The Human Microbiome Handbook

Edited by: Jason Tetro and Emma Allen-Vercoe

with an Introduction by Sydney M. Finegold

978-1-60595-159-1, ©2017, 370 pages, 6×9, Hardcover

  • Critical reference explains strategies of microbiome research in humans
  • Summarizes the microbiome’s effects on immunity, metabolism, genetics and psychology
  • Evaluates medical and nutritional therapies for modifying the microbiome
  • For healthcare researchers, nutritionists, microbiologists, and medical professionals

Written by a team of leading scientists, this book offers a concise technical reference covering human microbiome research and its ramifications for medicine and nutrition. The initial chapters furnish a scientific explanation of the microbiome in general and its ecology. The book then provides a detailed investigation of microbial populations as these pertain to physiology, metabolism and immunology. The final portions are devoted to exploration of the microbiome’s effects on chronic and autoimmune diseases and include assessments of clinical therapies and nutritional interventions designed to alter the microbiome to mitigate chronic health conditions.

Preface

Chapter 1. Some Historical Notes on Bowel Microflora
Sydney M. Finegold

Chapter 2. Ecology of the Human Microbiome
Kaludyna Borewicz and Hauke Smidt
2.1. Overview
2.2. Microbiota of the Gastrointestinal Tract
2.3. Microbial Composition in the GI Tract of Healthy Adults
2.4. Microbial Ecosystem Function in the GI Tract of Healthy Adults
2.5. Selected Diseases Associated with Dysbiosis of the Intestinal Microbiota
2.6. Acknowledgments
2.7. References

Chapter 3. From Birth to Old Age: Factors that Shape the Human Gut Microbiome
Alexandra Ntemiri, Catherine Stanton, R. Paul Ross and Paul W. O’Toole
3.1. Introduction
3.2. Establishment of the Gut Microbiota
3.3. Shaping Factors of Gut Microbiota Composition
3.4. Functional Gastrointestinal Disorders: Inflammatory Bowel Disease and Irritable Bowel Syndrome
3.5. Ageing and Microbiota Alterations
3.6. Concluding Remarks
3.7. References

Chapter 4. Microbial Biochemical Processes Critical to Human Health
Vicky De Preter and Kristin Verbeke
4.1. Introduction
4.2. Metabolic Function of the Colonic Microbiota
4.3. Carbohydrate Metabolism
4.4. Physiological Effects of Short-chain Fatty Acids
4.5. Short-chain Fatty Acids as Signaling Molecules
4.6. The Role of Short-chain Fatty Acids in the Immune Response
4.7. Fermentation of Proteins
4.8. Microbial Metabolism of Polyphenols
4.9. Conclusion
4.10. References

Chapter 5. The Gut Microbiome: Pathways to Brain, Stress, and Behavior
Aadil Bharwani, John Bienenstock and Paul Forsythe
5.1. Introduction
5.2. Evidence of Microbiota–CNS Interactions
5.3. Biological Underpinnings of Neural Communication
5.4. Conclusion
5.5. Acknowledgements
5.6. References

Chapter 6. Effects on Immunity
Leandro A. Lobo, Rosana B.R. Ferreira and L. Caetano M. Antunes
6.1. Introduction
6.2. Germ Free Mice
6.3. Galt Formation
6.4. Small Molecules, the Microbiome, and the Immune System
6.5. The Impact of Other Microbiomes on Host Immunity
6.6. The Impact of the Microbiota on Immune Disorders
6.7. Conclusion
6.8. References

Chapter 7. Microbiota-Related Modulation of Metabolic Processes in the Body
Tingting Ju, Jiaying Li and Benjamin P. Willing
7.1. Introduction
7.2. Short-chain Fatty Acids
7.3. Microbiota and Bile Acid Metabolism
7.4. Gut Microbiota, TMAO, and Atherosclerosis
7.5. Metabolic Inflammation
7.6. Early Life Microbiome Programming Metabolic Outcomes
7.7. Conclusion
7.8. References

Chapter 8. An Overview of Microbiota-Associated Gastrointestinal Diseases
Claudia Herrera, Virginia Robles-Alonso and Francisco Guarner
8.1. Host-microbes Interactions in the Gastrointestinal Tract
8.2. Antibiotics and Risk of Disease
8.3. The Gut Microbiota in Inflammatory Bowel Disease
8.4. The Gut Microbiota in Functional Bowel Disorders
8.5. The Gut Microbiota in Liver Diseases
8.6. References

Chapter 9. An Overview of Microbiota-Associated Epigenetic Disorders
Dawn D. Kingsbury and Holly H. Ganz
9.1. Introduction
9.2. Microbial Influence on Human Health
9.3. Conclusions
9.4. References

Chapter 10. Fecal Microbiota Transplantation in Gastrointestinal Disease
Rowena Almeida and Elaine O. Petrof
10.1. Introduction
10.2. Basic Concepts in Intestinal Microbiome Function
10.3. Introduction to Fecal Microbiota Transplantation
10.4. Applications of Fecal Microbiota Transplantation
10.5. Summary
10.6. References

Chapter 11. Probiotics and the Microbiome
Gregor Reid
11.1. A Long History of Time
11.2. Rationale for Modulating Health
11.3. The Constantly Growing List and How the Strains Function
11.4. Probiotics and Microbiome Mysteries
11.5. References

Chapter 12. Considering the Microbiome as Part of Future Medicine and Nutrition Strategies
Emma Allen-Vercoe
12.1. Introduction
12.2. Mining the Human Microbiota for New Drugs
12.3. Protecting the Gut Microbiota from Collateral Damage during Antibiotic Exposure
12.4. Microbial Ecosystem Therapeutics
12.5. Predicting the Influence of Xenobiotics on the Human Microbiota
12.6. Leveraging Microbiome Knowledge to Optimize Nutrition Strategies
12.7. Summary
12.8. References

Index

  1. :

    –A much needed deep introduction into microbiome research

    Poised as both an intro to beginners and a comprehensive review that every seasoned microbiome researcher should know, The Human Microbiome Handbook, edited by Jason A. Tetro and Emma Allen-Verco, covers a wide range of topics involving the microbiome in health and disease. With 12 focused chapters from 27 experts in the field, this book will prove to be a valuable resource for research scientists, medical professionals, and policy makers that interface with the microbiome in their work. The structure of the book can be divided into three areas, microbiome basics are covered in chapters 1-3, microbiome host interactions are described in chapters 4-7, and microbiome disease and related therapeutics are covered in chapters 8-12.

    Recently the microbiome has risen to be one of the hottest topics in science, and for those new to the field, it is easy to overlook the roots of microbiome research in decades-old studies in clinical anaerobic bacteriology. The “god-father” of anaerobes, Sydney Finegold, opens the book by discussing how microbiome research has changed over his greater than 60-year career. When he finished his training in 1943, there was a basic lack of understanding of anaerobic infectious diseases, with virtually no tools for anaerobic identification, even in the leading medical institutions. After tireless efforts to discover the etiologic agents and mechanisms of anaerobic infectious diseases, Finegold produces his encyclopedic work Anaerobic Bacteria in Human Diseases (1977), which was a first comprehensive look at the diverse and milti-organ clinical presentations of anaerobes in the infectious disease process. Nearly 40 years later, The Human Microbiome Handbook expands on this foundation and delves into complex interactions between microbial communities and their host. Finegold’s intro echoes many elements that researchers face today. While we are aware that the microbiota is involved in a great many physiologic processes, our knowledge is nascent and we are only now at beginning to develop the tools needed to understand the microbiome in health and clinical disease.

    The Human Microbiome Handbook is well referenced and makes a tremendous effort to cover the expansive and growing field of how the microbiota interacts with every organ system in the human body. Each chapter is well organized, with sub-headings for specific processes or diseases, and contains useful figures detailing interactions of bacteria and specific tissues systems, influence on immunity, or microbial chemical transformations. Several diseases are covered, including the role of the microbiota in inflammatory bowel disease, obesity, cardiovascular disease, immune disorders, cancer, and influence on neurologic diseases.

    With the field’s growing knowledge of the importance of the microbiome, tools and strategies to manipulate the microbiota are ever more needed. Common strategies such as prebiotics (nutrients that favor the growth of beneficial microbes, probiotics (live microbes), or fecal microbiota transplants are discussed. This book goes beyond the basics and discusses the rationale for modulating the microbiota, the practicality of developing microbial ecosystem therapeutics, and provides the provocative approach of mining the human microbiota for new drugs. In all, this handbook is an extremely relevant source of knowledge on all things microbiome.

    Laura M. Cox
    Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115

Emma Allen-Vercoe completed her BSc. (Hons.) In biochemistry from the University of London, UK, and her PhD in molecular microbiology. Allen-Vercoe’s lab at the University of Guelph in Ontario, Canada, houses an innovative platform that facilitates culturing of human microbiota ecosystems in vitro and permits study of microbial ecosystem responses to stressors affecting human health.

Jason A. Tetro earned his BSc. (Hons.) in Applied Biochemistry from the University of Guelph, Canada, and continued his research at the University of Ottawa as a member of the Centre for Research on Environmental Microbiology and the Emerging Pathogens Research Centre. His research primarily focused on the interruption of pathogen spread in food, blood, and both animate and inanimate surfaces.

978-1-60595-159-1, ©2017, 370 pages, 6×9, Hardcover

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