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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Discover the positive and helpful contributions made by microorganisms to various areas of human health, food preservation and production, biotechnology, industry, environmental clean up and sustainable agriculture. In Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation and Agriculture, a team of distinguished researchers delivers a comprehensive and eye-opening look at the positive side of bacteria and other microbes. The book explores the important and positive roles played by microorganisms. Divided into five sections, Good Microbes examines the use of microorganisms and the microbiome in human health, food production, industrial use, bioremediation, and sustainable agriculture. Coverage spans from food allergies, skin disorders, microbial food preservation and fermentation of various beverages and food products, also from an ethnical point of view to beneficial use of microbes in biotechnology, industry, bioeconomy, environmental remediation such as resource recovery, microbial-based environmental clean-up, plant-microbe interactions in biorestauration, biological control of plant diseases, and biological nitrogen fixation. * Provides basic knowledge on bacterial biology, biochemistry, genetics and genomics of beneficial microbes * Includes practical discussions of microbial biotechnology, including the contribution of microbial biotechnology to sustainable development goals * Features a comprehensive introduction and extensive index to facilitate the search for key terms. Perfect for scientists, researchers and anyone with an interest in beneficial microbes, Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation and Agriculture is also an indispensable resource for microbiology graduate students, applied microbiologists and policy makers.
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Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation, and Agriculture
Edited by
Frans J. de Bruijn
INRAE/CNRS, LIPME, Castanet Tolosan Cedex, France
Hauke Smidt
Wageningen University and Research, Wageningen, Netherlands
Luca S. Cocolin
University of Torino, Torino, Italy
Michael Sauer
University of Natural Resources and Life Sciences, Vienna, Austria
David Dowling
Institute of Technology Carlow, Carlow, Ireland
Linda Thomashow
USDA-ARS, Washington State University, Pullman, Washington, USA
This edition first published 2023
© 2023 John Wiley & Sons Ltd
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The right of Frans J. de Bruijn, Hauke Smidt, Luca S. Cocolin, Michael Sauer, David Dowling, and Linda Thomashow to be identified as the author(s) of the editorial material in this work has been asserted in accordance with law.
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Library of Congress Cataloging-in-Publication Data
Names: de Bruijn, Frans J., editor. | Smidt, Hauke, editor. | Cocolin, Luca S., editor. | Sauer, Michael, editor. | Dowling, David, editor. | Thomashow, Linda, editor. Title: Good microbes in medicine, food production, biotechnology, bioremediation and agriculture | edited by Frans J. de Bruijn, Hauke Smidt, Luca S. Cocolin, Michael Sauer, David Dowling, Linda Thomashow.Description: Hoboken, NJ : John Wiley & Sons, 2023. | Includes bibliographical references and index. Identifiers: LCCN 2021042854 (print) | LCCN 2021042855 (ebook) | ISBN 9781119762546 (hardback) | ISBN 9781119762379 (pdf) | ISBN 9781119762461 (epub) | ISBN 9781119762621 (obook) Subjects: LCSH: Microbiology. | Microorganisms.Classification: LCC QR41.2 .G66 2023 (print) | LCC QR41.2 (ebook) | DDC 579--dc23/eng/20211029 LC record available at https://lccn.loc.gov/2021042854LC ebook record available at https://lccn.loc.gov/2021042855
Cover images: © Morsa Images/Getty Images; © David Papazian/Getty Images; © vitranc/Getty Images; © STEVE GSCHMEISSNER/Getty Images; © sturti/Getty Images; © Raycat/Getty Images; © Dmitry Kalinovsky/Shutterstock
Cover design by Wiley
Set in 10.5/13pt STIXTwoText by Integra Software Services Pvt. Ltd, Pondicherry, India
This Book is dedicated to my two daughters, Waverly Klaw and Vanessa Mina for their love, support and interest even from a distance, and to my grandchildren Isabella, Ethan, Cassidy and Elliot, and to Sandrine Faure for her keen interest in the Book and its relevance to sustainability.
Contents
Cover
Title page
Copyright
Dedication
Preface
List of Contributors
Acknowledgments
Introduction
SECTION 1 Good Microbes in Medicine
CHAPTER 1 Modern Medicine Relies on the Help of Microorganisms – From Vaccine Production to Cancer Medication
1.1 Introduction: Good Microorganisms and Our Health
1.2 Bad Microorganisms: Epidemics Boosted Modern Medicine
1.3 Antimicrobial Peptides: A New Therapeutic Alternative to Antibiotics?
1.4 Microorganisms as Tools: Recombinant DNA Technology (rDNAT)
1.5 Vaccines: The Use of Microorganisms in the Frontline against Diseases
1.6 Anticancer Drugs: Many Ways to Fight Cancer with Good Microorganisms
1.7 Gene Therapy: The Future of Modern Medicine
1.8 Concluding Remarks and Perspectives
Acknowledgments
CHAPTER 2 How Nursing Mothers Protect Their Babies with Bifidobacteria
2.1 Bifidobacterium Species and Diversity
2.2 Human Milk Oligosaccharides
2.3 Bifidobacterial Metabolism
2.4 Benefits of Bifidobacterium
2.5 Global Distribution of Bifidobacterium
2.6 Supporting Persistent Bifidobacterium Populations
2.7 Summary
Acknowledgments
CHAPTER 3 Gut Microbiome and the Immune System: Role in Vaccine Response
3.1 Immunology of Vaccines
3.1.1 Induction of Protective Immunity by Vaccination
3.1.2 Evolution of Vaccines
3.1.3 Vaccine Limitations
3.2 Gut Microbiome and the Immune System
3.2.1 Microbiome Development in Life
3.2.2 Host–microbe Interactions: Impact on Health
3.3 Microbiome and Vaccine Response
3.3.1 Mechanistic Studies in Animal Models
3.4 Role of the Microbiome in Vaccine Response in Human Studies
3.5 Conclusions and Future Perspectives
CHAPTER 4 Probiotics for Prevention or Treatment of Food Allergies
4.1 Introduction
4.2 Prevention of Food Allergy
4.3 Treatment of Food Allergy
4.3.1 Clinical Use of Probiotics in Food Immunotherapy
4.3.2 Preclinical Studies of the Effects of Probiotics for Treatment of Food Allergy
4.4 Conclusion
CHAPTER 5 COVID-19, Microbiota, and Probiotics
5.1 Introduction
5.2 Relationship between COVID-19 and the Microbiota
5.3 Respiratory Microbiota in Patients with COVID-19
5.4 Gut Microbiota in Patients with COVID-19
5.5 Probiotics and COVID-19
CHAPTER 6 Underarm Body Odor, the Microbiome, and Probiotic Treatment
6.1 Skin Structure and Function
6.2 Sweat
6.2.1 Sweat Glands
6.2.1.1 Eccrine Glands
6.2.1.2 Apocrine Glands
6.2.1.3 Apoeccrine Glands
6.2.1.4 Sebaceous Glands
6.3 Skin and Underarm Microbiome
6.4 Axillary Microbiome
6.5 Bromhidrosis Pathophysiology
6.5.1 Steroid-based Malodor
6.5.2 Long-chain Fatty Acids (LCFAs)
6.5.3 VFA-based Malodor
6.5.4 Thioalcohol-based Malodor
6.6 Methods to Treat Body Odor
6.6.1 Conventional Methods
6.6.1.1 Deodorants
6.6.1.2 Antiperspirants
6.6.1.3 Antibiotics
6.6.1.4 Medication
6.6.1.5 Botox
6.6.1.6 Surgery
6.6.2 Alternative Methods
6.6.2.1 Pre-, Pro-, and Postbiotics
6.6.2.2 Armpit Bacterial Transplant
6.6.2.3 Bacteriotherapy
6.7 Conclusions
Acknowledgments
CHAPTER 7 The Enigma of Prevotella copri
7.1 Introduction
7.2 Prevotella copri Physiology, Growth, and Metabolism
7.3 Prevotella copri, an Important Member of the Human Gut Microbiota
7.4 The Unexplored Diversity of Prevotella copri
CHAPTER 8 Future Perspectives of Probiotics and Prebiotics in Foods and Food Supplements
8.1 Introduction
8.2 Function of the GI Tract Microbiota
8.3 Modulating the GI Tract Microbiota to Improve Health
8.3.1 Modulating the GI Tract Microbiota with Probiotics
8.3.2 Criteria for a Microorganism to Be Classified as Probiotic
8.4 Modulating the GI Tract Microbiota with Prebiotics
8.5 Modulating the GI Tract Microbiota with Synbiotics
8.6 Future Perspectives
8.6.1 Next Generation Probiotics
8.6.2 Next Generation Prebiotics
Acknowledgments
SECTION 2 Good Microbes in Food Production
CHAPTER 9 Bioprotective Cultures and Bacteriocins for Food
9.1 Introduction
9.1.1 Food Safety Hazards
9.1.2 Bioprotection: Fermentation, Protective Cultures, and Bacteriocins
9.1.3 Fermented Foods
9.1.4 Protective Cultures
9.1.5 Bacteriocins
9.1.6 Bacteriocin Classification
9.2 Bioprotection of Milk and Dairy Products
9.2.1 Milk Products and Their Importance in Society
9.2.2 Spoilage and Food-borne Pathogenic Bacteria in Milk and Dairy Products
9.3 Fermented Dairy Products
9.4 Application of Bacteriocins and Their Protective Cultures in Milk and Dairy Products
9.5 Bioprotection of Meat and Meat Products
9.5.1 Meat and Meat Products and Their Importance in Society
9.5.2 Spoilage and Food-borne Pathogenic Bacteria in Meat and Meat Products
9.6 Fermented Meat Products
9.7 Application of Protective Cultures and Their Bacteriocins in Meat and Meat Products
9.8 Bioprotection of Fresh Fish and Fish Products
9.8.1 Fish and Fish Products and Their Importance in Society
9.8.2 Spoilage and Food-borne Pathogenic Bacteria in Fish and Fish Products
9.9 Fermented Fish Products
9.10 Application of Protective Cultures and Their Bacteriocins in Fish and Fish Products
9.11 Bioprotection of Fruits and Vegetables
9.11.1 Fruit and Vegetables and Their Importance in Society
9.11.2 Spoilage and Pathogenic Bacteria in Fruit and Vegetables
9.12 Fermented Fruits and Vegetables Products
9.13 Application of Protective Cultures and Their Bacteriocins in Fruit, Vegetables, and By-products
9.14 Regulatory Issues in Bioprotection
9.15 Conclusions
Acknowledgments
CHAPTER 10 Aromatic Yeasts: Revealing Their Flavor Potential in Food Fermentations
10.1 Introduction
10.2 Yeast Aroma in Alcoholic Beverages
10.2.1 Yeast: Saccharomyces and Non-Saccharomyces
10.2.2 Aromatic Precursors
10.2.3 Fermentative Aroma Compounds
10.3 Yeast Aroma in Foods from Animal Sources
10.3.1 Yeast: Debaryomyces and Kluyveromyces
10.3.2 Fermentation Aroma Compounds
10.4 Yeast Aroma in Other Fermentations
10.4.1 Vegetables
10.4.2 Traditional Fermentations
10.5 Final Remarks
Acknowledgments
CHAPTER 11 Beneficial Microbiota in Ethnic Fermented Foods and Beverages
11.1 Introduction
11.2 Ethnic Fermented Foods
11.3 Diversity of Beneficial Microorganisms in Ethnic Fermented Foods
11.3.1 Lactic Acid Bacteria
11.3.2 Non-Lactic Acid Bacteria
11.3.3 Yeasts
11.3.4 Filamentous Molds
11.3.5 Probiotic Strains from Ethnic Fermented Foods
11.3.6 Functional Profiles of Beneficial Microorganisms
11.4 Conclusion
CHAPTER 12 No Microbes, No Cheese
12.1 Cheese for Life: The History
12.2 The Technology
12.3 The Market
12.4 Microbes, Milk, and Cheese: A Long Lasting Threesome Love Affair
12.5 Raw Milk Cheese versus Pasteurized Milk Cheese: A Thoughtful Debate about Cheese Quality and Safety
12.6 Starter Cultures versus Non-starter Cultures, Alias, Sprinters versus Marathon Runners
12.7 Cheese Microbial Communities Thrive while Cheese is Aging and Make a Fortune in Aroma, Flavor, Texture, and Color
12.8 Cheese Microbiota and Human Health: Myth or Reality?
12.9 Conclusions
CHAPTER 13 The Microbiome of Fermented Sausages
13.1 Introduction
13.2 The Microbiota of Fermented Sausages
13.3 The Importance of the Sausage’s Mycobiota
13.4 Use of the Autochthonous Microbiome to Improve the Quality and Safety of Fermented Sausages
13.5 Conclusion
CHAPTER 14 The Sourdough Microbiota and Its Sensory and Nutritional Performances
14.1 Introduction
14.2 How the Sourdough Microbiota is Assembled
14.2.1 House Microbiota
14.2.2 Flour
14.2.3 Water
14.2.4 Other Ingredients
14.3 Where and How to Use the Sourdough
14.3.1 Baked Goods and Flours
14.3.2 Conditions of Use
14.3.3 Microbiological and Biochemical Characteristics
14.4 Sourdough to Exploit the Potential of Non-conventional Flours
14.4.1 Legumes
14.4.2 Pseudo-cereals
14.4.3 Milling By-products
14.5 The Sensory Performances of Sourdough Baked Goods
14.6 The Nutritional Performances of Sourdough Baked Goods
14.6.1 Mineral Bioavailability
14.6.2 Dietary Fibers
14.6.3 Glycemic Index
14.6.4 Protein Digestibility
14.6.5 Degradation of Anti-nutritional Factors
14.7 Conclusions
CHAPTER 15 Beneficial Role of Microorganisms in Olives
15.1 Table Olives as Fermented Food
15.1.1 Microbiota of Fermented Olives
15.1.2 Microbial Starters in Olive Fermentation
15.2 Table Olives as Functional/Probiotic Food
15.2.1 Probiotic Microorganisms of Olives
15.2.2 Probiotic Microorganisms as Starters in Olive Fermentation
15.2.2.1 Non-olive Origin Probiotic Starters
15.2.2.2 Olive Origin Probiotic Starters
15.3 Conclusions
CHAPTER 16 The Functional and Nutritional Aspects of Cocobiota: Lactobacilli
16.1 Introduction
16.2 Characteristics of Liquorilactobacillus Cacaonum, Limosilactobacillus Fermentum, and Lactiplantibacillus Plantarum
16.2.1 Nutrition and Growth
16.2.2 Genetics
16.2.3 Metabolic Properties
16.2.4 Potential Food Application of Lactobacilli from Fermented Cocoa Pulp-bean Mass
16.2.5 Starter Cultures
16.2.6 Food Preservation Applications
16.2.7 Organoleptic Applications
16.2.8 Nutritional Applications
16.3 European Regulation of Food Cultures
16.3.1 Food Safety Assessment
16.4 Conclusions
CHAPTER 17 Microbiological Control as a Tool to Improve Wine Aroma and Quality
17.1 Introduction
17.2 Methods of Analysis: Classical and Molecular Methods
17.3 Grape Microbiome
17.4 Succession of Microorganisms during Alcoholic Fermentation
17.5 Microbial Interactions during Alcoholic Fermentation
17.6 Production of Aromas and Wine Quality
17.7 Conclusions
CHAPTER 18 Lambic Beer, A Unique Blend of Tradition and Good Microorganisms
18.1 Introduction
18.2 Lambic Beer, a Long-lasting Brew
18.3 A Unique Blend of Microorganisms
18.4 How Beer-spoiling Bacteria Can Be Wanted
18.5 Yeasts, More than a One-trick Pony
18.6 Conclusions
SECTION 3 Good Microbes in Biotechnology
CHAPTER 19 Microbiology and Bio-economy – Sustainability by Nature
19.1 Introduction
19.2 Economy, Employment, and Microbes – Some Numbers
19.3 Outlook into a Sustainable Future – Microbial Chemical Production as an Example
19.4 What Makes Microorganisms Useful for the Chemical Industry?
19.5 Metabolic Engineering Allows the Design of Microbial Cell Factories
19.6 From Plant to Microbe – Production of the Malaria Medication Artemisinin
19.7 Opening up the Chemical Space with the Tools of Synthetic Biology
19.8 Conclusions
CHAPTER 20 Role of Microorganisms in Environmental Remediation and Resource Recovery through Microbe-Based Technologies Having Major Potentials
20.1 Introduction
20.2 Microorganisms as Important Biological Entities in the Environment
20.2.1 Role of Microorganisms in Urgent Environmental Needs
20.2.1.1 Pollution Control
20.2.1.2 Carbon Sequestration
20.2.1.3 Biofuel Production
20.2.1.4 Biogas Production
20.2.1.5 Biofertilizer Production
20.2.1.6 Production of Single-cell Proteins
20.3 Different Microbial Technologies with High Potential for Environmental Exigencies
20.3.1 Omics Technologies
20.3.2 Nanobioremediation Technology
20.3.3 Electrobioremediation
20.3.4 Microbial Electrosynthesis for CO2 Sequestration
20.3.5 Microbial Fuel Cells (MFCs) for Electricity Generation
20.3.6 Microbial Electrolysis for Hydrogen Production
20.3.7 Consolidated Bioprocessing for Bioethanol Production
20.3.8 Microbial Technologies for Biogas Production
20.3.9 Bioaugmentation
20.3.10 Biogranulation
20.4 Conclusion
CHAPTER 21 Microbes Saving the World? How Microbial Carbon Dioxide Fixation Contributes to Storing Carbon in Goods of Our Daily Life
21.1 Introduction
21.2 Photoautrophic Microorganisms
21.2.1 Cultivation and Applications of Cyanobacteria and Microalgae
21.3 Chemoautotrophic Bacteria
21.3.1 Biotech Applications of Chemoautotrophs
21.4 Synthetic Biology: New-to-Nature CO2 Fixation Pathways
CHAPTER 22 The Biodiesel Biorefinery: Opportunities and Challenges for Microbial Production of Fuels and Chemicals
22.1 The Concept of a Biorefinery
22.1.1 Biorefinery Concept for Biodiesel Production
22.1.2 Microorganisms as Feedstocks for Biodiesel Production
22.1.3 Microbial Upgrading of Waste Streams from Biodiesel Production
22.2 Higher Value Chemicals from Aerobic Glycerol Metabolism
22.2.1 Anaerobic Glycerol Metabolism for Industrial Chemical Production
22.2.1.1 Dehydration of Glycerol to Industrial Relevant Building Blocks
22.2.1.2 Microbial Glycerol Reduction for Chemical Production
22.3 Concluding Remarks
Acknowledgments
CHAPTER 23 The Good Fungus – About the Potential of Fungi for Our Future
23.1 Introduction
23.2 Fungal Biotechnology: The Origins
23.3 Fungi for Moving Forward – Biofuels
23.4 Fungal Enzymes to the Rescue for Sustainable Industries
23.5 Fungal Organic Acids: Jacks of All Trades
23.6 Fungal Metabolites – Weapons against Diseases
23.7 Fungal Products on Demand
23.8 “Green” Fungi for a Sustainable Future
23.9 Biocomputers and Life in Space: The Future of Fungal Biotechnology
23.10 Conclusions
Acknowledgments
CHAPTER 24 Microbes and Plastic – A Sustainable Duo for the Future
24.1 Introduction
24.2 Training Microbes – Gene Technology at Work
24.3 Plastics – Problem or Opportunity?
24.3.1 Plastic Upcycling
24.3.2 The Role of Microbes in Plastic Degradation
24.3.3 Plastic-Eating Microbes
24.3.4 Enzymes – Molecular Scissors for the Breakdown of Recalcitrant Polymers
24.4 Plastic Monomers Generated by Microbes
24.4.1 Polyethylene (PE)
24.4.2 Polyurethane (PU)
24.4.2.1 2,3-butanediol (2,3-BDO)
24.4.2.2 1,4-butanediol (1,4-BDO)
24.4.2.3 Adipic Acid (AA)
24.4.3 Polyethylene Terephthalate (PET)
24.4.3.1 Ethylene Glycol (EG)
24.4.3.2 Terephthalic Acid (TA)
24.4.4 Polystyrene (PS)
24.5 Microbe-made Plastics
24.5.1 Using Bacterial “Fat” as Plastic
24.5.2 Lactic Acid Plastic
24.6 Microbes Work More Precisely than Chemists
24.6.1 How Do You Make a Polymer from Lactic Acid?
24.6.2 Engineered Enzymes as Environmentally Friendly Catalysts
24.7 Microbial Products as Plasticizers (HAA)
24.8 Sugars and More for Plastic-like Applications
24.9 Conclusion
Acknowledgments
CHAPTER 25 Food Waste as a Valuable Carbon Source for Bioconversion – How Microbes do Miracles
25.1 Introduction
25.2 Biofertilizers
25.3 Bioenergy
25.3.1 Hydrolysis
25.3.2 Acidogenesis
25.3.3 Acetogenesis
25.3.4 Methanogenesis
25.3.5 Bio-products
25.3.6 Biochemicals
25.3.7 Bioplastics
25.3.8 Biosurfactants
25.3.9 Biocatalysts
25.4 Conclusions
SECTION 4 Good Microbes and Bioremediation
CHAPTER 26 Microbial-based Bioremediation at a Global Scale: The Challenges and the Tools
26.1 Introduction
26.2 Bioremediation Beyond the Tipping Point
26.3 The Environmental Microbiome as a Global Catalyst
26.4 Designing Agents for Spreading New Traits through the Environmental Microbiome
26.5 Bacterial Chassis for Environmental Interventions
26.6 Inoculation of Newcomers in Existing Microbial Niches: No Piece of Cake
26.7 Programming Large-scale Horizontal Gene Transfer
26.8 Conclusion
Acknowledgments
CHAPTER 27 Ecopiling: Beneficial Soil Bacteria, Plants, and Optimized Soil Conditions for Enhanced Remediation of Hydrocarbon Polluted Soil
27.1 Introduction
27.2 Remediation of Hydrocarbons
27.3 Bioremediation
27.4 Biopiles
27.5 Phytoremediation
27.6 Rhizoremediation of Total Petroleum Hydrocarbons
27.7 Ecopiling
27.8 Conclusion
Acknowledgments
CHAPTER 28 Plant–Microbe Interactions in Environmental Restoration
28.1 Introduction to Plant–Microbe Interactions
28.2 Pollutants and Their Biodegradation
28.2.1 Persistent Organic Pollutants
28.2.2 Pollutants of Natural Origin
28.2.3 Biodegradation and Bioremediation
28.3 Catabolism versus Cometabolism
28.4 Secondary Plant Metabolite Hypothesis
28.4.1 SPM Hypothesis and the Degradation of PCBs
28.4.2 SPM Hypothesis and Other Pollutants as Examples
28.5 Conclusions
Acknowledgments
CHAPTER 29 Microbial Endophytes for Clean-up of Pollution
29.1 Introduction
29.2 Organic Pollutants
29.2.1 Background on Conventional Remediation and Phytoremediation of Common Organic Pollutants
29.2.2 Introduction to Endophyte-assisted Phytoremediation of Organic Pollutants
29.2.3 Endophyte-assisted Phytoremediation of TCE
29.2.4 Endophyte-assisted Phytoremediation of BTEX, PAHs, and Petroleum
29.2.5 Endophyte-assisted Phytoremediation of Herbicides and Pesticides
29.2.6 Endophyte-assisted Phytoremediation of More Recalcitrant Organic Pollutants
29.3 Inorganic Pollutants
29.3.1 Background of Inorganic Pollutants
29.3.2 Phytoremediation of Inorganic Pollutants
29.3.3 Endophytes for Enhanced Remediation of Inorganic Pollutants
29.4 Conclusions
CHAPTER 30 Metagenomics of Bacterial Consortia for the Bioremediation of Organic Pollutants
30.1 Introduction
30.2 Bacterial Consortia
30.2.1 Advantages and Limitations
30.3 Isolation from the Environment: Methods and Problems
30.3.1 Metagenomics
30.3.1.1 Targeted Metagenomics
30.3.1.2 Shotgun Metagenomics
30.4 Consortium-based Bioremediation: Case Studies
30.4.1 Petroleum Hydrocarbon Bioremediation
30.5 Aromatics Bioremediation
30.6 Prospects and Conclusions
Acknowledgments
CHAPTER 31 Soil Microbial Fuel Cells for Energy Harvesting and Bioremediation of Soil Contaminated with Organic Pollutants
31.1 Introduction to Soil Microbial Fuel Cells
31.2 Working Principle of SMFC
31.3 Key Factors Influencing the Performance
31.3.1 Electrode Material
31.3.2 Reactor Design
31.4 Soil Properties
31.5 SMFCs to Bioremediate Contaminated Soils
31.5.1 Petroleum Hydrocarbon
31.5.2 Pesticides
31.6 Conclusions and Future Perspective
CHAPTER 32 Biotechnology for the Management of Plastics and Microplastics
32.1 Introduction
32.2 Microplastics and Their Environmental Effects
32.3 Biotechnological Approaches to Management of Plastic Waste
32.3.1 Biodegradable Bioplastics for Circular Economy
32.3.2 Biodegradation of Synthetic Plastics
32.3.3 Biotechnology for Microplastics Management and Remediation
32.4 Conclusions
Acknowledgments
CHAPTER 33 Bio-electrochemical Systems for Monitoring and Enhancement of Groundwater Bioremediation
33.1 Introduction
33.2 Land/Groundwater Contamination and Remediation Design
33.2.1 In Situ Versus Ex Situ Methods
33.2.2 Active Versus Passive Methods
33.3 Sustainable Remediation
33.4 Verification of Remediation
33.5 Bio-electrochemical Systems
33.5.1 BES Hydrocarbon Remediation
33.5.1.1 BES Design and Remediation Technology
33.5.1.2 Scaling up BES Construction and Design
33.5.1.3 Pump and Treat BES (Ex Situ/Active Remediation Technology)
33.5.1.4 Biopile BES (Ex Situ/Active/Semi-Passive Remediation Technology)
33.5.1.5 Plume Biostimulation (In Situ Active/Semi-Passive Remediation Technology)
33.5.1.6 PRB BES (In Situ/Semi-Passive Remediation Technology)
33.5.1.7 Monitored Natural Attenuation BES – (In Situ/Passive Remediation Technology)
33.5.1.8 Monitoring the Microbe Geo-electric?
33.6 Conclusion
SECTION 5 Good Microbes and Agriculture
CHAPTER 34 Beneficial Microbes for Agriculture: From Discovery to Applications
34.1 Introduction
34.2 Beneficial Microbes Can Be Part of Microbiome Management Concepts
34.3 Beneficial Microbes Are Embedded in the Plant Microbiome: Facts and Problems
34.4 Concepts for Discovering and Capturing Novel Beneficial Microbes
34.4.1 Exploiting Novel Bio-resources for Discovering Beneficial Microbes
34.4.1.1 Wild Relatives – Exploiting The “Back to the Root” Concept
34.4.1.2 Suppressive Soils – Exploiting “Soil Immune Response”
34.4.2 Natural Systems – Harvesting the Best from Nature
34.4.3 Stressed Microbiomes – Exploiting the “Pathobiome” Concept
34.4.4 New Strategies for the Isolation and Cultivation of Beneficial Microbes
34.4.4.1 Cultivation and Isolation of Beneficial Microbes
34.4.5 Linking Cultivation-dependent and -independent Methods for Better Cultivation
34.4.6 Next Generation Physiology, Fingerprinting, and Cell Sorting
34.5 Concepts for Application of Beneficial Microbes
34.5.1 Designing Consortia – A Promising Alternative to Single Microbes?
34.6 Targeted Applications along the Food Supply Chain
34.7 The Vision and Future Challenges
34.8 Concluding Remarks
Acknowledgments
CHAPTER 35 Biological Control of Soilborne Plant Diseases
35.1 Introduction
35.2 Biological Control of Soilborne Pathogens, No Longer a Cottage Industry
35.3 The Holobiont: Functional Coordination of the Microbiome and Its Plant Host
35.4 Root Colonization: Breaching the Barrier
35.5 Host Immunity: Induced Systemic Resistance Links Roots and Foliar Tissues
35.6 Direct Antagonism of Pathogens: Microbial Warfare in the Rhizosphere
35.7 Chemical Warfare in the Rhizosphere
35.8 Antibiotics and the Sustainability of Wheat in the Pacific Northwest
35.9 Dual Control of Pathogens and Insects
35.10 Classic Biocontrol Agents: Bacillus
35.11 Perception and Response of Bacillus to Fungal and Bacterial Competitors
35.12 Streptomyces: “Plants’ Best Friends”?
35.13 Endosphere Colonization and a Tripartite System Benefitting Pollinators
35.14 Biological Control: Safety and Ecosustainability
35.15 Closing Thoughts
Acknowledgments
CHAPTER 36 Classification, Discovery, and Microbial Basis of Disease-Suppressive Soils
36.1 Microbe-based Plant Defense of Roots
36.2 Definitions and Examples of Disease-suppressive Soils
36.3 General Suppression
36.4 Specific Disease Suppression
36.5 Microbial Basis of Specific Suppressive Soils
36.6 Concluding Remarks
CHAPTER 37 Biological Nitrogen Fixation
37.1 Introduction
37.2 Free-living Diazotrophs
37.3 Symbiotic Nitrogen-fixing Bacteria
37.4 Evolution and Taxonomy of Nitrogen-fixing Organisms
37.5 Nodulation and Nitrogen Fixation
37.6 Inoculum Production
37.7 Application of Symbiotic Nitrogen Fixation in Agriculture
37.8 Economic, Social, and Environmental Implications
37.9 Conclusions
Acknowledgments
CHAPTER 38 A Primer on the Extraordinary Efficacy and Safety of Bacterial Insecticides Based on Bacillus Thuringiensis
38.1 Introduction
38.2 Summary of Bt Biology and Its Mode of Action
38.3 Summary of Earlier Studies on Bt Safety
38.4 Key Similarities and Differences between B. Thuringiensis and B. Cereus
38.5 Enterotoxins of B. Thuringiensis
38.6 Summary of Earlier Studies on Bt Safety
38.7 Safety of Bt Bacterial Insecticides to Humans
38.8 Safety and Non-target Effects of Bti Insecticides
38.9 Safety and Non-target Effects of Bt Crops
38.10 Summary and Conclusions
CHAPTER 39 Life of Microbes Inside the Plant: Beneficial Fungal Endophytes and Mycorrhizal Fungi
39.1 The Plant Microbiota
39.2 Fungal Endophytes of Plants
39.2.1 Epichloë spp.
39.2.2 Trichoderma spp.
39.2.3 Serendipita indica
39.2.4 Colletotrichum tofieldiae
39.3 Mycorrhizal Fungi: Ancient Allies of Plants
39.3.1 The AM Symbiosis: From the Origin to the Present
39.3.2 How to Establish a Mutualistic AM Relationship
39.3.3 Genetic Variation among the Partners Affects the Outcome of the Symbiosis
39.3.4 AM Translational Research: Pitfalls and Successes
39.4 Conclusions and Perspectives
Acknowledgments
CHAPTER 40 Aromatherapy: Improving Plant Health through Microbial Volatiles
40.1 Background
40.2 Microbial Volatiles Improving Plant Growth
40.3 Microbial Volatiles Inducing Systemic Resistance in Plants
40.4 Microbial Volatiles Directly Inhibiting Plant Pathogens
40.5 Application of Microbial Volatile Compounds
40.6 Conclusion
CHAPTER 41 Trichoderma for Biocontrol and Biostimulation – A Green Fungus Revolution in Agriculture
41.1 Modern Agriculture with Old Problems
41.2 Trichoderma Who’s Who
41.3 In the Beginning – Trichoderma, a BCA of Plant Pathogens
41.4 Induced Resistance to Biotic Factors for Crop Protection
41.5 Induced Resistance to Abiotic Stress – Cultivation in Adverse Conditions
41.6 Biostimulation – Plant Growth Promotion and Increased Production
41.7 Plant Physiological Benefits – Improved Quality
41.8 Trichoderma Products in Agriculture
41.8.1 Agricultural Sustainability – Reducing the Disparity
41.8.2 A Promising Role for Trichoderma in Agricultural Development
41.9 Conclusions
Acknowledgments
CHAPTER 42 Companies and Organizations Active in Agriculture and Horticulture
42.1 Introduction
42.2 Examples of Important Microbes
42.2.1 Arbuscular Mycorrhizas
42.2.2 Bacillus
42.2.3 Bacillus thuringiensis
42.2.4 Nitrogen-fixing Bacteria
42.2.5 Phosphate-solubilizing Bacteria
42.2.6 Rhizobium rhizogenes
42.2.7 Trichoderma
42.2.8 Pseudomonas
42.3 Great Discoveries
42.3.1 “The Indiana Jones of Fungus Hunters”
42.3.2 From Volatiles in the Rain Forest to Rocket Fuel and Plant Protection in Desert Soil
42.3.3 Using Fungi to Adapt Plants to Climate Change
42.3.4 Agrobacterium Tumefaciens, the Natural Genetic Engineer
42.4 Efficient Translation of Fundamental Research to Industry
42.4.1 Nanjing Agricultural University
42.4.2 Grasslanz Technology Ltd
42.4.3 LLC Bisolbi-Inter
42.5 Examples of Companies Producing Microbes
42.6 Examples of Companies for Registration and Other Forms of Consultation
42.6.1 Requirements for Registration
42.6.2 Companies Specialized in Registration
42.6.3 Small General Consultation Firms
42.7 Acquisitions, Mergers, and Alliances
42.8 Organizations in Biocontrol Science
Acknowledgments
Index
End User License Agreement
List of Tables
Chapter 03
TABLE 3.1 Studies that explore...
Chapter 08
TABLE 8.1 Selected examples of...
TABLE 8.2 Selected examples of...
TABLE 8.3 Selected examples of...
TABLE 8.4 Selected examples of...
Chapter 09
TABLE 9.1 Spoilage and pathogenic...
TABLE 9.2 Microorganisms isolated from...
TABLE 9.3 Types and examples of...
TABLE 9.4 Bioprotection of fish...
TABLE 9.5 Microorganisms used as...
TABLE 9.6 Bacteriocins used for...
TABLE 9.7 Commercial bioprotective cultures...
Chapter 11
TABLE 11.1 Some ethnic fermented...
TABLE 11.2 Some of the ethnic...
TABLE 11.3 Some of the ethnic...
TABLE 11.4 Some of the ethnic...
TABLE 11.5 Some of the ethnic...
TABLE 11.6 Some of the ethnic...
Chapter 12
TABLE 12.1 Main microbes involved...
TABLE 12.2 Representative significant cheese...
Chapter 14
TABLE 14.1 Main findings from...
Chapter 15
TABLE 15.1 Probiotic microorganisms isolated...
Chapter 16
TABLE 16.1 Phenotypic features of...
Chapter 17
TABLE 17.1 Summary of the most...
Chapter 25
TABLE 25.1 Summary of studies...
Chapter 31
TABLE 31.1 Field test performance...
TABLE 31.2 SMFC studies for...
Chapter 38
TABLE 38.1 Food sources and...
List of Illustrations
Chapter 01
FIGURE 1.1 Steps and methodologies...
Chapter 03
FIGURE 3.1 Figure scheme of vaccine...
FIGURE 3.2 Microbial translocation...
FIGURE 3.3 Microbial latency adapted...
Chapter 05
FIGURE 5.1 Interactions between the...
FIGURE 5.2 Frequent situations in...
Chapter 06
FIGURE 6.1 Structure of the skin...
FIGURE 6.2 Topographical distribution...
FIGURE 6.3 Microbiological and biochemical...
FIGURE 6.4 Schematic illustration of...
Chapter 08
FIGURE 8.1 Schematic representation...
FIGURE 8.2 Factors influencing...
Chapter 09
FIGURE 9.1 Examples of beneficial...
FIGURE 9.2 Spoilage and food-borne...
FIGURE 9.3 Main spoilage microorganisms...
Chapter 10
FIGURE 10.1 Modification of the...
FIGURE 10.2 Aroma profile of dry fermented...
FIGURE 10.3
D. hansenii effect
on the...
FIGURE 10.4 Volatile profile of ewe’s...
Chapter 13
FIGURE 13.1 Representation of the main factors...
FIGURE 13.2 Overview of the main bacteria...
Chapter 14
FIGURE 14.1
Lactobacillus
species...
FIGURE 14.2 Worldwide map listing sourdough...
FIGURE 14.3 Summarized characteristics...
FIGURE 14.4 Schematic representation of ...
Chapter 16
FIGURE 16.1 Microbial reactions...
FIGURE 16.2 Incidence of
Liq. cacaonum
...
FIGURE 16.3 Lactobacilli strains...
Chapter 17
FIGURE 17.1 Structure of the ribosomal...
FIGURE 17.2 Monitoring of alcoholic fermentation...
FIGURE 17.3 Monitoring of microbial...
FIGURE 17.4 Changes in chemical...
FIGURE 17.5 Analysis of volatile compounds...
FIGURE 17.6 Development of alcoholic fermentation...
Chapter 18
FIGURE 18.1 General classification...
FIGURE 18.2 Overview of the general...
Chapter 19
FIGURE 19.1 Size comparison of the global...
FIGURE 19.2 Our current economic model...
FIGURE 19.3 Lemons (left) have been...
FIGURE 19.4 EExamples for microbially...
FIGURE 19.5 The malaria drug...
Chapter 20
FIGURE 20.1 Two stage microbial electrosynthesis...
FIGURE 20.2 MFC system for...
FIGURE 20.3 Consolidated bioprocessing...
FIGURE 20.4 Enhanced remediation after...
Chapter 21
FIGURE 21.1 The global biological...
FIGURE 21.2 Photoautotrophic microorga...
FIGURE 21.3 Chemoautotrophic microorga...
FIGURE 21.4 The next generation...
Chapter 22
FIGURE 22.1 The general concept...
FIGURE 22.2 Microbial glycerol...
Chapter 23
FIGURE 23.1
Trichoderma reesei...
FIGURE 23.2
Aspergillus niger...
FIGURE 23.3 Hyphae constituting the my...
Chapter 24
FIGURE 24.1 The four main categories...
FIGURE 24.2 (A) The state-of-the-art...
FIGURE 24.3 Schematic representation...
Chapter 25
FIGURE 25.1 Food waste degradation by...
FIGURE 25.2 Typical composting stages ...
FIGURE 25.3 Food waste degradation...
FIGURE 25.4 Microbial mediated...
Chapter 26
FIGURE 26.1 Stability regimes of...
FIGURE 26.2 Breakdown contributors to ...
FIGURE 26.3 Engineering physical...
FIGURE 26.4 The bacterial surface as...
FIGURE 26.5 Refactoring the...
FIGURE 26.6 Engineering propagation of...
Chapter 27
FIGURE 27.1 Structure of an ecopile....
FIGURE 27.2 Ecopiles used to treat ...
FIGURE 27.3 Bacterial communities...
FIGURE 27.4 Bacterial communities...
FIGURE 27.5 Top 10–12 most abund...
FIGURE 27.6 TPH levels in the ecopile ...
Chapter 28
FIGURE 28.1 Examples of plant–mi...
FIGURE 28.2 Typical logic of...
FIGURE 28.3 Difference between...
FIGURE 28.4 Capability of secondary...
Chapter 31
FIGURE 31.1 Schematic and working...
FIGURE 31.2 Design variants with...
FIGURE 31.3 SMFC reactor designs: (A) ...
FIGURE 31.4 Schematic of configuration...
Chapter 32
FIGURE 32.1 Comparison of brine shrimp...
FIGURE 32.2 Life cycle of plastics in ...
FIGURE 32.3 Predicted pathway for PET ...
FIGURE 32.4 Waxworms and their gut bac...
Chapter 33
FIGURE 33.1 Simple bio-electrochemical...
FIGURE 33.2 Standard remediation...
Chapter 34
FIGURE 34.1 Strategies for the discove...
FIGURE 34.2 CLSM images visualizing...
Chapter 35
FIGURE 35.1 The rhizosphere is the...
FIGURE 35.2 Cells of Pseudomonas...
FIGURE 35.3 Systemic acquired resistan...
FIGURE 35.4 Infection of the cabbage..
FIGURE 35.5 The rhizosphere bacterium ...
Chapter 37
FIGURE 37.1 Nodulation at the root...
FIGURE 37.2 Phylogenetic 16S rRNA...
FIGURE 37.3 Approximate order of...
FIGURE 37.4 Soybean grown in the first...
Chapter 38
FIGURE 38.1 Typical parasporal bodies ...
FIGURE 38.2 Schematic illustration of ...
Chapter 39
FIGURE 39.1 Beneficial effects of plan...
FIGURE 39.2 Scheme of the main cellula...
Chapter 40
FIGURE 40.1 Beneficial effects of micr...
FIGURE 40.2 Application modes of micro...
Chapter 41
FIGURE 41.1 (A) Plate cultures of...
FIGURE 41.2 Evaluation of...
FIGURE 41.3 Plant growth promotion or ...
FIGURE 41.4 (A) Isolation of fungi fro...
FIGURE 41.5 Production of...
FIGURE 41.6 Field applications
Guide
Cover
Title page
Copyright
Dedication
Table of Contents
Preface
List of Contributors
Acknowledgments
Introduction
Begin Reading
Index
End User License Agreement
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Preface
The idea for a book on “Good Microbes” came out of a discussion among scientists of different backgrounds touching on microbiology when the question was raised “why do we always talk and write about microbes in a negative fashion, as pathogens especially in medicine, but also in the preparation of food and in agriculture?”. Human bacteria are often associated with antibiotics, food bacteria with spoilage and sterilization, and agricultural bacteria with pesticides. So the challenge became to think of “good microbes” in different environments and their unique benefits to humanity. Out of these discussions an impressive list of beneficial microbes and their mode of action resulted and a book on “Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation, and Agriculture” materialized. A book that does not aim to exhaustively cover all “Good Microbes” in the latter five disciplines but to introduce several examples of interest in each of the five areas. The book is written for non-specialist scientists as well as an informed public with some basic knowledge of microbiology. The idea is to have five co-editors, who specialize in Medical Microbiology, Food Microbiology, Biotechnical Microbiology, Bio(phyto)remediation, or Agricultural Microbiology. The five specialists have chosen up to ten topics of interest and have selected corresponding authors to contribute the chapters, resulting in a book of approximately 500 pages surveying the five fields. The resulting chapters were edited by the section editor and subsequently by the editor-in-chief, especially for the scientific content and format.
The book aims to highlight the positive aspects of microbes, therefore, the topics chosen clearly emphasize this assumption. The chosen topics are such that non-scientists can also relate to it. For example, in the medical section the reader is led to consider the use of probiotics, in the food section the reader is able to relate to the microbe-initiated fermentation of beer, dough, wine, and cheese, and in the biotechnology section to biofuels, biohydrogen, or bioplastics production or degradation. In the bioremediation section the reader will become familiar with various methods using microbes, sometimes in conjunction with plants in environmental clean-up and in the agriculture section with various approaches without pesticides to use good bacteria and fungi to enhance plant growth and defense against pathogens and under stressful environmental conditions. This is clearly reflected in the introduction of each chapter. It will be clear that often consortia of good microbes (microbiota) are involved and their analysis is complex but possible because of high power “omics” technologies, which can even be used to identify and characterize non-culturable microbes.
The science presented is of high quality and has been reviewed/edited as such by the co-editors and editor-in-chief. The book is written for non-specialist scientists, as well as well-educated citizens, physicians, teachers, and regulators.
Frans J. de Bruijn (Editor in Chief)
List of Contributors
Ahmed AbdelfattahLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam, Germany
Altaf AlBahoQueen’s University BelfastBelfast, Ireland
Hana AmeurFree University of BolzanoBolzano, Italy
Tomás AparicioUniversidad Autónoma de MadridMadrid, Spain
Sara ArbuluUniversity College CorkCork, Ireland
and
Teagasc Food Research Centre Cork, Ireland
Anthoula A. ArgyriHellenic Agricultural Organization DIMITRAAthens, Greece
Kashika AroraFree University of BolzanoBolzano, Italy
Özge AtaUniversity of NaturalResources and Life Sciences 1190 Vienna, Austria
Carmela BellochInstituto de Agroquímica y Tecnología de AlimentosValencia, Spain
Gemma BeltranUniversitat Rovira i VirgiliTarragona, Spain
Gabriele BergGraz University of TechnologyGraz, Austria
Lars M. BlankRWTH Aachen UniversityAachen, Germany
Varsha BohraHong Kong Baptist UniversityKowloon Tong, Hong Kong
Larissa BrumanoUniversity of Sao PauloFederal University of ABCSao Paulo, Brazil
Chris CallewaertGhent University Gent, Belgium
Tomislav CernavaGraz University of TechnologyGraz, Austria
and
Austrian Center for Industrial BiotechnologyGraz, Austria
John ClearyInstitute of TechnologyCarlow, Ireland
Luca S.CocolinUniversity of Turin Torino, Italy
Robert ConlonInstitute of Technology CarlowCarlow, Ireland
Paul D. CotterUniversity College CorkCork, Ireland
and
Teagasc Food Research CentreCork, Ireland
Rune DaneelsGhent UniversityGent, Belgium
Frans J. de BruijnINRA/CNRS Laboratoire des Interactions Plant-Microorganismes et EnvironmentCastanet-Tolosan, France
Jorgen De JongeNational Institute for Public Health and the Environment (RIVM)The Netherlands
Victor de LorenzoUniversidad Autónoma de Madrid Madrid, Spain
Britta De PessemierGhent UniversityGent, Belgium
Jonas De RoosVrije Universiteit BrusselBrussels, Belgium
Luc De VuystVrije Universiteit BrusselBrussels, Belgium
Mirella Di LorenzoUniversity of BathBath, UK
Rory DohertyQueen’s University BelfastBelfast, Ireland
Sharon L. DotyUniversity of WashingtonSeattle, USA
David DowlingInstitute of Technology CarlowCarlow, Ireland
Jakub DziegielowskiUniversity of BathBath, UK
Michael EgermeierBOKU-VIBT University of Natural Resources and Life SciencesVienna, Austria
Valeria EllenaAustrian Centre of Industrial Biotechnology (ACIB GmbH)Vienna, Austria
and
Institute of Chemical, Environmental and Bioscience EngineeringVienna, Austria
Brian FedericiUniversity of CaliforniaRiverside, USA
Leónides FernándezUniversidad Complutense de MadridSpain
Ilario FerrocinoUniversity of TurinTorino, Italy
Valentina FiorilliUniversity of TurinTorino, Italy
Mónica FloresInstituto de Agroquímica y Tecnología de Alimentos Valencia, Spain
Irene FranciosaUniversity of TurinTorino, Italy
Susana FuentesNational Institute for Public Health and the Environment (RIVM)The Netherlands
Amparo GameroUniversitat de ValènciaValencia, Spain
Paolina GarbevaNetherlands Institute of Ecology (NIOO-KNAW) Wageningen, The Netherlands
Enriqueta Garcia-GutierrezUniversity College CorkCork, Ireland
and
Teagasc Food Research CentreCork, Ireland
Daniel Garrido-SanzUniversidad Autónoma de MadridMadrid, Spain
Thomas GasslerUniversity of Natural Resources and Life Sciences1190 Vienna, Austria
Kieran J. GermaineInstitute of TechnologyCarlow, Ireland
Xuemei Liu GermaineInstitute of TechnologyCarlow, Ireland
Marco GobbettiFree University of BolzanoBolzano, Italy
Beatriz Gómez-SalaUniversity College CorkCork, Ireland
and
Teagasc Food Research CentreCork, Ireland
Helena Ipe Pinheiro GuimaraesNational Institute for Public Health and the Environment (RIVM)The Netherlands
Z. H. HassanIndonesian Center for Agricultural Postharvest Research and Development Indonesian Agency for AgriculturalResearch and Development (IAARD)West Java, Indonesia
and
Wageningen University & ResearchWageningen, The Netherlands
Britta E. HeissUniversity of California DavisDavis, USA
Henric M.T. HintzenRWTH Aachen UniversityAachen, Germany
F. HugenholtzWageningen University & ResearchThe Netherlands
and
The Dutch Research Council (NWO)The Hague, The Netherlands
Mariangela HungriaEMBRAPA SojaParaná, Brazil
Nick M. JensenUniversity of California DavisDavis, USA
Maria KazouAgricultural University of AthensAthens, Greece
Bongkyu KimUniversity of BathBath, UK
Eduardo KleingesindsUniversity of Sao PauloSao Paulo, Brazil
Petia Kovatcheva-DatcharyUniversity of WürzburgWürzburg, Germany
Rajat KumarHong Kong Baptist UniversityKowloon Tong, Hong Kong
Peter KusstatscherGraz University of TechnologyGraz, Austria
Luisa LanfrancoUniversity of TurinTorino, Italy
Ana Shein Lee DiazNetherlands Institute of Ecology (NIOO-KNAW)Wageningen, The Netherlands
Melissa LeTourneauWheat Health, Genetics and Quality Research UnitPullman, USA
Agnes S. Y. LeungThe Chinese University of Hong KongHong Kong
Wenyin LohDepartment of PaediatricsSingapore
Matteo LoritoUniversity of Naples Federico IINaples, Italy
and
Institute for Sustainable Plant ProtectionNational Research Council (CNR-ISPP)Naples, Italy
Ben LugtenbergLeiden UniversityLeiden, The Netherlands
Tomas MacekUniversity of Chemistry and Technology, PraguePrague, Czechia
Piyush MalaviyaUniversity of JammuJammu and Kashmir, India
Rajesh MaliInstitute of Technology CarlowCarlow, Ireland
Manu MkHong Kong Baptist UniversityKowloon Tong, Hong Kong
Marta MartinUniversidad Autónoma de MadridMadrid, Spain
Esteban Martínez-GarcíaUniversidad Autónoma de MadridMadrid, Spain
Albert MasUniversitat Rovira i VirgiliTarragona, Spain
Diethard MattanovichUniversity of Natural Resources and Life SciencesVienna, Austria
David A. MillsUniversity of California DavisDavis, USA
Jatziri Mota-GutierrezUniversity of TurinTorino, Italy
Marta MozotaUniversidad Complutense de MadridSpain
Loriane MurphyInstitute of Technology CarlowCarlow, Ireland
Deepak PantFlemish Institute for Technological Research VITO Mol, Belgium
Jakub PapikUniversity of Chemistry and Technology, PraguePrague, Czechia
Letícia ParizottoUniversity of Sao PauloSao Paulo, Brazil
Adalberto Pessoa JuniorUniversity of Sao PauloSao Paulo, Brazil
Andrea PoloFree University of BolzanoBolzano, Italy
Kalliopi RantsiouUniversity of Turin
Torino, Italy
Miguel Redondo-NietoUniversidad Autónoma de MadridMadrid, Spain
Rafael RivillaUniversidad Autónoma de MadridMadrid, Spain
Juan Miguel RodríguezUniversidad Complutense de MadridMadrid, Spain
Lily RoneyQueen’s University BelfastBelfast, Ireland
Hannes RussmayerBOKU-VIBT University of Natural Resources and Life SciencesVienna, Austria
Paula Sansegundo-LobatoUniversidad Autónoma de MadridMadrid, Spain
Michael SauerUniversity of Natural Resources and Microbial BiotechnologyVienna, Austria
Rozi SharmaUniversity of Jammu
Jammu and Kashmir, India
Smiley SharmaUniversity of JammuJammu and Kashmir, India
Hauke SmidtWageningen University & ResearchWageningen, The Netherlands
Matthias SteigerAustrian Centre of Industrial Biotechnology ACIB Vienna, Austria
Michal StrejcekUniversity of Chemistry and TechnologyPrague, Czechia
Jachym SumanUniversity of Chemistry and TechnologyPrague, Czechia
Jyoti Prakash TamangSikkim UniversitySikkim, India
Mimi L. K. TangThe Royal Children’s HospitalMelbourne, Australia
Chrysoula C. TassouHellenic Agricultural Organization DIMITRAAthens, Greece
Namrata ThapaSikkim UniversitySikkim, India
Linda ThomashowUSDA ARS, Washington State University Washington, USA
Till TisoRWTH Aachen UniversityAachen, Germany
María Jesús TorijaUniversitat Rovira i VirgiliTarragona, Spain
Robert J. TournayUniversity of WashingtonSeattle, USA
Effie TsakalidouAgricultural University of AthensAthens, Greece
Ondrej UhlikUniversity of Chemistry and Technology, Prague Prague, Czechia
Debbie Van BaarleNational Institute for Public Health and the Environment (RIVM)The Netherlands
and
University Medical Center Groningen (UMCG)The Netherlands
Tom Van De WieleGhent UniversityGent, Belgium
Mutian WangInstitute of TechnologyCarlow, Ireland
Birgit WassermannGraz University of TechnologyGraz, Austria
and
Austrian Center for Industrial Biotechnology Graz, Austria
David M. WellerUSDA ARS, Washington State UniversityWashington, USA
Gina WelsingRWTH Aachen University
Aachen, Germany
Birger WolterRWTH Aachen UniversityAachen, Germany
Jonathan W. C. WongHong Kong Baptist UniversityKowloon Tong, Hong Kong
Sheridan Lois WooUniversity of Naples Federico IINaples, Italy
Mingming YangNorthwest A&F UniversityYangling, P. R. China
E. G. ZoetendalWageningen UniversityWageningen, The Netherlands
Acknowledgments
Frans J. de Bruijn would like to thank INRAE/CNRS and the Labex Tulip for their support of his editorial work. He would also like to thank Claudine Hendriksen for her relentless support during the edition of this volume. Linda Thomashow would like to thank the USDA for their support for her editorial work on the book.
Introduction
The majority of well educated lay people and even researchers in non-related fields, when asked “what is the impact of bacteria or microbes on medicine, food production, and agriculture?”, are likely to respond that the microbes are nocive, pathogenic, must be controlled by antibiotics and sterilization and combatted by pesticides. This general negative notion is quite strong, ubiquitous and general throughout the population. Microbiology as a discipline is slated the same way and many microbiology texts are oriented in this direction. Here we would like to introduce an opposite point of view that bacteria and other microbes play important positive roles in medicine, food production, biotechnology, bioremediation and agriculture. In this book “Good Microbes in Medicine, Food, Biotechnology, Bioremediation and Agriculture” we would like to present a number of strong examples of the positive application of microbes in the above mentioned five fields.
SECTION 1: GOOD MICROBES IN MEDICINE, CO-EDITED BY HAUKE SMIDT
In Section 1 Chapter 1, we will focus on the role of good microbes in modern medicine; after that the focus will shift to their roles in a new field of medicine, namely probiotics or the use of microbes to positively influence the human microbiota, especially of the gastrointestinal tract, and thereby control diseases. The human gastrointestinal (GI) tract harbours a complex community of 3.9 × 1013 microbial cells, equalling the number of human cells that is 3.7 × 1013 (Chapter 8). This complex community, known as microbiota, comprises diverse microorganisms, including bacteria, archaea, and eukaryotes, of which bacteria is the predominant domain, that contributes to host metabolism and the immune system (Chapter 8). The composition and metabolic activity of the microbiota are considered to be among the critical factors in maintaining and improving host health. In turn, imbalances regarding microbial composition and metabolic activity have been associated with development of several intestinal and other diseases including, e.g., inflammatory bowel disease, obesity, diabetes, allergic diseases and psychiatric disorders such as cardiovascular disease and psychiatric disorders such as depression. Modulating the GI tract microbiota through dietary intervention, including administration of probiotics, is considered to be a promising strategy to restore and maintain the composition and metabolic activity of the GI tract microbiota (Chapter 8). Probiotics are preparations of microbes that have a beneficial effect on the intestinal flora. Several examples of their use to positively influence the intestinal microbiota of nursing babies, mitigate medical problems associated with vaccine responses, allergies, COVID-19 infections and bad body odor will be introduced below.
Good Microbes in Modern Medicine
Our survival relies on many good microorganisms. They can act in their living form directly on our bodies, and they are also widely used as microbioreactors to produce relevant therapeutic products for the treatment of diseases. Good microorganisms have played an essential role in the development of modern medicine, which started with the fight against infectious diseases that promoted the search for antipathogenic agents. The discovery of penicillin, the first therapeutic product isolated from microbial sources against pathogens, was the precursor of new biological medicines. Antibiotics revolutionized the treatment of infectious diseases. However, due to very resistant superbugs, we have recently been facing a threat to public health. Therefore, new antimicrobial agents are needed. In addition, we deal with new epidemics, a growing number of cancer cases, and other genetic conditions for which a cure seemed improbable. Fortunately, DNA recombinant technology has given new applications to good microorganisms in treating these diseases as well. They can be used as production platforms (hosts), tools for replication, plasmid stock or as a source of enzymes necessary for methodologies employed in genetic modification processes. Thus, new sophisticated biopharmaceuticals have been developed, such as vaccines, anticancer drugs, and gene therapy. Thanks to good microorganisms, vaccines can be produced more safely, economically, and quickly. Moreover, microorganisms contribute to producing anticancer drugs as natural producers of biomolecules, platforms for recombinant expression, or agents in immunotherapies. Recently, they have also been applied as carriers of nucleic acids in gene therapy, mainly to treat hereditary diseases. Therefore, good microorganisms have been supporting modern treatments that led to rapid responses to epidemic outbreaks, new therapies for preventable diseases and a chance of curing incurable diseases. In Chapter 1, some of the main applications of good microorganisms in modern medicine are presented.
Beneficial Infant-associated Bifibacterium
Bifidobacterium species are common residents of the human gastrointestinal tract. While they colonize people of all ages, they are most strikingly found in the infant gut, where they degrade human milk oligosaccharides (HMOs) found in breast milk. Individual Bifidobacterium strains encode unique sets of transport proteins and enzymes called glycoside hydrolases (GHs) to metabolize these diverse carbohydrates in milk (see Chapter 2). By fermenting HMOs, bifidobacteria produce bioactive end products such as lactate and acetate. These molecules reduce the pH of the gut, protect against invasion by harmful pathogens, and likely support healthy childhood growth and immune development. Although Bifidobacterium colonization promotes infant health, levels of these bacteria vary based on geography, breastfeeding rates and other factors. However, recent trials suggest that providing infants with probiotic Bifidobacterium, in combination with HMOs that sustain their nutrient niche, can support the persistent growth of these beneficial bacteria. These observations will be presented in Chapter 2.
Role of the Microbiome in Vaccine Response
Vaccination mediated protection is one of the best ways to control infectious diseases. However, inter-individual variation in vaccination responses, regardless of the type of vaccine, affects the effectiveness of vaccines. Demographics, comorbidities and aging are a few variables that may influence the differences in vaccination response and effectiveness. Novel strategies aimed at increasing immunogenicity of vaccines and thereby protecting all individuals is a major public health interest. The gastrointestinal tract is an ecosystem for various microorganisms and a hotspot for microbiota-derived molecules.
These compounds found in the gut can travel through the bloodstream and are able to enter the systemic circulation from the intestinal lumen. Thus, bacteria or bacteria-derived products may act as natural adjuvants and their interplay with immune cells could ultimately impact immune responses to infectious diseases and vaccination (see Chapter 3). Animal and human population studies indeed indicate that this hypothesis might play an important role in the shaping of a proper systemic immune response to vaccination. The effector mechanisms by which the gut microbiota can impact immune response and how these can be adjusted for a more efficient response to vaccinations will be discussed in Chapter 3.
Probiotics and Food Allergies
The search for effective preventive and treatment strategies for food allergy is becoming ever more important as the prevalence of food allergy increases. Since the hygiene hypothesis was first proposed, there has been growing evidence that dysbiosis plays an important role in the pathogenesis and development of food allergy. Chapter 4 presents the evidence for probiotics in the prevention and treatment of food allergy. Published studies show an inconsistent role for probiotics in prevention of disease, likely due to differences in probiotic strains used, as well as the dose and duration of therapy in the different studies. Application of probiotics for the treatment of food allergy appear more promising, with favourable results in both clinical and preclinical studies. It is noteworthy that probiotic effects appear to be species and strain-specific, with benefits primarily reported for L. rhamnosus GG and certain Clostridia strains (see Chapter 4).
COVID-19, Microbiota and Probiotics
SARS-CoV-2 is the agent of the current COVID-2 pandemic. This virus interacts with the mucosal surface lining the upper respiratory tract, which is associated with complex microbiota. Recent studies suggest an implication of the microbiota of the respiratory and gastrointestinal tracts in the modulation of the infection by this virus (see Chapter 5). In fact, the susceptibility to the infection and the severity of the disease seems higher when there is a depletion of butyrate-producing strict anaerobes in the gut microbiome. Few clinical trials involving the use of probiotics to prevent or minimize the impact of COVID-19 have been published so far, but they show a significant impact by shortening the duration of diarrheal episodes and decreasing the risk of respiratory failure and death. These observations will be discussed in Chapter 5.
Underarm Microbiome and Probiotics
Bromhidrosis or excessively foul-smelling body odor is a chronic pathologic condition that usually comes from axillary skin regions. This offensive body odor can have a significant impact on the quality of life and can cause professional, social, and emotional distress. There are two main reasons for underarm malodor: the presence of apocrine sweat, which is the precursor of body odor, and the underarm microbiome, which converts the precursors into malodorous volatiles. Secretions from either apocrine and eccrine glands are primarily odorless but become malodorous after bacterial catabolism. Factors that worsen the condition are poor hygiene or underlying complications that promote bacterial overgrowth, including obesity, intertrigo, diabetes, and erythrasma. Conventional therapies usually focus on antimicrobial treatments (e.g., deodorants containing antibacterial agents and antibiotics) or prevention of sweating (e.g., antiperspirants, medication, botox, surgery). However, alternative therapies promote the growth of beneficial and good-smelling bacteria and inhibit the growth of odor-causing bacteria. Promicrobiome therapies could rebalance the composition of the cutaneous microbiota and reduce smelly body odor in a sustainable manner. The latter will be discussed in Chapter 6.
Prevotella Copri: Beneficial or Detrimental
The gut microbiota plays an important role in human metabolism and health by interacting with host diet. An example of such a bacterium is Prevotella copri, the most abundant Prevotella species in the human gut that has been associated with diet, improved or impaired host metabolic health, and gut inflammation. Thus, there is a growing body of interest in research to further elucidate the drivers of the potentially beneficial or detrimental effect of P. copri
