Principles in Microbiome Engineering

Cover
Title Page
Copyright
Contents
Preface
1 Diet‐Based Microbiome Modulation: You are What You Eat
1.1 Introduction
1.1.1 Microbiome Diversity in Human Body
1.1.1.1 Oral Microbiome
1.1.1.2 Gastrointestinal Microbiome
1.1.1.3 Skin Microbiome
1.1.1.4 Respiratory Microbiome
1.1.1.5 Urogenital Microbiome
1.1.2 Elements that Influence Microbiome Development
1.1.2.1 Prebiotics
1.1.2.2 Probiotics
1.1.2.3 Diet and Nutrition
1.1.3 Current Approaches Employed in Studying the Human Microbiome
1.2 Dietary Lifestyle Variation Affecting Host Microbiome
1.2.1 Dietary Role in Shaping the Microbiome
1.2.1.1 Protein and Polypeptides
1.2.1.2 Soluble Saccharides
1.2.1.3 Dietary Fibers
1.2.1.4 Lipids
1.2.2 The Socioeconomic Impact on Diet‐Related Microbiome Changes
1.2.3 Age Groups and Dietary‐Related Microbiome Changes
1.2.4 Continental Dietary Difference and Its Effect of the Local Microbiome
1.2.4.1 Asia
1.2.4.2 Europe
1.2.4.3 Australia
1.2.4.4 Africa
1.2.4.5 South America
1.2.4.6 North America
1.3 Dietary Modulation of Microbiome for Disease Treatment
1.3.1 Infection
1.3.1.1 Fecal Microbiota Transplantation (FMT)
1.3.1.2 Prebiotic‐, Diet‐, and Probiotic‐Mediated Prevention of Pathogenic Infections
1.3.2 Inflammatory Disease
1.3.3 Cancer
1.3.4 Psychological Disease
1.3.4.1 Autism Spectrum Disorder
1.3.4.2 Neurodegenerative Diseases
1.3.5 Metabolic Disorder
1.3.5.1 Obesity
1.3.5.2 Diabetes
1.3.5.3 Non‐alcoholic Fatty Liver Disease (NAFLD)
1.4 Challenges and Opportunities
1.4.1 Limitations in the Field
1.4.2 Current Microbiome Project Supporting Infrastructures
1.4.2.1 International and Local Initiatives
1.4.2.2 Global Foundations
1.5 Concluding Remarks
Acknowledgments
References
2 Microbiome Engineering for Metabolic Disorders
2.1 Introduction
2.2 Microbiome Engineering for Diabetes and Obesity
2.2.1 Microbiome Engineering for the Hypoglycemic Effect to Treat Diabetes and Obesity
2.2.2 Microbiome Engineering for Immune Modulation to Treat Diabetes
2.3 Microbiome Engineering to Modulate Gut–Liver Axis
2.3.1 Microbiome Engineering to Modulate Ammonia Metabolism
2.3.2 Microbiome Engineering to Modulate Phenylalanine Metabolism
2.3.3 Microbiome Engineering to Modulate Bile‐Salt Metabolism
2.3.4 Microbiome Engineering to Modulate Fat Metabolism
2.4 Microbiome Engineering for Cardiovascular Diseases
2.4.1 Gut Microbiome Interventions for Cardiovascular Diseases
2.4.2 Role of Microbiome‐Derived TMAO in Cardiovascular Diseases
2.5 Microbiome Engineering to Modulate Gut–Brain Axis
2.5.1 Exploratory Studies on the Development of Psychobiotics
2.6 Clinical Translation of Live Biotherapeutic Products
2.7 Conclusion and Future Directions
References
3 Repurposing Microbes for Therapeutic Applications in Humans
3.1 Introduction
3.2 A Brief Overview of Microbiota and Human Health
3.2.1 Interactions Between Microbes and Their Compositions Affect the Host Metabolic Status
3.2.2 Host–Microbe Interactions Constitute an Essential Part of Host Metabolism
3.3 Systems Biology Approach to Analyze the Gut Microbiota Functions
3.3.1 Rational Design of Gut Microbiome Editing Strategies
3.3.2 High‐Throughput Data‐Driven Understanding of Gut Microbiota
3.4 Engineering Microbiome to Treat Diseases
3.4.1 Strain Selection for Microbiome Engineering
3.4.2 Engineering Microbes to Sense and Respond to Disease‐Related Perturbations
3.4.3 Engineering Microbes to Express Therapeutic Proteins for Disease Treatment
3.5 Perspectives and Conclusion
References
4 Modulating Residence Time and Biogeography of Engineered Probiotics
4.1 Introduction
4.2 Adhesion Mechanisms
4.3 Adhesion Modulation
4.4 Functional Encapsulations and Biofilms that Modify Gastrointestinal Dynamics of Probiotics
4.5 Metabolic Engineering to Modulate Gut Adaptation
4.6 Conclusions
References
5 Microbiome Engineering for Next‐Generation Precision Agriculture
5.1 Background
5.2 Systems Approach to Microbiome Engineering
5.2.1 DBTL Framework for Microbiome Engineering
5.2.2 Computational Tools for Robust Microbiome Engineering
5.2.3 Genome‐Scale Metabolic Modeling
5.3 Synthetic Biology for Genome and Genetic Engineering of Phytobiomes
5.4 Conclusion and Future Perspectives
Acknowledgments
References
6 Biological Sensors for Microbiome Diagnostics
6.1 Introduction
6.1.1 The Malleable Microbiome
6.1.2 Engineered Probiotics
6.2 Diagnosing the Microbiome
6.2.1 Microbiome Analyses
6.2.1.1 Small Subunit rRNA Analysis
6.2.1.2 Metagenomics and Metatranscriptomics
6.2.1.3 Proteomics and Metabolomics
6.2.2 Considerations and Future of Microbiome Diagnosis
6.3 Types of Biosensors
6.3.1 Riboswitches
6.3.1.1 Riboswitches and Their Regulatory Mechanisms
6.3.1.2 Design and Selection of Synthetic Riboswitches
6.3.1.3 Riboswitches in Molecular Detection of Microbiome Metabolites
6.3.2 Transcription Factors
6.3.2.1 Transcription Factor Mining
6.3.2.2 Engineering Transcription Factors
6.3.2.3 Applications of Transcription Factors
6.3.3 Two‐Component Systems
6.3.3.1 Introduction to Two‐Component Systems
6.3.3.2 Expression of Natural TCS Systems for Gut Diagnostics
6.3.3.3 Engineering TCS‐Based Sensors for the Microbiome
6.3.4 G Protein‐Coupled Receptors
6.3.4.1 GPCRs and the Gut Microbiome
6.3.4.2 GPCRs Engineered Into Yeast
6.3.4.3 Recent Advances in Yeast GPCR‐Based Sensors
6.4 Testing and Utilizing Engineered Biosensors
6.4.1 Cell‐Free Protein Expression Systems (CFPS) for Biosensing
6.4.2 In Vitro Testing
6.4.2.1 In Vitro Models
6.4.2.2 Organ‐on‐a‐Chip
6.4.2.3 In Vitro Host–Microbe Characterization
6.4.3 Examples of Engineered Microbes
6.4.3.1 Identifying Microbiome Changes In Situ
6.4.3.2 Engineered Microbes for Disease Diagnostics
6.4.3.3 Cancer
6.4.3.4 Inflammatory Bowel Disease
6.4.3.5 Infection
6.4.3.6 Future Translation
6.5 Conclusions/Summary
Acknowledgments
References
7 Principles, Tools, and Applications of Synthetic Consortia Toward Microbiome Engineering
7.1 Introduction
7.2 Advantages of Labor Division via Synthetic Microbial Consortia
7.2.1 Providing Optimal Conditions
7.2.2 Reducing the Metabolic Burden on the Host
7.2.3 Reducing Crosstalk and Competition Within Synthetic Pathways
7.3 Tools for Engineering Synthetic Consortia
7.3.1 Genetic Manipulation Tools
7.3.2 Cell‐to‐Cell Communication
7.3.3 External and Intercellular Signal Molecules for Regulating Gene Expression and Population Composition
7.3.4 Secretion and Exchange of Metabolites
7.3.5 Analysis Tools
7.3.6 Computational Models
7.3.6.1 Dynamic/Deterministic Models
7.3.6.2 Agent‐Based Models
7.3.6.3 Stoichiometric and Genome‐Scale Metabolic Models
7.4 Engineering Syntrophy
7.5 Engineering Population Control
7.6 Synthetic Microbial Consortia and the Human Microbiome
7.7 Conclusions and Future Perspectives
References
8 Fecal Microbiota Transplantation for Microbiome Modulation: A Clinical View
8.1 Introduction
8.2 Fecal Microbiota Transplantation (FMT)
8.2.1 Recruitment of Potential Donors
8.2.2 Administration of FMT
8.2.3 Safety
8.3 Clinical Application of Fecal Microbiota Therapy
8.3.1 C. difficile Infection (CDI)
8.3.2 Inflammatory Bowel Disease
8.3.3 FMT as a Therapeutic Option to Eradicate Highly Drug‐Resistant Enteric Bacteria Carriage
8.3.4 FMT and Irritable Bowel Syndrome
8.3.5 FMT and Slow‐Transit Constipation
8.3.6 FMT and Liver Diseases
8.4 FMT – Novel Indications
8.4.1 Chemotherapy‐Induced Diarrhea
8.4.2 Obesity and Metabolic Syndrome
8.4.3 Graft‐versus‐Host Disease (GvHD)
8.4.4 Autoimmune Diseases
8.4.5 Neuropsychiatric Disorders
8.5 Conclusion
References
9 Maternal Microbiota as a Therapeutic Target
9.1 Introduction
9.2 Human Maternal Microbiota
9.2.1 Oral Microbiota
9.2.2 Vaginal Microbiota
9.2.3 Endometrial Microbiome
9.2.4 Gut Microbiome
9.2.4.1 Maternal Gut Microbiome and Immune Functions
9.2.4.2 Gut and Brain Axis
9.2.4.3 Epigenetic Regulation of Gut Microbiota
9.2.5 Placental Microbime and Meconium
9.3 Maternal Microbiota and Health
9.3.1 Developmental Origins of Adult‐Onset Diseases: Barker Hypothesis
9.3.2 Maternal Microbiota and Obesity
9.3.2.1 Maternal Diet and Gut Microbiota
9.3.2.2 Body Mass Index, Insulin Resistance, and Obesity in Pregnancy
9.3.2.3 Childhood Obesity
9.3.3 Miscarriages and Microbiome
9.3.4 Postpartum Microbiome
9.3.4.1 Mode of Delivery
9.3.4.2 Vaginal Seeding
9.3.5 Maternal Microbiota and Gestational Age at Birth
9.3.6 Maternal Microbiota and Maternal Inflammation and Intrauterine Infections
9.4 Human Milk Microbiota and Infant Health
9.5 Drug Treatment, Unhealthy Conditions, and Microbiome
9.5.1 Perinatal Antibiotic Treatment
9.5.2 Smoking
9.5.3 Stress Under Pregnancy
9.5.4 Autism Spectrum Disorders
9.5.5 Critical Illness of Newborns
9.6 Probiotic and Prebiotic Therapies as Modulators of Microbiome
References
10 Transcription Factor‐Based Biosensors and Their Application in Microbiome Engineering
Summary
10.1 Design: TF‐Based Biosensors
10.1.1 Transcriptional Repressors
10.1.2 Transcriptional Activators
10.1.3 One‐Component Regulatory System or Two‐Component Regulatory System
10.1.4 Types of Output Modules
10.1.5 Layered Genetic Circuits
10.2 Build: TF‐Based Biosensors
10.2.1 Construction of Genetic Circuits
10.2.1.1 Gene Synthesis
10.2.1.2 Restriction Enzyme–Based Cloning
10.2.1.3 Gibson Assembly
10.2.2 Chassis
10.3 Test: TF‐Based Biosensors Application in Microbiome
10.3.1 Diagnostics
10.3.2 Therapeutics
10.3.3 Biocontainment
10.4 Learn: Strategies for TF‐Based Biosensor Improvement
10.5 Conclusions
Acknowledgments
References
Index
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