Principles in Microbiome Engineering

Principles in Microbiome Engineering
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Principles in Microbiome Engineering Provides an overview of the techniques and applications insight into the complex composition and interactions of microbiomes Microbiomes, the communities of microorganisms that inhabit specific ecosystems or organisms, can be engineered to modify the structure of microbiota and reestablish ecological balance. In recent years, a better understanding of microbial composition and host-microbe interactions has led to the development of new applications for improving human health and increasing agricultural productivity and quality. Principles in Microbiome Engineering introduces readers to the tools and applications involved in manipulating the composition of a microbial community to improve the function of an eco-system. Covering a range of key topics, this up-to-date volume discusses current research in areas such as microbiome-based therapeutics for human diseases, crop plant breeding, animal husbandry, soil engineering, food and beverage applications, and more. Divided into three sections, the text first describes the critical roles of systems biology, synthetic biology, computer modelling, and machine learning in microbiome engineering. Next, the volume explores various state-of-the-art applications, including cancer immunotherapy and prevention of diseases associated with the human microbiome, followed by a concluding section offering perspectives on the future of microbiome engineering and potential applications. Introduces a variety of applications of microbiome engineering in the fields of medicine, agriculture, and food and beverage products Presents current research into the complex interactions and relationships between microbiomes and biotic and abiotic elements of their environments Examines the use of technologies such as Artificial Intelligence (AI), Machine Learning (ML), and Big Data analytics to advance understanding of microbiomes Discusses the engineering of microbiomes to address human health conditions such as neuro psychiatric disorders and autoimmune and inflammatory diseases Edited and authored by leading researchers in the rapidly evolving field, Principles in Microbiome Engineering is an essential resource for biotechnologists, biochemists, microbiologists, pharmacologists, and practitioners working in the biotechnology and pharmaceutical industries.

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Группа авторов. Principles in Microbiome Engineering

Table of Contents

List of Tables

List of Illustrations

Guide

Pages

Further Volumes of the “Advanced Biotechnology” Series:

Principles in Microbiome Engineering

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

Notes

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

Note

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

List of Abbreviations

Acknowledgments

References

Note

Index. a

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Edited by

Matthew W. Chang

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The initial development of the human gut microbiota is shaped during birth through microbial colonization introduced by the environment. During gestation, fetuses are generally considered germ‐free in utero, where the gut microbes of the individual microbiota are introduced post‐delivery. The microbiome is shaped by initial microbes introduced during childbirth, where infants delivered through natural birth and Caesarean‐section (C‐section) have different microbiota composition [18, 112, 113]. The GI tract of infants delivered by natural birth is primarily colonized by maternal vaginal and fecal bacteria with the enriched abundance of Lactobacillus and Bifidobacterium spp. [114], whereas the GI tract of C‐section infants is colonized by other environmental bacteria [112]. The microbiome is further shaped by the infants' diet, where the breast‐fed infants have more heterogeneous microbiota with higher taxonomic diversity than formula‐fed babies [115]. These variations in the delivery method and diet contribute to the maturation of the infant's immune system through the gut microbiome development [116]. Breast‐fed infants have further exposed microbes present in the milk and breast surface, accounting for over 700 species of bacteria [117] made up primarily of Streptococci and Staphylococci [118]. Breast milk is also rich in complex oligosaccharides that stimulates the growth of beneficial microbial groups such as Staphylococci [118] and Bifidobacteria [119]. In comparison, the microbiota of formula‐fed babies adapts a microbiota similar to that of an adult, with an increased abundance of E. coli, Clostridium difficile, Bacteroides fragilis, and Lactobacilli [120, 121]. The microbiota during the age of 0–3 years old is highly dynamic, which stabilizes after the age of 3 years [122].

Children (3–10 years old) undergo massive changes in the microbiota composition, particularly due to the introduction of solid dietary foods. Food solids comprise various nutrients and fibers that facilitate the colonization of various microbial groups including butyrate producers such as Bacteroides and certain Clostridium species [110, 123]. The diet introduced during the pre‐adolescence phase influences how the microbiome takes shape, where children provided with a balanced diet (meat/fish, fruit, vegetables, eggs/beans, and bread/pasta) showed different microbiota shift compared to those given an unhealthy diet (processed, sugar‐rich, and fatty foods) [124]. A study conducted in Japan discovered that Ruminococcus and Bacteroides were found to be enriched in children provided with unprocessed foods (e.g. meat/fish, fruit), whereas Blautia and Clostridium were abundant in the GI tract of children provided with processed food. Additionally, micronutrients provided through nutritional beverages were found to influence the microbiota population. Children provided with the Growing Up Milk‐Lite (GUMLi) was found to have increased bifidobacterial abundance compared to natural bovine milk and other milk formulations [124], indicating that micronutrients can be used to alter the microbiota.

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