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

Frans J. de Bruijn, PhD, was Director of the Laboratory for Plant-Microbe Interactions and Environment, a mixed INRAE/CNRS research facility with about 100 scientists and support staff in Toulouse, France. He is presently Director of Recherche DR1 and editor of multiple books on a variety of topics. Hauke Schmidt, PhD, is a member of the management team at the National BE-Basic Program and Senior Scientist and Theme Council member at TI Food & Nutrition. Luca S. Cocolin is Full Professor in the Department of Agricultural, Forest, and Food Sciences at the University of Torino, Italy. Michael Sauer is Assistant Professor at the Department of Biotechnology of BOKU—University of Natural Resources and Life Sciences in Vienna, Austria. David Dowling, PhD, co-founded MicroGen Biotechnology Limited and is the Head of the Faculty of Science at the Institute of Technology Carlow. Linda Thomashow, PhD, Research Geneticist at the USDA Agricultural Research Service's Wheat Health, Genetics and Quality Research Unit and Professor in Plant Pathology and Molecular Plant Sciences at Washington State University, USA.

• Preface xxiList of Contributors xxiiAcknowledgments xxviiiIntroduction xxixSection 1 Good Microbes in Medicine 1Co-Edited by Hauke Smidt and Frans J. de BruijnChapter 1 Modern Medicine Relies on the Help of Microorganisms – From Vaccine Production to Cancer Medication 3Letícia Parizotto, Larissa Brumano, Eduardo Kleingesinds, and Adalberto Pessoa Junior1.1 Introduction: Good Microorganisms and Our Health 31.2 Bad Microorganisms: Epidemics Boosted Modern Medicine 41.3 Antimicrobial Peptides: A New Therapeutic Alternative to Antibiotics? 41.4 Microorganisms as Tools: Recombinant DNA Technology (rDNAT) 51.5 Vaccines: The Use of Microorganisms in the Frontline against Diseases 71.6 Anticancer Drugs: Many Ways to Fight Cancer with Good Microorganisms 81.7 Gene Therapy: The Future of Modern Medicine 91.8 Concluding Remarks and Perspectives 10Acknowledgments 10Chapter 2 How Nursing Mothers Protect Their Babies with Bifidobacteria 13Nick M. Jensen, Britta E. Heiss, and David A. Mills2.1 Bifidobacterium Species and Diversity 132.2 Human Milk Oligosaccharides 142.3 Bifidobacterial Metabolism 142.4 Benefits of Bifidobacterium 152.5 Global Distribution of Bifidobacterium 162.6 Supporting Persistent Bifidobacterium Populations 162.7 Summary 18Acknowledgments 18Chapter 3 Gut Microbiome and the Immune System: Role in Vaccine Response 22Helena Ipe Pinheiro Guimaraes, Jorgen De Jonge, Debbie Van Baarle, and Susana Fuentes3.1 Immunology of Vaccines 223.1.1 Induction of Protective Immunity by Vaccination 223.1.2 Evolution of Vaccines 233.1.3 Vaccine Limitations 243.2 Gut Microbiome and the Immune System 243.2.1 Microbiome Development in Life 243.2.2 Host–microbe Interactions: Impact on Health 253.3 Microbiome and Vaccine Response 273.3.1 Mechanistic Studies in Animal Models 273.4 Role of the Microbiome in Vaccine Response in Human Studies 283.5 Conclusions and Future Perspectives 29Chapter 4 Probiotics for Prevention or Treatment of Food Allergies 35Agnes S. Y. Leung, Wenyin Loh, and Mimi L. K. Tang4.1 Introduction 354.2 Prevention of Food Allergy 364.3 Treatment of Food Allergy 374.3.1 Clinical Use of Probiotics in Food Immunotherapy 384.3.2 Preclinical Studies of the Effects of Probiotics for Treatment of Food Allergy 394.4 Conclusion 39Chapter 5 COVID-19, Microbiota, and Probiotics 43Marta Mozota, Leónides Fernández, and Juan Miguel Rodríguez5.1 Introduction 435.2 Relationship between COVID-19 and the Microbiota 445.3 Respiratory Microbiota in Patients with COVID-19 455.4 Gut Microbiota in Patients with COVID-19 455.5 Probiotics and COVID-19 46Chapter 6 Underarm Body Odor, the Microbiome, and Probiotic Treatment 52Britta De Pessemier, Rune Daneels, Tom Van De Wiele, and Chris Callewaert6.1 Skin Structure and Function 526.2 Sweat 526.2.1 Sweat Glands6.2.1.1 Eccrine Glands 536.2.1.2 Apocrine Glands 536.2.1.3 Apoeccrine Glands 536.2.1.4 Sebaceous Glands 546.3 Skin and Underarm Microbiome 546.4 Axillary Microbiome 546.5 Bromhidrosis Pathophysiology 566.5.1 Steroid-based Malodor 566.5.2 Long-chain Fatty Acids (LCFAs) 566.5.3 VFA-based Malodor 576.5.4 Thioalcohol-based Malodor 576.6 Methods to Treat Body Odor 576.6.1 Conventional Methods 576.6.1.1 Deodorants 576.6.1.2 Antiperspirants 586.6.1.3 Antibiotics 586.6.1.4 Medication 586.6.1.5 Botox 586.6.1.6 Surgery 586.6.2 Alternative Methods 586.6.2.1 Pre-, Pro-, and Postbiotics 596.6.2.2 Armpit Bacterial Transplant 606.6.2.3 Bacteriotherapy 606.7 Conclusions 60Acknowledgments 61Chapter 7 The Enigma of Prevotella copri 64Petia Kovatcheva-Datchary7.1 Introduction 647.2 Prevotella copri Physiology, Growth, and Metabolism 647.3 Prevotella copri, an Important Member of the Human Gut Microbiota 657.4 The Unexplored Diversity of Prevotella copri 65Chapter 8 Future Perspectives of Probiotics and Prebiotics in Foods and Food Supplements 69Z. H. Hassan, F. Hugenholtz, E. G. Zoetendal, and Hauke Smidt8.1 Introduction 698.2 Function of the GI Tract Microbiota 718.3 Modulating the GI Tract Microbiota to Improve Health 718.3.1 Modulating the GI Tract Microbiota with Probiotics 728.3.2 Criteria for a Microorganism to Be Classified as Probiotic 728.4 Modulating the GI Tract Microbiota with Prebiotics 738.5 Modulating the GI Tract Microbiota with Synbiotics 748.6 Future Perspectives 768.6.1 Next Generation Probiotics 788.6.2 Next Generation Prebiotics 80Acknowledgments 82Section 2 Good Microbes in Food Production 89Co-Edited by Luca S. Cocolin and Frans J. de BruijnChapter 9 Bioprotective Cultures and Bacteriocins for Food 91Sara Arbulu, Beatriz Gómez-Sala, Enriqueta Garcia-Gutierrez,and Paul D. Cotter9.1 Introduction 919.1.1 Food Safety Hazards 919.1.2 Bioprotection: Fermentation, Protective Cultures, and Bacteriocins 929.1.3 Fermented Foods 929.1.4 Protective Cultures 929.1.5 Bacteriocins 929.1.6 Bacteriocin Classification 929.2 Bioprotection of Milk and Dairy Products 939.2.1 Milk Products and Their Importance in Society 939.2.2 Spoilage and Food-borne Pathogenic Bacteria in Milk and Dairy Products 939.3 Fermented Dairy Products 939.4 Application of Bacteriocins and Their Protective Cultures in Milk and Dairy Products 949.5 Bioprotection of Meat and Meat Products 959.5.1 Meat and Meat Products and Their Importance in Society 959.5.2 Spoilage and Food-borne Pathogenic Bacteria in Meat and Meat Products 959.6 Fermented Meat Products 959.7 Application of Protective Cultures and Their Bacteriocins in Meat and Meat Products 969.8 Bioprotection of Fresh Fish and Fish Products 979.8.1 Fish and Fish Products and Their Importance in Society 979.8.2 Spoilage and Food-borne Pathogenic Bacteria in Fish and Fish Products 979.9 Fermented Fish Products 989.10 Application of Protective Cultures and Their Bacteriocins in Fish and Fish Products 1009.11 Bioprotection of Fruits and Vegetables 1009.11.1 Fruit and Vegetables and Their Importance in Society 1009.11.2 Spoilage and Pathogenic Bacteria in Fruit and Vegetables 1039.12 Fermented Fruits and Vegetables Products 1039.13 Application of Protective Cultures and Their Bacteriocins in Fruit, Vegetables, and By-products 1049.14 Regulatory Issues in Bioprotection 1049.15 Conclusions 106Acknowledgments 106Chapter 10 Aromatic Yeasts: Revealing Their Flavor Potential in Food Fermentations 113Amparo Gamero, Mónica Flores, and Carmela Belloch10.1 Introduction 11310.2 Yeast Aroma in Alcoholic Beverages 11310.2.1 Yeast: Saccharomyces and Non-Saccharomyces 11410.2.2 Aromatic Precursors 11510.2.3 Fermentative Aroma Compounds 11610.3 Yeast Aroma in Foods from Animal Sources 11610.3.1 Yeast: Debaryomyces and Kluyveromyces 11710.3.2 Fermentation Aroma Compounds 11710.4 Yeast Aroma in Other Fermentations 12010.4.1 Vegetables 12110.4.2 Traditional Fermentations 12210.5 Final Remarks 125Acknowledgments 125Chapter 11 Beneficial Microbiota in Ethnic Fermented Foods and Beverages 130Jyoti Prakash Tamang and Namrata Thapa11.1 Introduction 13011.2 Ethnic Fermented Foods 13011.3 Diversity of Beneficial Microorganisms in Ethnic Fermented Foods 13211.3.1 Lactic Acid Bacteria 13311.3.2 Non-Lactic Acid Bacteria 13411.3.3 Yeasts 13511.3.4 Filamentous Molds 13511.3.5 Probiotic Strains from Ethnic Fermented Foods 13611.3.6 Functional Profiles of Beneficial Microorganisms 13611.4 Conclusion 137Chapter 12 No Microbes, No Cheese 149Maria Kazou and Effie Tsakalidou12.1 Cheese for Life: The History 14912.2 The Technology 15012.3 The Market 15112.4 Microbes, Milk, and Cheese: A Long Lasting Threesome Love Affair 15112.5 Raw Milk Cheese versus Pasteurized Milk Cheese: A Thoughtful Debate about Cheese Quality and Safety 15412.6 Starter Cultures versus Non-starter Cultures, Alias, Sprinters versus Marathon Runners 15512.7 Cheese Microbial Communities Thrive while Cheese is Aging and Make a Fortune in Aroma, Flavor, Texture, and Color 15612.8 Cheese Microbiota and Human Health: Myth or Reality? 15712.9 Conclusions 158Chapter 13 The Microbiome of Fermented Sausages 160Ilario Ferrocino, Irene Franciosa, Kalliopi Rantsiou, and Luca S. Cocolin13.1 Introduction 16013.2 The Microbiota of Fermented Sausages 16113.3 The Importance of the Sausage’s Mycobiota 16413.4 Use of the Autochthonous Microbiome to Improve the Quality and Safety of Fermented Sausages 16513.5 Conclusion 166Chapter 14 The Sourdough Microbiota and Its Sensory and Nutritional Performances 169Hana Ameur, Kashika Arora, Andrea Polo, and Marco Gobbetti14.1 Introduction 16914.2 How the Sourdough Microbiota is Assembled 17014.2.1 House Microbiota 17014.2.2 Flour 17114.2.3 Water 17214.2.4 Other Ingredients 17214.3 Where and How to Use the Sourdough 17314.3.1 Baked Goods and Flours 17314.3.2 Conditions of Use 17314.3.3 Microbiological and Biochemical Characteristics 17414.4 Sourdough to Exploit the Potential of Non-conventional Flours 17514.4.1 Legumes 17514.4.2 Pseudo-cereals 17714.4.3 Milling By-products 17714.5 The Sensory Performances of Sourdough Baked Goods 17814.6 The Nutritional Performances of Sourdough Baked Goods 17814.6.1 Mineral Bioavailability 17814.6.2 Dietary Fibers 17914.6.3 Glycemic Index 17914.6.4 Protein Digestibility 17914.6.5 Degradation of Anti-nutritional Factors 18014.7 Conclusions 181Chapter 15 Beneficial Role of Microorganisms in Olives 185Anthoula A. Argyri and Chrysoula C. Tassou15.1 Table Olives as Fermented Food 18515.1.1 Microbiota of Fermented Olives 18515.1.2 Microbial Starters in Olive Fermentation 18615.2 Table Olives as Functional/Probiotic Food 18615.2.1 Probiotic Microorganisms of Olives 18715.2.2 Probiotic Microorganisms as Starters in Olive Fermentation 19115.2.2.1 Non-olive Origin Probiotic Starters 19115.2.2.2 Olive Origin Probiotic Starters 19215.3 Conclusions 193Chapter 16 The Functional and Nutritional Aspects of Cocobiota: Lactobacilli 199Jatziri Mota-Gutierrez and Luca S. Cocolin16.1 Introduction 19916.2 Characteristics of Liquorilactobacillus Cacaonum, Limosilactobacillus Fermentum, and Lactiplantibacillus Plantarum 20016.2.1 Nutrition and Growth 20016.2.2 Genetics 20116.2.3 Metabolic Properties 20216.2.4 Potential Food Application of Lactobacilli from Fermented Cocoa Pulp-bean Mass 20316.2.5 Starter Cultures 20316.2.6 Food Preservation Applications 20516.2.7 Organoleptic Applications 20516.2.8 Nutritional Applications 20616.3 European Regulation of Food Cultures 20716.3.1 Food Safety Assessment 20716.4 Conclusions 207Chapter 17 Microbiological Control as a Tool to Improve Wine Aroma and Quality 213Albert Mas, Gemma Beltran, and María Jesús Torija17.1 Introduction 21317.2 Methods of Analysis: Classical and Molecular Methods 21317.3 Grape Microbiome 21517.4 Succession of Microorganisms during Alcoholic Fermentation 21617.5 Microbial Interactions during Alcoholic Fermentation 21817.6 Production of Aromas and Wine Quality 21917.7 Conclusions 222Chapter 18 Lambic Beer, A Unique Blend of Tradition and Good Microorganisms 225Jonas De Roos and Luc De Vuyst18.1 Introduction 22518.2 Lambic Beer, a Long-lasting Brew 22618.3 A Unique Blend of Microorganisms 22818.4 How Beer-spoiling Bacteria Can Be Wanted 22918.5 Yeasts, More than a One-trick Pony 23118.6 Conclusions 232Section 3 Good Microbes in Biotechnology 237Co-Edited by Michael Sauer and Frans J. de BruijnChapter 19 Microbiology and Bio-economy – Sustainability by Nature 239Michael Sauer19.1 Introduction 23919.2 Economy, Employment, and Microbes – Some Numbers 23919.3 Outlook into a Sustainable Future – Microbial Chemical Production as an Example 24019.4 What Makes Microorganisms Useful for the Chemical Industry? 24119.5 Metabolic Engineering Allows the Design of Microbial Cell Factories 24319.6 From Plant to Microbe – Production of the Malaria Medication Artemisinin 24319.7 Opening up the Chemical Space with the Tools of Synthetic Biology 24419.8 Conclusions 245Chapter 20 Role of Microorganisms in Environmental Remediation and Resource Recovery through Microbe-Based Technologies Having Major Potentials 247Piyush Malaviya, Rozi Sharma, Smiley Sharma, and Deepak Pant20.1 Introduction 24720.2 Microorganisms as Important Biological Entities in the Environment 24820.2.1 Role of Microorganisms in Urgent Environmental Needs 24820.2.1.1 Pollution Control 24820.2.1.2 Carbon Sequestration 24920.2.1.3 Biofuel Production 24920.2.1.4 Biogas Production 25020.2.1.5 Biofertilizer Production 25020.2.1.6 Production of Single-cell Proteins 25020.3 Different Microbial Technologies with High Potential for Environmental Exigencies 25020.3.1 Omics Technologies 25020.3.2 Nanobioremediation Technology 25120.3.3 Electrobioremediation 25120.3.4 Microbial Electrosynthesis for CO2 Sequestration 25120.3.5 Microbial Fuel Cells (MFCs) for Electricity Generation 25220.3.6 Microbial Electrolysis for Hydrogen Production 25420.3.7 Consolidated Bioprocessing for Bioethanol Production 25520.3.8 Microbial Technologies for Biogas Production 25620.3.9 Bioaugmentation 25620.3.10 Biogranulation 25720.4 Conclusion 257Chapter 21 Microbes Saving the World? How Microbial Carbon Dioxide Fixation Contributes to Storing Carbon in Goods of Our Daily Life 265Diethard Mattanovich, Özge Ata, and Thomas Gassler21.1 Introduction 26521.2 Photoautrophic Microorganisms 26721.2.1 Cultivation and Applications of Cyanobacteria and Microalgae 26821.3 Chemoautotrophic Bacteria 27021.3.1 Biotech Applications of Chemoautotrophs 27221.4 Synthetic Biology: New-to-Nature CO 2 Fixation Pathways 272Chapter 22 The Biodiesel Biorefinery: Opportunities and Challenges for Microbial Production of Fuels and Chemicals 276Hannes Russmayer and Michael Egermeier22.1 The Concept of a Biorefinery 27622.1.1 Biorefinery Concept for Biodiesel Production 27722.1.2 Microorganisms as Feedstocks for Biodiesel Production 27722.1.3 Microbial Upgrading of Waste Streams from Biodiesel Production 27922.2 Higher Value Chemicals from Aerobic Glycerol Metabolism 28022.2.1 Anaerobic Glycerol Metabolism for Industrial Chemical Production 28122.2.1.1 Dehydration of Glycerol to Industrial Relevant Building Blocks 28122.2.1.2 Microbial Glycerol Reduction for Chemical Production 28222.3 Concluding Remarks 282Acknowledgments 283Chapter 23 The Good Fungus – About the Potential of Fungi for Our Future 287Valeria Ellena and Matthias Steiger23.1 Introduction 28723.2 Fungal Biotechnology: The Origins 28723.3 Fungi for Moving Forward – Biofuels 28823.4 Fungal Enzymes to the Rescue for Sustainable Industries 28823.5 Fungal Organic Acids: Jacks of All Trades 28923.6 Fungal Metabolites – Weapons against Diseases 28923.7 Fungal Products on Demand 29023.8 “Green” Fungi for a Sustainable Future 29023.9 Biocomputers and Life in Space: The Future of Fungal Biotechnology 29123.10 Conclusions 292Acknowledgments 292Chapter 24 Microbes and Plastic – A Sustainable Duo for the Future 294Birger Wolter, Henric M.T. Hintzen, Gina Welsing, Till Tiso, and Lars M. BlankList of Abbreviations 29424.1 Introduction 29424.9 Conclusion 306Acknowledgments 306Chapter 25 Food Waste as a Valuable Carbon Source for Bioconversion – How Microbes do Miracles 312Rajat Kumar, Varsha Bohra, Manu Mk, and Jonathan W. C. Wong25.1 Introduction 31225.2 Biofertilizers 31325.3 Bioenergy 31525.3.1 Hydrolysis 31525.3.2 Acidogenesis 31625.3.3 Acetogenesis 31625.3.4 Methanogenesis 31725.3.5 Bio-products 31725.3.6 Biochemicals 31825.3.7 Bioplastics 31825.3.8 Biosurfactants 31925.3.9 Biocatalysts 31925.4 Conclusions 319Section 4 Good Microbes and Bioremediation 323Co-Edited by David Dowling and Frans J. de BruijnChapter 26 Microbial-based Bioremediation at a Global Scale: The Challenges and the Tools 325Victor de Lorenzo, Esteban Martínez-García, and Tomás Aparicio26.1 Introduction 32526.2 Bioremediation Beyond the Tipping Point 32626.3 The Environmental Microbiome as a Global Catalyst 32626.4 Designing Agents for Spreading New Traits through the Environmental Microbiome 32826.5 Bacterial Chassis for Environmental Interventions 32926.6 Inoculation of Newcomers in Existing Microbial Niches: No Piece of Cake 33126.7 Programming Large-scale Horizontal Gene Transfer 33126.8 Conclusion 332Acknowledgments 333Chapter 27 Ecopiling: Beneficial Soil Bacteria, Plants, and Optimized Soil Conditions for Enhanced Remediation of Hydrocarbon Polluted Soil 337Robert Conlon, Mutian Wang, Xuemei Liu Germaine, Rajesh Mali,David Dowling, and Kieran J. Germaine27.1 Introduction 33727.2 Remediation of Hydrocarbons 33827.3 Bioremediation 33827.4 Biopiles 33927.5 Phytoremediation 33927.6 Rhizoremediation of Total Petroleum Hydrocarbons 34027.7 Ecopiling 34027.8 Conclusion 345Acknowledgments 346Chapter 28 Plant–Microbe Interactions in Environmental Restoration 348Ondrej Uhlik, Jachym Suman, Jakub Papik, Michal Strejcek, and Tomas Macek28.1 Introduction to Plant–Microbe Interactions 34828.5 Conclusions 353Acknowledgments 354Chapter 29 Microbial Endophytes for Clean-up of Pollution 358Robert J. Tournay and Sharon L. Doty29.1 Introduction 35829.4 Conclusions 367Chapter 30 Metagenomics of Bacterial Consortia for the Bioremediation of Organic Pollutants 372Daniel Garrido-Sanz, Paula Sansegundo-Lobato, Marta Martin,Miguel Redondo-Nieto, and Rafael Rivilla30.1 Introduction 372Acknowledgments 382Chapter 31 Soil Microbial Fuel Cells for Energy Harvesting and Bioremediation of Soil Contaminated with Organic Pollutants 385Bongkyu Kim, Jakub Dziegielowski, and Mirella Di Lorenzo31.1 Introduction to Soil Microbial Fuel Cells 38531.6 Conclusions and Future Perspective 392Chapter 32 Biotechnology for the Management of Plastics and Microplastics 396Loriane Murphy and John Cleary32.1 Introduction 39632.4 Conclusions 406Acknowledgments 407Chapter 33 Bio-electrochemical Systems for Monitoring and Enhancement of Groundwater Bioremediation 412Rory Doherty, Altaf AlBaho, and Lily Roney33.1 Introduction 41233.6 Conclusion 422Section 5 Good Microbes and Agriculture 427Co-Edited by Linda Thomashow and Frans J. de BruijnChapter 34 Beneficial Microbes for Agriculture: From Discovery to Applications 429Gabriele Berg, Peter Kusstatscher, Birgit Wassermann, Tomislav Cernava,and Ahmed Abdelfattah34.1 Introduction 42934.8 Concluding Remarks 438Acknowledgments 438Chapter 35 Biological Control of Soilborne Plant Diseases 444Linda Thomashow and David M. Weller35.1 Introduction 444Acknowledgments 454Chapter 36 Classification, Discovery, and Microbial Basis of Disease-Suppressive Soils 457David M. Weller, Melissa LeTourneau, and Mingming Yang36.1 Microbe-based Plant Defense of Roots 457Chapter 37 Biological Nitrogen Fixation 466Frans J. de Bruijn and Mariangela Hungria37.1 Introduction 46637.9 Conclusions 472Acknowledgments 473Chapter 38 A Primer on the Extraordinary Efficacy and Safety of Bacterial Insecticides Based on Bacillus Thuringiensis 476Brian Federici38.1 Introduction 47638.2 Summary of Bt Biology and Its Mode of Action 47738.3 Summary of Earlier Studies on Bt Safety 479Chapter 39 Life of Microbes Inside the Plant: Beneficial Fungal Endophytes and Mycorrhizal Fungi 488Luisa Lanfranco and Valentina Fiorilli39.1 The Plant Microbiota 48839.4 Conclusions and Perspectives 497Acknowledgments 498Chapter 40 Aromatherapy: Improving Plant Health through Microbial Volatiles 506Ana Shein Lee Diaz and Paolina Garbeva40.1 Background 506Chapter 41 Trichoderma for Biocontrol and Biostimulation – A Green Fungus Revolution in Agriculture 515Sheridan Lois Woo and Matteo Lorito41.1 Modern Agriculture with Old Problems 51541.9 Conclusions 526Acknowledgments 527Chapter 42 Companies and Organizations Active in Agriculture and Horticulture 531Ben Lugtenberg42.1 Introduction 53142.2 Examples of Important Microbes 53242.2.1 Arbuscular Mycorrhizas 53242.2.2 Bacillus 53242.2.3 Bacillus thuringiensis 532Acknowledgments 539Index 541