Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation, and Agriculture

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 Letícia 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, Leónides Fernández, and Juan Miguel Rodríguez 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 Gómez-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, Mónica 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 María Jesús 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 Martínez-García, and Tomás 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