Agriculture
Department of Food Science and Technology
Minufiya University
Minufiya Government
Egypt

Joshua Gong
Guelph Research and Development Center
Agriculture and Agri‐Food Canada
Guelph, Ontario, Canada

Moni Gupta
Division of Biochemistry
Faculty of Basic Sciences
Sher‐e‐Kashmir University of Agricultural Sciences and Technology of Jammu
Jammu & Kashmir
India

Sachin Gupta
Division of Plant Pathology
Faculty of Agriculture
Sher‐e‐Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu & Kashmir
India

Agni Hadjilouka
Laboratory of Food Quality Control and Hygiene
Department of Food Science and Human Nutrition
Agricultural University of Athens
Athens, Greece

Wenjing Hua
Department of Biology
McMaster University
Hamilton, Ontario, Canada

Malik Altaf Hussain
Department of Wine
Food and Molecular Biosciences
Lincoln University
Christchurch
New Zealand

Ehsan Khafipour
Department of Animal Science
University of Manitoba
Winnipeg, Manitoba
Canada

Mohamed Koubaa
Laboratoire Transformations Intégrées de la Matière Renouvelable
Centre de Recherche de Royallieu
Université de Technologie de Compiègne
Sorbonne Universités
Compiègne
France

Robert E. Levin
Department of Food Science
University of Massachusetts
Massachusetts, Amherst
USA

Gláucia E.O. Midorikawa
Laboratório de Microbiologia: Interação Planta‐Praga
Instituto de Ciências Biológicas
Departamento de Biologia Celular
Universidade de Brasília
Brasília
Brazil

Robert N.G. Miller
Laboratório de Microbiologia: Interação Planta‐Praga
Instituto de Ciências Biológicas
Departamento de Biologia Celular
Universidade de Brasília
Brasília
Brazil

Nadège Donkeng Nganou
Department of Food Science and Nutrition
Food Microbiology Laboratory
National School of Agro‐Industrial Sciences
University of Ngaoundere
Ngaoundere
Cameroon

Spiros Paramithiotis
Laboratory of Food Quality Control and Hygiene
Department of Food Science and Human Nutrition
Agricultural University of Athens
Athens
Greece

Francisco Quilez
Valencian School for Health Studies (EVES)
Professional Training Unit
Valencia
Spain

Sudip Kumar Rakshit
Biorefining Research Institute
Lakehead University
Thunder Bay
Canada

R.M.U.S.K. Rathnayaka
Faculty of Applied Science
Sabaragamuwa University
Belihuloya
Sri Lanka

Shahin Roohinejad
Department of Food Technology and Bioprocess Engineering
Max Rubner‐Institut
Federal Research Institute of Nutrition and Food
Karlsruhe
Germany

Burn and Wound Healing Research Center
Division of Food and Nutrition
Shiraz University of Medical Sciences
Shiraz
Iran

Elena Roselló‐Soto
Faculty of Pharmacy
Preventive Medicine and Public Health
Food Sciences
Toxicology and Forensic Medicine Department
University of Valencia
Valencia
Spain

Deepika Sharma
Division of Plant Pathology
Faculty of Agriculture
Sher‐e‐Kashmir University of Agricultural Sciences and Technology of Jammu
Jammu & Kashmir
India

Neeta Sharma
Department of Botany
Lucknow University
Lucknow
India

Baby Summuna
Division of Plant Pathology
Faculty of Agriculture
Sher‐e‐Kashmir University of Agricultural Sciences and Technology of Jammu
Jammu & Kashmir
India

Justine Ting
Department of Biology
McMaster University
Hamilton
Ontario, Canada

Jianping Xu
Department of Biology
Mc
Master University
Hamilton
Ontario, Canada

Rui Xu
Department of Biology
Mc
Master University
Hamilton
Ontario, Canada

Chengbo Yang
Department of Animal Science
University of Manitoba
Winnipeg
Manitoba, Canada

Preface

With increasing population size and heightened awareness of food quality, safety, and authenticity, food production and food safety have never been more important in human history. Over the decades since the introduction of molecular biology, significant improvements have been made to enhance food production, enrich food nutrition, and increase food quality and food authenticity. This book describes recent advances in food biology from the viewpoint of the development and use of molecular techniques. Our focus is the microbes associated with food and food products and the diversity of microbe‐food interactions.

Molecular Techniques in Food Biology: Safety, Biotechnology, Authenticity & Traceability presents a summary of the broad microbe‐food interactions, covering food microbiology, food mycology, biochemistry, microbial ecology, food biotechnology and bioprocessing, food authenticity, food origin, and food science and technology. Particular emphasis is placed on how modern molecular techniques have been and can be used to enhance food biology research, to help monitor and assess food safety and quality, and to establish effective food traceability and inspection systems.

The book comprises 19 chapters, broadly divided into six sections. The first section contains five chapters that deal with general topics to provide a global overview of safety, biotechnology, authenticity, and traceability issues related to plant‐ and animal‐based foods. The second section includes two chapters on the molecular techniques used in studying microbes found in fruits and vegetables. The third section consists of two chapters dealing with the assessment of microbial ecology of non‐fermented fish and meat products at the molecular level. The fourth section includes five chapters capturing the excitement of recent advances in molecular approaches made to decipher the microbial mechanisms in fermented foods and beverages. The fifth section comprises four chapters covering the detection of foodborne pathogens by new molecular strategies. The last chapter provides an overview of the current status and future prospects of molecular food fingerprinting.

An emerging theme among these chapters is that the detection, differentiation, and identification of microorganisms associated with food are ambiguous when they are exclusively based on morphological, physiological, and biochemical characteristics. The application of molecular tools has vastly enhanced our ability to identify these microbes and analyze their activities. In addition, there is increasing recognition that a systematic view of food products is needed in order to reveal the complexities of microbe‐food interactions. These complexities include the changing trophic relationships among interacting organisms throughout the food production process. For example, beneficial microbes can help plant and animal growth while pathogenic ones cause diseases and deter their growth. During harvesting, environmental microbes from their immediate environments are introduced which could cause spoilage. During the preparation of fine processed food, microbes and/or microbial enzymes are often needed to achieve desirable properties. Throughout these processes, microbes leave their signatures on the food that can be used for tracking and authentication purposes. For contaminated foods associated with disease outbreaks, analyses of microbial communities and populations are needed to help track the origins and spread of the specific pathogens.

We are fortunate to have experts from diverse backgrounds and agencies contributing to this book. They bring perspectives from academia, research institutes, industry, and government agencies. We believe the book will be a useful reference for research scientists, regulatory authorities, food microbiologists and technologists, epidemiologists, biotechnologists, food manufacturers, policymakers involved in food regulation, and the general public interested in food biology.

Aly Farag El Sheikha
Robert E. Levin
Jianping Xu

Molecular Techniques in Food Biology

Safety, Biotechnology, Authenticity and Traceability

List of Contributors

Preface

Acknowledgments

Section I
General Topics