Microbial Engineering for Therapeutics

Description

This book highlights the recent advances in the field of microbial engineering and its application in human healthcare. It underscores the systemic and synthetic biology approaches for engineering microbes and discusses novel treatments for inflammatory bowel diseases based on engineered probiotics. The book also reviews the different options and methods for engineering microbes, ranging from recombinant DNA technology to designing microbes for targeting specific sites and delivering therapeutics. Further, it discusses genetically engineered microorganisms for smart diagnostics and describes current approaches in microbial gene editing using CRISPR-Cas9-based tools. Lastly, it summarizes the potential applications of human microbiome engineering in improving human health and explores potential strategies for scaling-up the production of engineered microbial strains for commercial purposes, as well as the challenges. Given its scope, this book is a valuable resource for students, researchers, academics and entrepreneurs interested in understanding microbial engineering for the production of commercial products. Contents Editors and Contributors Part I: Introduction to Microbial Engineering 1: Exploring the Potential of Microbial Engineering: The Prospect, Promise, and Essence 1.1 Introduction: The Prospect 1.1.1 Origins of the Use of Microbes for Disease Therapy 1.2 Toolbox for Engineering Living Therapeutics 1.2.1 Chassis Selection 1.2.2 Sense and Control 1.2.3 Memory Circuits 1.2.4 Production and Delivery of Therapeutic Molecules 1.2.4.1 Genetic Actuators: Reporters 1.2.5 Biocontainment and Biosafety 1.2.6 Probiotics Collection at the Registry of Standard Biological Parts 1.3 Engineering Microbes for Human Health: The Promise 1.4 Engineering Microbes to Rewire Metabolism 1.4.1 Phenylketonuria 1.4.2 Hyperammonemia 1.4.3 Diabetes 1.5 Engineered Bacteria to Modulate the Immune System 1.5.1 Inflammatory Bowel Disease 1.5.2 Mucositis 1.6 Engineering Probiotics for the Treatment of Bacterial Infections 1.6.1 Pseudomonas aeruginosa 1.6.2 Vibrio cholerae 1.6.3 Salmonella Species 1.6.4 Enterococcus Species 1.7 Engineering Probiotics for Disease Diagnosis 1.7.1 Quorum-Sensing System 1.7.2 Biosensing to Detect Gut Inflammation 1.7.3 Biosensing for Cancer Diagnosis 1.8 Future Prospects: The Essence References Part II: Microbial Engineering Approaches 2: Role of System Biology in Microbial System 2.1 Introduction 2.2 Industrial Microbial Systems 2.2.1 Production of Anti-Listeria Chemicals 2.2.2 Isobutanol Production 2.2.3 Food Microbiology 2.3 Plant Microbial Systems 2.3.1 Bioremediation 2.3.2 Plant-Associated Microbiomes 2.4 Biomedical Microbial Systems 2.4.1 Metabolic Network Modelling of the Gut Microbiome 2.4.2 Studying Host-Pathogen Interaction 2.4.3 Adaptation of Microbes to Nutritional Conditions Inside the Cell 2.4.4 Modelling the Population Dynamics of the Microbes 2.4.5 Vaccine Development 2.5 Challenges and Ways to Overcome Them References 3: Synthetic Biology: Refining Human Health 3.1 Introduction 3.2 Applications of Synthetic Biology in Human Health 3.2.1 Pathogen Mechanisms 3.2.2 Immune Systems 3.2.3 Vaccines 3.2.4 Drug Discovery 3.2.5 Drug Production and Drug Delivery 3.2.6 Breaking Bacterial Resistance by Designer Phages 3.3 Applications of Engineered Synthetic Ecosystems 3.3.1 Targeting Microbial Communities in Engineering 3.3.2 Biosensors and Biosensing 3.3.3 Biodegradation 3.3.4 Biosynthesis 3.3.5 Microbial Biofuel Production 3.4 Some Limitations of Synthetic Biology 3.4.1 Biosafety Concerns 3.4.2 Allergies 3.4.3 Carcinogens 3.4.4 Pathogenicity or Toxicity 3.4.5 Change or Depletion of the Environment 3.4.6 Horizontal Gene Transfer 3.5 Conclusion and Future Prospect in Synthetic Biology for Humans References 4: Gut Microbiome and Obesity: Connecting Link 4.1 Introduction to Obesity 4.1.1 Obesity and Comorbidities 4.1.2 Metabolic Syndrome 4.2 Etiologies of Obesity 4.2.1 Polygenic Nature of Obesity: Leptin and Ghrelin 4.2.2 Incidence and Prevalence 4.2.3 Difference Between Agrarian and Western Diet 4.2.4 Diet and Microbiome 4.2.5 Connection Between Diet and Disease 4.3 Current Interventions to Obesity 4.3.1 Non-pharmacological Interventions 4.3.2 Pharmacological Interventions (Fig. 4.2) 4.3.2.1 Orlistat (Xenical) 4.3.2.2 Phentermine and Topiramate Extended Release 4.3.2.3 Lorcaserin (Belviq) 4.3.2.4 Bupropion SR and Naltrexone SR (Contrave) 4.3.2.5 Liraglutide (Saxenda, Victoza) 4.3.3 Bariatric Surgery 4.3.4 Shortcomings of Intervention 4.4 Gut Microbiome and Obesity 4.4.1 Gut Microbiome and Energy Harvest from Foods 4.4.2 Firmicutes and Bacteroidetes Phyla 4.4.3 Gut Microbiome and Leaky Gut Syndrome 4.5 Inflammation and Obesity 4.5.1 Low-Grade Chronic Inflammation 4.5.2 Inflammation and Metabolic Consequences 4.5.3 Vagal Afferent Neurons 4.6 New Frontiers in the Treatment of Obesity and Associated Comorbidities 4.6.1 Vagal Nerve Blockade 4.6.2 Fecal Microbiota Transplant 4.7 Conclusion References 5: Engineering Microbes for Smart Diagnostics and Lab-on-Chip 5.1 Introduction 5.2 Microbial Engineering 5.2.1 Factors Affecting the Choice of Microbial Species for Diagnostics and Therapeutics 5.2.2 Engineered Microbes as Sensors for Diagnosis 5.2.3 Genetic Circuits in Microbial Diagnostics 5.3 Microfluidics and Microbial Engineering 5.3.1 Engineered Microbes as a Functional Part of Microfluidics 5.3.2 Toxicity Detection 5.3.3 Sensing of Biomolecules 5.4 Microbial Engineering Facilitated by Microfluidics 5.4.1 DNA Recombination 5.4.2 Transformation 5.4.3 Microbial Selection/Screening 5.4.4 Genotyping 5.4.5 Phenotyping 5.5 Microbial Consortia Engineering in Microfluidics 5.6 Future Scope of Microfluidics and Microbial Engineering in Diagnostics 5.7 Conclusion References 6: Bacteriophage and Virus Engineering 6.1 Introduction 6.2 Engineering Bacteriophage for Biotechnological Applications 6.2.1 Phage for Delivery of Drug Molecules 6.2.2 Phage to Deliver Peptides/Protein Molecules 6.2.3 Phage for Gene Therapy 6.2.4 Phage Display Technology 6.3 Engineering Bacteriophage for Medical Applications 6.3.1 Phage-Based Biosensors for Pathogen Detection 6.3.2 Phage for Biomedical Imaging 6.3.3 Phage for Treatment of Infections (Phage Therapy) 6.3.4 Phage for Treating Anti-Microbial Resistance 6.4 Engineering Bacteriophage for Biocontrol of Pathogens in Food and Agriculture 6.5 Future Scope References 7: CRISPR Technologies: A Tool for Engineering Microbes 7.1 Introduction 7.2 Bacterial CRISPR System 7.2.1 Adaptation 7.2.2 crRNA Maturation 7.2.3 Interference 7.2.3.1 Class 1 Interference Machinery 7.2.3.2 Class 2 Interference Machinery 7.3 Technological Overview of CRISPR/Cas9 7.3.1 Genetic Engineering with CRISPR-Cas9 7.3.2 Regulation of Gene Transcription by Using dCas9 7.3.3 Infectious Disease Applications 7.3.4 Understanding Host-Pathogen Interactions 7.3.5 Infectious Disease Diagnostic Development 7.3.5.1 Diagnostics Using CRISPR-Cas9 7.3.5.2 Applications Based on CRISPR/Cas12 and CRISPR/Cas13 7.3.6 CRISPR-Based Therapies in the Treatment of Acute and Chronic Viral Infections 7.3.7 CRISPR ``Vaccines´´ 7.3.8 CRISPR-Based Therapies for Bacterial Infections 7.4 Impediments to CRISPR Therapeutics References Part III: Health Benefits 8: Recombinant Vaccines: The Revolution Ahead 8.1 Introduction 8.2 Vaccine Immunology 8.3 Herd Immunity 8.4 Types of Vaccines 8.4.1 Whole Pathogen Live-Attenuated Vaccines 8.4.2 Whole Pathogen Killed or Inactivated Vaccines 8.4.3 Subunit Vaccines 8.4.3.1 Toxoid Vaccines 8.4.3.2 Recombinant Vaccines Recombinant Protein-Based Vaccines Recombinant Virus-Like Particles Polysaccharide and/or Glycoconjugate Vaccines 8.5 New Era of Vaccinology: Shaping the Future of Immunization 8.5.1 Adjuvants and Novel Vaccine Delivery Systems 8.5.2 Bacterial and Viral Vaccine Vectors 8.5.3 Nucleic Acid Vaccines 8.5.4 Reverse and Structure-Based Vaccinology 8.5.5 Vaccine Development Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) 8.6 Clinical Trials 8.7 Conclusion: The Challenges and Revolution Ahead References 9: Microbe-Host Metabolic Interaction: Probiotic Approach 9.1 Introduction 9.2 Probiotics 9.2.1 Gut Microbial Composition 9.2.2 Probiotics-Pathogen in the Host GIT 9.2.3 Immunomodulation 9.2.3.1 Epithelial Barrier 9.2.3.2 Innate Immunity 9.2.3.3 Adaptive Immunity 9.3 Probiotics in Clinical Practices 9.4 Gut-Brain-Immune Axis 9.5 Gut Microbiome and Malnutrition 9.6 Gut Microbiome and Covid-19 9.7 Emerging Trends and Innovations 9.7.1 Next-Generation Probiotics 9.7.2 Postbiotics-Parabiotics 9.7.3 Faecal Microbiota Transplantation 9.7.3.1 Mechanism of Action of FMT on Recurrent CDI 9.7.4 CRISPR/Cas9 System 9.8 Summary and Future Perspectives References 10: Designer Microbes: Oncotherapy Approach 10.1 Introduction 10.2 Brief History of Usage of Bacteria and Virus in Oncotherapy 10.3 Bacterial Oncotherapy 10.3.1 Bacteria Producing Anti-cancer Drugs 10.3.1.1 Streptomyces antibioticus 10.3.1.2 Streptomyces verticillus 10.3.1.3 Streptomyces peucetius var. caesius 10.3.1.4 Streptomyces caespitosus 10.4 Probiotics in Anti-cancer Therapy 10.5 Microbial Engineering for Anti-cancer Therapy 10.5.1 Designer Bacteria in Cancer Immunotherapy 10.5.2 Clinical Trials of Bacterial Oncotherapy 10.6 Viral Oncotherapy 10.6.1 Viruses in Oncotherapy 10.6.1.1 Vaccinia Virus 10.6.1.2 Herpes Virus 10.6.2 Strategies to Improve Oncolytic Viral Therapy 10.7 Conclusion and Future Prospects References 11: The Human Gut Microbiome in Health, Disease, and Therapeutics 11.1 Introduction: The Human Gut Microbiota and Why Do We Care? 11.2 The Assembly of the Gut Microbiota and Their Composition 11.3 Impaired Gut Microbiome and Its Attribution to Chronic Diseases 11.3.1 Inflammatory Bowel Disease (IBD) 11.3.2 Autoimmune Disease 11.3.3 Cardiovascular Disease 11.3.4 Obesity 11.3.5 Type 2 Diabetes Mellitus 11.3.6 Behavioral Disorders 11.4 Gut Microbiome as Therapeutic Target 11.5 Future Perspective References 12: Use of Engineered Bacteria for the Production of Green Chemical and Pharmaceuticals 12.1 Introduction 12.2 Enzymes 12.3 Polysaccharides 12.4 Nutrients 12.5 Antibiotics and Chemotherapeutic Agents 12.6 How to Engineer Bacterial for the Production of Green Chemical 12.6.1 Bacteria and Its Engineering to Produce Chemicals 12.6.1.1 Organic Acids 12.6.1.2 Rare Sugars and Sugar Alcohol 12.6.1.3 1,3-Propanediol 12.6.1.4 Vitamins and Amino Acid 12.6.1.5 Biofuels 12.6.1.6 Use of Lignocellulosic Feedstocks 12.6.2 Pharmaceutical Industries and Use of Engineered Bacteria 12.6.3 Advances in Bacterial Engineering 12.6.4 Development of New Bacterial Strain for the Production of Green Chemicals 12.6.4.1 Alkaloids 12.6.4.2 Terpenoids 12.6.4.3 Flavonoids 12.6.4.4 Polyketides and Non-ribosomal Peptides 12.6.5 Leap Between Laboratory to Industry for Product Development 12.6.5.1 Metabolism and Physiology 12.6.5.2 Volume Change Effect 12.6.5.3 Final Product Toxicity 12.7 Conclusion and Future Prospects References 13: Fat Fighting Microbes 13.1 Introduction 13.2 Relationship Between ``Gut Microbiota and Obesity´´ 13.3 Evidence That Gut Microbiota Have a Role in Obesity and Dysbiosis 13.4 Gut Microbiota Link with Obesity: Mechanistic Insight 13.5 Gut Microbiota in Energy Harvesting from Indigestible Food 13.6 Gut Microbiota Influence Fatty Acid Oxidation 13.7 Gut Microbiota Influences Fasting Induced Adipose 13.8 Microbial Enterotypes of Obesity 13.9 Mechanisms Linking Gut Microbiome and Obesity 13.10 Microbiome-Based Therapy for Obesity Treatment 13.11 Prebiotics Increase Bifidobacterium, as well as Reduce Obesity 13.12 Engineered Microbes Lessen Food Intake and Lower Body Weight 13.13 Probiotics in Modulation of Gut Microbiota in Context to Obesity 13.14 Conclusion References Part IV: Innovation and Translation 14: Scale-Up of Engineering Strain for Industrial Applications 14.1 Introduction 14.2 Selection of a Host Strain 14.3 Pathway Construction, Engineering, and Optimization for Product Formation 14.3.1 Introduction of Heterologous Pathways to Non-native Producers 14.3.2 Development of De Novo Pathways 14.4 Scale-Up of Fermentation 14.4.1 Principles of Scale-Up Process 14.4.2 Standard Procedures for Successful Scale-Up Procedures 14.5 Problems Associated with Scale-Up 14.5.1 Metabolic Shifts 14.5.2 Reduced Mixing Quality and Enhanced Exposure to Stress 14.5.3 Plasmid Stability 14.6 Process Characterization 14.7 Optimizing Scale-Up Fermentation Processes 14.7.1 A Brief Illustration of the Theoretical Steps with the Stages of Fermentation Optimization and Scale-Up 14.8 Conclusion References 15: Affordable Therapeutics Through Engineered Microbes 15.1 Introduction 15.2 Toolbox Used for Tailoring Living Therapeutics 15.2.1 Sense and Control 15.2.2 Living Chassis 15.2.3 Memory 15.3 Development and Distribution of Therapeutic Molecules 15.4 Role of Genetically Tailored Microbial Species in Delivering Therapeutics 15.4.1 In Drug Delivery 15.4.2 For the Treatment of Metabolic Disorders 15.4.3 For Diagnosis and Detection of Diseases 15.4.4 To Combat Cancer 15.5 Synthesis of Natural Compounds with Pharmaceutical Significance 15.6 Stem Cell Reprogramming and Genome Edition Using Engineered Bacteria 15.7 Challenges and Outlook References 16: COVID-19: Lesson Learnt from Diagnostics to Therapeutics 16.1 Introduction 16.2 Look Back at the Past 16.3 COVID-19 Pandemic: What Lessons Have Been Learned? 16.4 The Phase of Quarantine and Isolation 16.5 Psychological Implications of COVID-19 16.6 Drug Repurposing and Treatment Strategies: Dynamic Area 16.7 Diagnosis for COVID 19 16.8 Lessons Learned from COVID-19 Research 16.9 A Glance at the Vaccine World of COVID-19 16.10 The Future of Critical Care: Lessons from the COVID-19 Crisis 16.11 Human Lessons Extracted from COVID-19 Pandemic 16.12 COVID-19 and Indian Perspective 16.13 Conclusion References