Quantitative Microbiology in Food Processing
Modeling the Microbial Ecology

List of contributors xvi

Part I Introductory section 1

1 Introduction to the microbial ecology of foods 3
D. Roy and G. LaPointe

1.1 Introduction 3

1.2 Role of food characteristics and environment on microbial fate 4

1.3 Understanding microbial growth, death, persistence, competition, antagonism and survival in food 8

1.4 Methods to study the microbial ecology of foods 11

1.5 Perspectives on applying food ecosystem modeling 12

References 13

2 Predictive microbiology: mathematics towards understanding the fate of food‐borne microorganisms in food processing 16
P.N. Skandamis and E.Z. Panagou

2.1 Introduction 16

2.2 Probability and kinetic models for food processing and HACCP 18

2.3 Thermal inactivation 32

2.4 Non‐thermal inactivation and modeling stress‐adaptation strategies 34

2.5 Fermentation: a dynamic environment for microbial growth and pathogen inactivation 38

2.6 Colonial versus planktonic type of growth: modes of microbial existence on surfaces and in liquid, semi‐liquid, and solid foods 41

2.7 Modeling microbial transfer between processing equipment and foods 45

2.8 Alternative multivariate approaches: the use of bioinformatics for characterizing spoilage and product classification 49

References 51

3 Principles of unit operations in food processing 68
A. Ibarz and P.E.D. Augusto

3.1 Introduction 68

3.2 Principles of transport phenomena 68

3.3 Principles and unit operations of momentum transfer 69

3.4 Principles and unit operations of heat transfer 73

3.5 Principles and unit operations of mass transfer 81

3.6 Conclusions 82

References 83

Part II Impact of unit operations on microorganisms of relevance in foods 85

4 Impact of materials handling at pre‐ and post‐harvest operations on the microbial ecology of foods of vegetable origin 87
A.N. Olaimat, P.J. Delaquis, and R.A. Holley

4.1 Introduction 87

4.2 The production environment 90

4.3 Soil 91

4.4 Fertilizers derived from animal wastes 92

4.5 Irrigation 93

4.6 Harvesting and handling 98

4.7 Postharvest processing 99

4.8 Packaging, storage, and transportation 101

4.9 Conclusions 103

References 103

5 Impact of heating operations on the microbial ecology of foods 117
E. Xanthakis and V.P. Valdramidis

5.1 Background and basic information of heating operations 117

5.2 Quantitative aspects and how unit operations impact on food‐borne microorganisms 131

5.3 Application of F‐value concept 132

5.4 Dealing with non‐linearity 133

5.5 Development of new concepts to assess heat processes 135

5.6 Microbial safety and stability of heating operations: challenges and perspectives 136

References 136

6 Impact of refrigeration operations on the microbial ecology of foods 142
L. Huang

6.1 Introduction 142

6.2 Refrigeration as a unit operation 143

6.3 Dynamic effect of chilling on growth of C. perfringens during cooling 147

References 158

7 Impact of dehydration and drying operations on the microbial ecology of foods 160
F. Pérez‐Rodríguez, E. Carrasco, and A. Valero

7.1 Introduction 160

7.2 Modeling the drying process in food 161

7.3 Modeling microbial survival/inactivation in drying/dehydration processes 163

7.4 Example of application/development of predictive microbiology models for describing microbial death during drying processes 169

7.5 Conclusions 173

References 173

8 Impact of irradiation on the microbial ecology of foods 176
S. Unluturk

8.1 Introduction 176

8.2 Ionizing radiation 176

8.3 Non‐ionizing radiation 180

References 187

9 Impact of high‐pressure processing on the microbial ecology of foods 194
S. Mukhopadhyay, D.O. Ukuku, V. Juneja, and R. Ramaswamy

9.1 Introduction 194

9.2 Processing operation 195

9.3 Bacteria and enzyme inactivation 195

9.4 Effect of high pressure on fruit and vegetable products 198

9.5 Effect of HHP on meat and other food products 198

9.6 Effect of added antimicrobial on pathogen inactivation by high‐pressure processing (hurdle approach) 199

9.7 High‐pressure carbon dioxide (HPCD) disinfection 200

9.8 Effect of HHP on bacteria, virus, insects, and other organisms 201

9.9 Effect of HHP on quality: color, flavor, texture, sugar, totally soluble, and insolubles 203

9.10 Advantages and disadvantages of using HHP 205

9.11 Applications and conclusions 205

References 206

10 Impact of Vacuum packaging, modified and controlled atmosphere on the microbial ecology of foods 217
L. Angiolillo, A. Conte, and M.A.D. Nobile

10.1 Introduction 217

10.2 Vacuum packaging 218

10.3 Controlled atmosphere 219

10.4 Modified atmosphere packaging 220

References 223

11 Impact of fermentation on the microbial ecology of foods 226
M. Mataragas, K. Rantsiou, and L. Cocolin

11.1 Introduction 226

11.2 Fermentations: microbial ecology and activity 227

11.3 Factors affecting food‐borne pathogen inactivation during fermentation 227

11.4 Challenge tests 229

11.5 Predictive modeling 230

11.6 Conclusions 236

References 236

12 Impact of forming and mixing operations on the microbial ecology of foods: focus on pathogenic microorganisms 241
J.C.C.P. Costa, G.D. Posada‐Izquierdo, F. Perez‐Rodriguez, and R.M. Garcia‐Gimeno

12.1 Forming 241

12.2 Homogenizing 244

12.3 Mixing 246

References 248

13 Impact of specific unit operations on food‐borne microorganisms: curing, salting, extrusion, puffing, encapsulation, absorption, extraction, distillation, and crystallization 250
E. Ortega‐Rivas, S.B. Perez‐Vega, and I. Salmeron

13.1 Introductory remarks 250

13.2 Burden of food‐borne illnesses 250

13.3 Food safety and food quality 251

13.4 Prevention and control through processing 251

13.5 Conclusions and prospects for the future 260

References 261

14 Impact of food unit operations on virus loads in foods 263
D. Li, A.D. Keuckelaere, and M. Uyttendaele

14.1 Introduction 263

14.2 The use of surrogate viruses to assess inactivation processes 263

14.3 Virus contamination in food processing 264

14.4 Survival of virus in the food processing chain 267

14.5 Effect of food preservation techniques on the virus load 267

14.6 Conclusion and perspectives 280

References 281

15 Impact of food unit operations on parasites in foods: focus on selected parasites within the fresh produce industry 288
L.J. Robertson

15.1 Background and introduction 288

15.2 Detection of selected parasites in fresh produce 299

15.3 Effects of fresh produce treatments on selected parasites 303

15.4 Conclusion 315

References 316

16 Impact of food unit operations on probiotic microorganisms 327
A. Gandhi and N.P. Shah

16.1 Introduction 327

16.2 Probiotic products 328

16.3 probiotics and environmental stress: cellular mechanisms and resistance 328

16.4 Enhancing stress resistance of probiotics 332

16.5 Conclusion 334

References 334

Part III Microbial ecology of food products 339

17 Microbial ecology of fresh vegetables 341
J. Zheng, J. Kase, A. De Jesus, S. Sahu, A.E. Hayford, Y. Luo, A.R. Datta, E.W. Brown, and R. Bell

17.1 Introduction 341

17.2 Prevalence and diversity of microbial communities on fresh vegetables (post‐harvest) 341

17.3 Post‐harvest persistence, colonization, and survival on fresh vegetables 342

17.4 Routes of contamination during post‐harvest handling of fresh and fresh‐cut vegetables 345

17.5 Microbial adaptation on produce commodity 347

17.6 Effective post‐harvest intervention technologies 348

References 350

18 Microbial ecology of fruits and fruit‐based products 358
S. Paramithiotis, E.H. Drosinos, and P.N. Skandamis

18.1 Introduction 358

18.2 Fresh whole fruits 359

18.3 Minimally processed fruits 367

18.4 Processed fruits 372

Acknowledgments 374

References 374

19 Microbial ecology of cereal and cereal‐based foods 382
A. Bevilacqua, M. Sinigaglia, and M.R. Corbo

19.1 Introduction 382

19.2 Sourdough 382

19.3 Ethnic fermented foods 384

19.4 Spoilage of cereals and cereal products 385

References 388

20 Microbial ecology of nuts, seeds, and sprouts 390
M.S. Rhee, S.A. Kim, and N.H. Kim

20.1 Introduction 390

20.2 Definition and classification of nuts, seeds, and sprouts 390

20.3 Microbial ecology of nuts and seeds 391

20.4 Microbial ecology of sprouts and their corresponding seeds 400

20.5 Implications and perspectives 409

References 410

21 Microbial ecology of eggs: a focus on Salmonella and microbial contamination in post‐harvest table shell egg production 416
S.C. Ricke

21.1 Introduction 416

21.2 Historical and current trends in commercial egg production 417

21.3 Egg production management on the farm and incidence of Salmonella 420

21.4 Egg processing and microbial contamination: general aspects 421

21.5 Microbial contamination during egg collection at the farm to in‐line processing 423

21.6 Microbial contamination during transportation to off‐line egg processing facilities 424

21.7 Microbial contamination during egg processing 425

21.8 Egg washwater and sanitation 426

21.9 Egg retail and microbial contamination 428

21.10 Conclusions and future directions 429

Acknowledgment 431

References 431

22 Microbial ecology of beef carcasses and beef products 442
X. Yang

22.1 Introduction 442

22.2 Carcass production process 442

22.3 Carcass breaking 451

References 455

23 Microbial ecology of pork meat and pork products 463
L. Iacumin and J. Carballo

23.1 Introduction 463

23.2 Pork meat as a substrate for microbial growth: chemical and physical characteristics 464

23.3 Microbial ecology of fresh pork meat: sources of contamination and microbial groups 465

23.4 Microbial ecology of chilled pork meat 467

23.5 Microbial ecology of vacuum/modified atmosphere packaged pork meat 468

23.6 Microbial ecology of marinated pork meat 469

23.7 Microbial ecology of cured and fermented/ripened pork meats 470

23.8 Microbial ecology of high‐pressure preserved pork meat 473

References 474

24 Microbial ecology of poultry and poultry products 483
S. Buncic, D. Antic, and B. Blagojevic

24.1 Introduction 483

24.2 Microbial hazard identification and prioritization 483

24.3 Microbial aspects of poultry processing at abattoirs 484

24.4 Microbial aspects of derived poultry meat products 492

References 497

25 Microbial ecology of seafoods: a special emphasis on the spoilage microbiota of North Sea seafood 499
K. Broekaert, G. Vlaemynck, and M. Heyndrickx

25.1 Introduction 499

25.2 Total viable counts (TVC s) and microorganisms identified depends on the method used 499

25.3 The initial microbiota of marine fish 501

25.4 Raw seafood 503

25.5 Processing – lightly preserved seafood 506

25.6 A case study: brown shrimp (Crangon crangon) (adapted from Broekaert et al. 2013) 509

References 513

26 Microbial ecology of mayonnaise, margarine, and sauces 519
O. Sagdic, F. Tornuk, S. Karasu, M.Z. Durak, and M. Arici

26.1 Introduction 519

26.2 Mayonnaise 519

26.3 Margarine 523

26.4 Sauces and salad dressings 525

26.5 Conclusion 527

References 529

27 Microbial ecology of confectionary products, honey, sugar, and syrups 533
M. Nascimento and A. Mondal

27.1 Introduction 533

27.2 Cocoa and chocolate 533

27.3 Nuts and peanut butter 535

27.4 Honey 538

27.5 Sugar 539

27.6 Syrups 539

27.7 Conclusion 540

References 540

28 Microbial ecology of wine 547
E. Vaudano, A. Costantini, and E. Garcia‐Moruno

28.1 Introduction 547

28.2 Biodiversity of grape microorganisms 547

28.3 Microorganism ecology in winemaking 548

28.4 Microorganism ecology during aging 550

28.5 Microbial identification by classical methods 551

28.6 Microbial identification by molecular methods 551

References 555

29 Microbial diversity and ecology of bottled water 560
C.M. Manaia and O.C. Nunes

29.1 Definitions of bottled water 560

29.2 Characteristics of mineral and spring water 562

29.3 Useful methods to study bottled water microbiota 565

29.4 Microbiological diversity 568

29.5 Bottling effect 573

29.6 Microbiological contamination 574

29.7 A new perspective on microbiological quality and safety 576

Acknowledgments 577

References 577

Part IV Closing section 581

30 Microbial risk assessment: integrating and quantifying the impacts of food processing operations on food safety 583
J.‐C. Augustin, M. Ellouze, and L. Guillier

30.1 Introduction 583

30.2 Basic processes encountered during food processing operations 584

30.2.1 Microbial processes 584

30.3 Risk‐based objectives for each processing operation 590

30.4 Conclusion 595

References 596

31 Quorum sensing and microbial ecology of foods 600
V.A. Blana, A. Lianou, and G.‐J.E. Nychas

31.1 Introduction 600

31.2 Quorum sensing and microbial behavior 601

31.3 Quorum sensing and food ecology 606

31.4 Quorum quenching 610

References 611

32 Heterogeneity in Bacillus subtilis spore germination and outgrowth: an area of key challenges for “omics” in food microbiology 617
R. Pandey and S. Brul

32.1 Bacterial spores in the food industry 617

32.2 The Bacillus genus 618

32.3 Sporulation cycle 618

32.4 Endospore structure and its resistance 619

32.5 Spore germination and outgrowth 620

32.6 Heterogeneity in bacterial (spore) physiology during germination and outgrowth 623

32.7 Steps towards single‐cell physiology and “omics” measurements 625

References 626

33 Role of stress response on microbial ecology of foods and its impact on the fate of food‑borne microorganisms 631
A. Alvarez‐Ordóñez, M. López, and M. Prieto

33.1 Introduction 631

33.2 Acquisition of permanent stress tolerance through adaptive mutagenesis 631

33.3 Transient adaptive responses to stress: modulation of membrane fluidity as an example 634

33.4 Using food components to survive under harsh conditions 636

33.5 The balance between self‐preservation and nutritional competence (SPANC) 639

33.6 Conclusions and future prospects 641

Acknowledgment 643

References 643

Index 649

Prof. Dr. Anderson de Souza Sant'Ana, Department of Food science, Faculty of Food Engineering, University of Campinas, Sao Paulo, Brazil.
Anderson de Souza Sant'Ana is an Industrial Chemist, Master and PhD in Food Science. As an Industrial Chemist his interests are focused on the microbiological aspects involving the handling and transformation of raw materials into processed food products. He has authored more than 40 articles in international referred journals and is reviewer of more than 40 scientific peer-reviewed journals in food science area. Currently, he is editor-in-chief of Food Research International, Regional editor (South America) of the British Food Journal, associate editor of Acta Amazonica, handling editor of Journal of Applied Microbiology (Wiley) and Letters in Applied Microbiology (Wiley), and editorial board member of Food Bioscience (Elsevier) and Applied and Environmental Microbiology (Wiley). Currently, he is Professor of Food Microbiology, in the Faculty of Food Engineering at University of Campinas in Sao Paulo, Brazil, where he teaches Microbiology of Food Processing, Thermobacteriology Applied to Food Processing, and Microbiology and Fermentations for undergraduate course in Food Engineering, and Quantitative Microbiology of Food Processing and Quantitative Aspects of Food Stability and Safety for the Graduation Program in Food Science.