Microbial Engineering for Therapeutics

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