Preface xxi
List of Contributors xxii
Acknowledgments xxviii
Introduction xxix
Section 1 Good Microbes in Medicine 1
Co-Edited by Hauke Smidt and Frans J. de Bruijn
Chapter 1 Modern Medicine Relies on the Help of Microorganisms – From Vaccine Production to Cancer Medication 3
Leticia Parizotto, Larissa Brumano, Eduardo Kleingesinds, and Adalberto Pessoa Junior
1.1 Introduction: Good Microorganisms and Our Health 3
1.2 Bad Microorganisms: Epidemics Boosted Modern Medicine 4
1.3 Antimicrobial Peptides: A New Therapeutic Alternative to Antibiotics? 4
1.4 Microorganisms as Tools: Recombinant DNA Technology (rDNAT) 5
1.5 Vaccines: The Use of Microorganisms in the Frontline against Diseases 7
1.6 Anticancer Drugs: Many Ways to Fight Cancer with Good Microorganisms 8
1.7 Gene Therapy: The Future of Modern Medicine 9
1.8 Concluding Remarks and Perspectives 10
Acknowledgments 10
Chapter 2 How Nursing Mothers Protect Their Babies with Bifidobacteria 13
Nick M. Jensen, Britta E. Heiss, and David A. Mills
2.1 Bifidobacterium Species and Diversity 13
2.2 Human Milk Oligosaccharides 14
2.3 Bifidobacterial Metabolism 14
2.4 Benefits of Bifidobacterium 15
2.5 Global Distribution of Bifidobacterium 16
2.6 Supporting Persistent Bifidobacterium Populations 16
2.7 Summary 18
Acknowledgments 18
Chapter 3 Gut Microbiome and the Immune System: Role in Vaccine Response 22
Helena Ipe Pinheiro Guimaraes, Jorgen De Jonge, Debbie Van Baarle, and Susana Fuentes
3.1 Immunology of Vaccines 22
3.1.1 Induction of Protective Immunity by Vaccination 22
3.1.2 Evolution of Vaccines 23
3.1.3 Vaccine Limitations 24
3.2 Gut Microbiome and the Immune System 24
3.2.1 Microbiome Development in Life 24
3.2.2 Host–microbe Interactions: Impact on Health 25
3.3 Microbiome and Vaccine Response 27
3.3.1 Mechanistic Studies in Animal Models 27
3.4 Role of the Microbiome in Vaccine Response in Human Studies 28
3.5 Conclusions and Future Perspectives 29
Chapter 4 Probiotics for Prevention or Treatment of Food Allergies 35
Agnes S. Y. Leung, Wenyin Loh, and Mimi L. K. Tang
4.1 Introduction 35
4.2 Prevention of Food Allergy 36
4.3 Treatment of Food Allergy 37
4.3.1 Clinical Use of Probiotics in Food Immunotherapy 38
4.3.2 Preclinical Studies of the Effects of Probiotics for Treatment of Food Allergy 39
4.4 Conclusion 39
Chapter 5 COVID-19, Microbiota, and Probiotics 43
Marta Mozota, Leonides Fernandez, and Juan Miguel Rodriguez
5.1 Introduction 43
5.2 Relationship between COVID-19 and the Microbiota 44
5.3 Respiratory Microbiota in Patients with COVID-19 45
5.4 Gut Microbiota in Patients with COVID-19 45
5.5 Probiotics and COVID-19 46
Chapter 6 Underarm Body Odor, the Microbiome, and Probiotic Treatment 52
Britta De Pessemier, Rune Daneels, Tom Van De Wiele, and Chris Callewaert
6.1 Skin Structure and Function 52
6.2 Sweat 52
6.2.1 Sweat Glands
6.2.1.1 Eccrine Glands 53
6.2.1.2 Apocrine Glands 53
6.2.1.3 Apoeccrine Glands 53
6.2.1.4 Sebaceous Glands 54
6.3 Skin and Underarm Microbiome 54
6.4 Axillary Microbiome 54
6.5 Bromhidrosis Pathophysiology 56
6.5.1 Steroid-based Malodor 56
6.5.2 Long-chain Fatty Acids (LCFAs) 56
6.5.3 VFA-based Malodor 57
6.5.4 Thioalcohol-based Malodor 57
6.6 Methods to Treat Body Odor 57
6.6.1 Conventional Methods 57
6.6.1.1 Deodorants 57
6.6.1.2 Antiperspirants 58
6.6.1.3 Antibiotics 58
6.6.1.4 Medication 58
6.6.1.5 Botox 58
6.6.1.6 Surgery 58
6.6.2 Alternative Methods 58
6.6.2.1 Pre-, Pro-, and Postbiotics 59
6.6.2.2 Armpit Bacterial Transplant 60
6.6.2.3 Bacteriotherapy 60
6.7 Conclusions 60
Acknowledgments 61
Chapter 7 The Enigma of Prevotella copri 64
Petia Kovatcheva-Datchary
7.1 Introduction 64
7.2 Prevotella copri Physiology, Growth, and Metabolism 64
7.3 Prevotella copri, an Important Member of the Human Gut Microbiota 65
7.4 The Unexplored Diversity of Prevotella copri 65
Chapter 8 Future Perspectives of Probiotics and Prebiotics in Foods and Food Supplements 69
Z. H. Hassan, F. Hugenholtz, E. G. Zoetendal, and Hauke Smidt
8.1 Introduction 69
8.2 Function of the GI Tract Microbiota 71
8.3 Modulating the GI Tract Microbiota to Improve Health 71
8.3.1 Modulating the GI Tract Microbiota with Probiotics 72
8.3.2 Criteria for a Microorganism to Be Classified as Probiotic 72
8.4 Modulating the GI Tract Microbiota with Prebiotics 73
8.5 Modulating the GI Tract Microbiota with Synbiotics 74
8.6 Future Perspectives 76
8.6.1 Next Generation Probiotics 78
8.6.2 Next Generation Prebiotics 80
Acknowledgments 82
Section 2 Good Microbes in Food Production 89
Co-Edited by Luca S. Cocolin and Frans J. de Bruijn
Chapter 9 Bioprotective Cultures and Bacteriocins for Food 91
Sara Arbulu, Beatriz Gomez-Sala, Enriqueta Garcia-Gutierrez,
and Paul D. Cotter
9.1 Introduction 91
9.1.1 Food Safety Hazards 91
9.1.2 Bioprotection: Fermentation, Protective Cultures, and Bacteriocins 92
9.1.3 Fermented Foods 92
9.1.4 Protective Cultures 92
9.1.5 Bacteriocins 92
9.1.6 Bacteriocin Classification 92
9.2 Bioprotection of Milk and Dairy Products 93
9.2.1 Milk Products and Their Importance in Society 93
9.2.2 Spoilage and Food-borne Pathogenic Bacteria in Milk and Dairy Products 93
9.3 Fermented Dairy Products 93
9.4 Application of Bacteriocins and Their Protective Cultures in Milk and Dairy Products 94
9.5 Bioprotection of Meat and Meat Products 95
9.5.1 Meat and Meat Products and Their Importance in Society 95
9.5.2 Spoilage and Food-borne Pathogenic Bacteria in Meat and Meat Products 95
9.6 Fermented Meat Products 95
9.7 Application of Protective Cultures and Their Bacteriocins in Meat and Meat Products 96
9.8 Bioprotection of Fresh Fish and Fish Products 97
9.8.1 Fish and Fish Products and Their Importance in Society 97
9.8.2 Spoilage and Food-borne Pathogenic Bacteria in Fish and Fish Products 97
9.9 Fermented Fish Products 98
9.10 Application of Protective Cultures and Their Bacteriocins in Fish and Fish Products 100
9.11 Bioprotection of Fruits and Vegetables 100
9.11.1 Fruit and Vegetables and Their Importance in Society 100
9.11.2 Spoilage and Pathogenic Bacteria in Fruit and Vegetables 103
9.12 Fermented Fruits and Vegetables Products 103
9.13 Application of Protective Cultures and Their Bacteriocins in Fruit, Vegetables, and By-products 104
9.14 Regulatory Issues in Bioprotection 104
9.15 Conclusions 106
Acknowledgments 106
Chapter 10 Aromatic Yeasts: Revealing Their Flavor Potential in Food Fermentations 113
Amparo Gamero, Monica Flores, and Carmela Belloch
10.1 Introduction 113
10.2 Yeast Aroma in Alcoholic Beverages 113
10.2.1 Yeast: Saccharomyces and Non-Saccharomyces 114
10.2.2 Aromatic Precursors 115
10.2.3 Fermentative Aroma Compounds 116
10.3 Yeast Aroma in Foods from Animal Sources 116
10.3.1 Yeast: Debaryomyces and Kluyveromyces 117
10.3.2 Fermentation Aroma Compounds 117
10.4 Yeast Aroma in Other Fermentations 120
10.4.1 Vegetables 121
10.4.2 Traditional Fermentations 122
10.5 Final Remarks 125
Acknowledgments 125
Chapter 11 Beneficial Microbiota in Ethnic Fermented Foods and Beverages 130
Jyoti Prakash Tamang and Namrata Thapa
11.1 Introduction 130
11.2 Ethnic Fermented Foods 130
11.3 Diversity of Beneficial Microorganisms in Ethnic Fermented Foods 132
11.3.1 Lactic Acid Bacteria 133
11.3.2 Non-Lactic Acid Bacteria 134
11.3.3 Yeasts 135
11.3.4 Filamentous Molds 135
11.3.5 Probiotic Strains from Ethnic Fermented Foods 136
11.3.6 Functional Profiles of Beneficial Microorganisms 136
11.4 Conclusion 137
Chapter 12 No Microbes, No Cheese 149
Maria Kazou and Effie Tsakalidou
12.1 Cheese for Life: The History 149
12.2 The Technology 150
12.3 The Market 151
12.4 Microbes, Milk, and Cheese: A Long Lasting Threesome Love Affair 151
12.5 Raw Milk Cheese versus Pasteurized Milk Cheese: A Thoughtful Debate about Cheese Quality and Safety 154
12.6 Starter Cultures versus Non-starter Cultures, Alias, Sprinters versus Marathon Runners 155
12.7 Cheese Microbial Communities Thrive while Cheese is Aging and Make a Fortune in Aroma, Flavor, Texture, and Color 156
12.8 Cheese Microbiota and Human Health: Myth or Reality? 157
12.9 Conclusions 158
Chapter 13 The Microbiome of Fermented Sausages 160
Ilario Ferrocino, Irene Franciosa, Kalliopi Rantsiou, and Luca S. Cocolin
13.1 Introduction 160
13.2 The Microbiota of Fermented Sausages 161
13.3 The Importance of the Sausage’s Mycobiota 164
13.4 Use of the Autochthonous Microbiome to Improve the Quality and Safety of Fermented Sausages 165
13.5 Conclusion 166
Chapter 14 The Sourdough Microbiota and Its Sensory and Nutritional Performances 169
Hana Ameur, Kashika Arora, Andrea Polo, and Marco Gobbetti
14.1 Introduction 169
14.2 How the Sourdough Microbiota is Assembled 170
14.2.1 House Microbiota 170
14.2.2 Flour 171
14.2.3 Water 172
14.2.4 Other Ingredients 172
14.3 Where and How to Use the Sourdough 173
14.3.1 Baked Goods and Flours 173
14.3.2 Conditions of Use 173
14.3.3 Microbiological and Biochemical Characteristics 174
14.4 Sourdough to Exploit the Potential of Non-conventional Flours 175
14.4.1 Legumes 175
14.4.2 Pseudo-cereals 177
14.4.3 Milling By-products 177
14.5 The Sensory Performances of Sourdough Baked Goods 178
14.6 The Nutritional Performances of Sourdough Baked Goods 178
14.6.1 Mineral Bioavailability 178
14.6.2 Dietary Fibers 179
14.6.3 Glycemic Index 179
14.6.4 Protein Digestibility 179
14.6.5 Degradation of Anti-nutritional Factors 180
14.7 Conclusions 181
Chapter 15 Beneficial Role of Microorganisms in Olives 185
Anthoula A. Argyri and Chrysoula C. Tassou
15.1 Table Olives as Fermented Food 185
15.1.1 Microbiota of Fermented Olives 185
15.1.2 Microbial Starters in Olive Fermentation 186
15.2 Table Olives as Functional/Probiotic Food 186
15.2.1 Probiotic Microorganisms of Olives 187
15.2.2 Probiotic Microorganisms as Starters in Olive Fermentation 191
15.2.2.1 Non-olive Origin Probiotic Starters 191
15.2.2.2 Olive Origin Probiotic Starters 192
15.3 Conclusions 193
Chapter 16 The Functional and Nutritional Aspects of Cocobiota: Lactobacilli 199
Jatziri Mota-Gutierrez and Luca S. Cocolin
16.1 Introduction 199
16.2 Characteristics of Liquorilactobacillus Cacaonum, Limosilactobacillus Fermentum, and Lactiplantibacillus Plantarum 200
16.2.1 Nutrition and Growth 200
16.2.2 Genetics 201
16.2.3 Metabolic Properties 202
16.2.4 Potential Food Application of Lactobacilli from Fermented Cocoa Pulp-bean Mass 203
16.2.5 Starter Cultures 203
16.2.6 Food Preservation Applications 205
16.2.7 Organoleptic Applications 205
16.2.8 Nutritional Applications 206
16.3 European Regulation of Food Cultures 207
16.3.1 Food Safety Assessment 207
16.4 Conclusions 207
Chapter 17 Microbiological Control as a Tool to Improve Wine Aroma and Quality 213
Albert Mas, Gemma Beltran, and Maria Jesus Torija
17.1 Introduction 213
17.2 Methods of Analysis: Classical and Molecular Methods 213
17.3 Grape Microbiome 215
17.4 Succession of Microorganisms during Alcoholic Fermentation 216
17.5 Microbial Interactions during Alcoholic Fermentation 218
17.6 Production of Aromas and Wine Quality 219
17.7 Conclusions 222
Chapter 18 Lambic Beer, A Unique Blend of Tradition and Good Microorganisms 225
Jonas De Roos and Luc De Vuyst
18.1 Introduction 225
18.2 Lambic Beer, a Long-lasting Brew 226
18.3 A Unique Blend of Microorganisms 228
18.4 How Beer-spoiling Bacteria Can Be Wanted 229
18.5 Yeasts, More than a One-trick Pony 231
18.6 Conclusions 232
Section 3 Good Microbes in Biotechnology 237
Co-Edited by Michael Sauer and Frans J. de Bruijn
Chapter 19 Microbiology and Bio-economy – Sustainability by Nature 239
Michael Sauer
19.1 Introduction 239
19.2 Economy, Employment, and Microbes – Some Numbers 239
19.3 Outlook into a Sustainable Future – Microbial Chemical Production as an Example 240
19.4 What Makes Microorganisms Useful for the Chemical Industry? 241
19.5 Metabolic Engineering Allows the Design of Microbial Cell Factories 243
19.6 From Plant to Microbe – Production of the Malaria Medication Artemisinin 243
19.7 Opening up the Chemical Space with the Tools of Synthetic Biology 244
19.8 Conclusions 245
Chapter 20 Role of Microorganisms in Environmental Remediation and Resource Recovery through Microbe-Based Technologies Having Major Potentials 247
Piyush Malaviya, Rozi Sharma, Smiley Sharma, and Deepak Pant
20.1 Introduction 247
20.2 Microorganisms as Important Biological Entities in the Environment 248
20.2.1 Role of Microorganisms in Urgent Environmental Needs 248
20.2.1.1 Pollution Control 248
20.2.1.2 Carbon Sequestration 249
20.2.1.3 Biofuel Production 249
20.2.1.4 Biogas Production 250
20.2.1.5 Biofertilizer Production 250
20.2.1.6 Production of Single-cell Proteins 250
20.3 Different Microbial Technologies with High Potential for Environmental Exigencies 250
20.3.1 Omics Technologies 250
20.3.2 Nanobioremediation Technology 251
20.3.3 Electrobioremediation 251
20.3.4 Microbial Electrosynthesis for CO2 Sequestration 251
20.3.5 Microbial Fuel Cells (MFCs) for Electricity Generation 252
20.3.6 Microbial Electrolysis for Hydrogen Production 254
20.3.7 Consolidated Bioprocessing for Bioethanol Production 255
20.3.8 Microbial Technologies for Biogas Production 256
20.3.9 Bioaugmentation 256
20.3.10 Biogranulation 257
20.4 Conclusion 257
Chapter 21 Microbes Saving the World? How Microbial Carbon Dioxide Fixation Contributes to Storing Carbon in Goods of Our Daily Life 265
Diethard Mattanovich, Özge Ata, and Thomas Gassler
21.1 Introduction 265
21.2 Photoautrophic Microorganisms 267
21.2.1 Cultivation and Applications of Cyanobacteria and Microalgae 268
21.3 Chemoautotrophic Bacteria 270
21.3.1 Biotech Applications of Chemoautotrophs 272
21.4 Synthetic Biology: New-to-Nature CO 2 Fixation Pathways 272
Chapter 22 The Biodiesel Biorefinery: Opportunities and Challenges for Microbial Production of Fuels and Chemicals 276
Hannes Russmayer and Michael Egermeier
22.1 The Concept of a Biorefinery 276
22.1.1 Biorefinery Concept for Biodiesel Production 277
22.1.2 Microorganisms as Feedstocks for Biodiesel Production 277
22.1.3 Microbial Upgrading of Waste Streams from Biodiesel Production 279
22.2 Higher Value Chemicals from Aerobic Glycerol Metabolism 280
22.2.1 Anaerobic Glycerol Metabolism for Industrial Chemical Production 281
22.2.1.1 Dehydration of Glycerol to Industrial Relevant Building Blocks 281
22.2.1.2 Microbial Glycerol Reduction for Chemical Production 282
22.3 Concluding Remarks 282
Acknowledgments 283
Chapter 23 The Good Fungus – About the Potential of Fungi for Our Future 287
Valeria Ellena and Matthias Steiger
23.1 Introduction 287
23.2 Fungal Biotechnology: The Origins 287
23.3 Fungi for Moving Forward – Biofuels 288
23.4 Fungal Enzymes to the Rescue for Sustainable Industries 288
23.5 Fungal Organic Acids: Jacks of All Trades 289
23.6 Fungal Metabolites – Weapons against Diseases 289
23.7 Fungal Products on Demand 290
23.8 “Green” Fungi for a Sustainable Future 290
23.9 Biocomputers and Life in Space: The Future of Fungal Biotechnology 291
23.10 Conclusions 292
Acknowledgments 292
Chapter 24 Microbes and Plastic – A Sustainable Duo for the Future 294
Birger Wolter, Henric M.T. Hintzen, Gina Welsing, Till Tiso, and Lars M. Blank
List of Abbreviations 294
24.1 Introduction 294
24.9 Conclusion 306
Acknowledgments 306
Chapter 25 Food Waste as a Valuable Carbon Source for Bioconversion – How Microbes do Miracles 312
Rajat Kumar, Varsha Bohra, Manu Mk, and Jonathan W. C. Wong
25.1 Introduction 312
25.2 Biofertilizers 313
25.3 Bioenergy 315
25.3.1 Hydrolysis 315
25.3.2 Acidogenesis 316
25.3.3 Acetogenesis 316
25.3.4 Methanogenesis 317
25.3.5 Bio-products 317
25.3.6 Biochemicals 318
25.3.7 Bioplastics 318
25.3.8 Biosurfactants 319
25.3.9 Biocatalysts 319
25.4 Conclusions 319
Section 4 Good Microbes and Bioremediation 323
Co-Edited by David Dowling and Frans J. de Bruijn
Chapter 26 Microbial-based Bioremediation at a Global Scale: The Challenges and the Tools 325
Victor de Lorenzo, Esteban Martinez-Garcia, and Tomas Aparicio
26.1 Introduction 325
26.2 Bioremediation Beyond the Tipping Point 326
26.3 The Environmental Microbiome as a Global Catalyst 326
26.4 Designing Agents for Spreading New Traits through the Environmental Microbiome 328
26.5 Bacterial Chassis for Environmental Interventions 329
26.6 Inoculation of Newcomers in Existing Microbial Niches: No Piece of Cake 331
26.7 Programming Large-scale Horizontal Gene Transfer 331
26.8 Conclusion 332
Acknowledgments 333
Chapter 27 Ecopiling: Beneficial Soil Bacteria, Plants, and Optimized Soil Conditions for Enhanced Remediation of Hydrocarbon Polluted Soil 337
Robert Conlon, Mutian Wang, Xuemei Liu Germaine, Rajesh Mali,
David Dowling, and Kieran J. Germaine
27.1 Introduction 337
27.2 Remediation of Hydrocarbons 338
27.3 Bioremediation 338
27.4 Biopiles 339
27.5 Phytoremediation 339
27.6 Rhizoremediation of Total Petroleum Hydrocarbons 340
27.7 Ecopiling 340
27.8 Conclusion 345
Acknowledgments 346
Chapter 28 Plant–Microbe Interactions in Environmental Restoration 348
Ondrej Uhlik, Jachym Suman, Jakub Papik, Michal Strejcek, and Tomas Macek
28.1 Introduction to Plant–Microbe Interactions 348
28.5 Conclusions 353
Acknowledgments 354
Chapter 29 Microbial Endophytes for Clean-up of Pollution 358
Robert J. Tournay and Sharon L. Doty
29.1 Introduction 358
29.4 Conclusions 367
Chapter 30 Metagenomics of Bacterial Consortia for the Bioremediation of Organic Pollutants 372
Daniel Garrido-Sanz, Paula Sansegundo-Lobato, Marta Martin,
Miguel Redondo-Nieto, and Rafael Rivilla
30.1 Introduction 372
Acknowledgments 382
Chapter 31 Soil Microbial Fuel Cells for Energy Harvesting and Bioremediation of Soil Contaminated with Organic Pollutants 385
Bongkyu Kim, Jakub Dziegielowski, and Mirella Di Lorenzo
31.1 Introduction to Soil Microbial Fuel Cells 385
31.6 Conclusions and Future Perspective 392
Chapter 32 Biotechnology for the Management of Plastics and Microplastics 396
Loriane Murphy and John Cleary
32.1 Introduction 396
32.4 Conclusions 406
Acknowledgments 407
Chapter 33 Bio-electrochemical Systems for Monitoring and Enhancement of Groundwater Bioremediation 412
Rory Doherty, Altaf AlBaho, and Lily Roney
33.1 Introduction 412
33.6 Conclusion 422
Section 5 Good Microbes and Agriculture 427
Co-Edited by Linda Thomashow and Frans J. de Bruijn
Chapter 34 Beneficial Microbes for Agriculture: From Discovery to Applications 429
Gabriele Berg, Peter Kusstatscher, Birgit Wassermann, Tomislav Cernava,
and Ahmed Abdelfattah
34.1 Introduction 429
34.8 Concluding Remarks 438
Acknowledgments 438
Chapter 35 Biological Control of Soilborne Plant Diseases 444
Linda Thomashow and David M. Weller
35.1 Introduction 444
Acknowledgments 454
Chapter 36 Classification, Discovery, and Microbial Basis of Disease-Suppressive Soils 457
David M. Weller, Melissa LeTourneau, and Mingming Yang
36.1 Microbe-based Plant Defense of Roots 457
Chapter 37 Biological Nitrogen Fixation 466
Frans J. de Bruijn and Mariangela Hungria
37.1 Introduction 466
37.9 Conclusions 472
Acknowledgments 473
Chapter 38 A Primer on the Extraordinary Efficacy and Safety of Bacterial Insecticides Based on Bacillus Thuringiensis 476
Brian Federici
38.1 Introduction 476
38.2 Summary of Bt Biology and Its Mode of Action 477
38.3 Summary of Earlier Studies on Bt Safety 479
Chapter 39 Life of Microbes Inside the Plant: Beneficial Fungal Endophytes and Mycorrhizal Fungi 488
Luisa Lanfranco and Valentina Fiorilli
39.1 The Plant Microbiota 488
39.4 Conclusions and Perspectives 497
Acknowledgments 498
Chapter 40 Aromatherapy: Improving Plant Health through Microbial Volatiles 506
Ana Shein Lee Diaz and Paolina Garbeva
40.1 Background 506
Chapter 41 Trichoderma for Biocontrol and Biostimulation – A Green Fungus Revolution in Agriculture 515
Sheridan Lois Woo and Matteo Lorito
41.1 Modern Agriculture with Old Problems 515
41.9 Conclusions 526
Acknowledgments 527
Chapter 42 Companies and Organizations Active in Agriculture and Horticulture 531
Ben Lugtenberg
42.1 Introduction 531
42.2 Examples of Important Microbes 532
42.2.1 Arbuscular Mycorrhizas 532
42.2.2 Bacillus 532
42.2.3 Bacillus thuringiensis 532
Acknowledgments 539
Index 541
