The Human Microbiome in Health and Disease

Biology

The Human Microbiome in Health and Disease: An Introduction

Margaret Riley

How the trillions of microbes in our bodies influence nearly every aspect of our health

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Published:: Sep 16, 2025
Copyright:: 2025
Illus:: 272 color illus.

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Published:: Sep 16, 2025
Copyright:: 2025
Illus:: 272 color illus.

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ISBN:
Published:: Sep 16, 2025
Copyright:: 2025
Illus:: 272 color illus.

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Each of our bodies is home to trillions of microorganisms that shape our health, prevent disease, and influence conditions ranging from depression to allergies. This book offers a detailed look at how our microbial inhabitants鈥攌nown as the microbiome鈥攁ffect almost every facet of our health. It takes readers from the microbiome鈥檚 primordial origins and their symbiosis with humans to the latest microbiome research, utilizing real-world case studies and current clinical insights to show how shifts in the microbiome can play a role in obesity, autoimmune disorders, depression, and other conditions. Each chapter incorporates cutting-edge research findings, exploring both traditional and new therapeutic approaches to restoring microbiome balance. The text emphasizes the interactions between diet and microbiome health, showing how personalized dietary choices can serve as preventive and therapeutic tools, and describes emerging microbiome-based diagnostics and treatments.

鈥� Fills the need for an introductory textbook on the human microbiome
鈥� Presents complex information in an accessible way, with illustrations, summaries, and key takeaways
鈥� Integrates research and examples
鈥� Draws on the author鈥檚 years of undergraduate teaching experience

Margaret Riley is professor in the Biology Department at the University of Massachusetts Amherst. She is the coauthor of Empowering Underrepresented Students in Science: STEM Students Speak, the editor of Research and Applications in Bacteriocins, and the coeditor of Current Knowledge and Future Prospects and Bacteriocins: Ecology and Evolution. Riley has published over 100 research articles related to antibiotic resistance and the discovery of novel antimicrobials.

Preface
CHAPTER 1 The Ancient Origin of Microbes
- 1.1 In the Beginning
  - Origin of Life
  - The Very First Cell
  - Box 1.1 RESEARCH IN ACTION Building Life from Scratch鈥擳he Quest for a Protocell
  - Competition Drives Diversification
  - Anaerobic versus Aerobic Respiration
  - Photosynthesis Evolves
  - Endosymbiosis and the Origin of Eukaryotes
- 1.2 The Great Tree of Life
  - A Molecular Tree of Life
  - The Three Domains of Life
  - The Tiniest Microbes
- 1.3 Making the Invisible Visible
  - The First Sightings of Bacteria
  - Culturing the Invisible
  - Extremophiles, Life on the Edge
- 1.4 The Microbes within Us
  - A Universe of Microbes within Us
  - How Much of You Is Human?
- 1.5 Our Microbiomes, Our Health
  - Microbiomes and Human Nutrition
  - Microbial Metabolites, Key to Human Health
  - Reflections on Your Microbiome
CHAPTER 2 A Brief History of Microbiome Research
- 2.1 Our First View of Microbes
  - Spontaneous Generation, or Not?
  - Box 2.1 Redi鈥檚 Exemplary Experimental Design
  - Modern Experimental Design
  - The Germ Theory of Disease
  - Koch鈥檚 Postulates
  - The Discovery of Antibiotics
  - Box 2.2 Discovery of Penicillin
- 2.2 The Golden Age of Microbiology
  - Discovering Colonization Resistance
  - Not Just Germs
  - Anaerobic Culturing Methods
- 2.3 Genomics and Bioinformatics
  - Environmental Metagenomics
  - Fecal Microbiota Transplantation
  - Germ-Free Mice
- 2.4 Bringing It All Together
  - Fluorescing Microbes
  - The Father of Microbiome Research
  - Human Microbiome Project
  - No One Else Has Your Exact Microbiome
  - The Normal Human Microbiome
CHAPTER 3 The Human Holobiont
- 3.1 The Human Holobiont
- 3.2 The Many Human Microbiomes
  - A Healthy versus Normal Microbiome
  - Microbiome in Names and Numbers
  - Microbial Taxonomy
  - The Core Microbiome
  - Primary Functions of the Core
  - Hallmarks of a Healthy Microbiome
- 3.3 The Microbes in Our GI Tract
  - Crowdsourcing for Carbs
  - Cooperation and Conflict in the Large Intestine
  - The Friendly Gut Phageome
  - Box 3.1 Communication between the Large Intestine Microbiome and Immune System
  - Dysbiosis of the Large Intestine Microbiome
  - Box 3.2 Bacteriophages Protect Epithelial Cells in the Large Intestine
  - Inflammatory Bowel Disease
  - Box 3.3 RESEARCH IN ACTION Fecal Amino Acids and Dysbiosis鈥擴nlocking Crohn鈥檚 Disease Therapies
- 3.4 The Microbes in Our Mouth
  - Archaeal Syntrophy
  - Fungal Diversity of Unknown Function
  - Creation of Dental Plaque
  - The Diverse Roles of the Oral Microbiome
  - Our Evolving Oral Microbiota
  - Oral Microbiome Dysbiosis
  - Box 3.4 The Gum Microbiome and Gum Disease
- 3.5 The Microbes on Our Skin
  - A Nutritional Desert
  - Primary Functions of the Skin Microbiome
  - Skin Microbiome Dysbiosis
  - Acne and Your Skin Microbes
- 3.6 Sampling Your Own Microbiome
  - Identifying a Testable Hypothesis
  - Box 3.5 Bacterial Growth Media Protocol
  - Preparing Nutrient Media
  - Experimental Controls Are Key
  - Sampling Your Skin
  - Box 3.6 Culturing Your Skin Microbiome
CHAPTER 4 Generating Microbiome Data
- 4.1 An Opportunity and Many Challenges
  - Training to Become a Microbiome Scientist
  - Designing a Microbiome Study
  - Using Model Organisms When Practical
  - A Testable Hypothesis Is Key
  - Experimental Variables
  - Exploring the Primary Literature
  - Performing a Literature Search
- 4.2 Designing Our Study
  - Choosing Our Subjects
  - Statistical Power Is Key
  - Testing for Statistical Significance
  - The Power of Our Sample Size
  - Taking Control of Our Experiment
  - Cross-Sectional versus Longitudinal Study Design
  - Experimental Data versus Metadata
- 4.3 Entering the Experimental Phase
  - Obtaining Our Samples
  - DNA Chemistry
  - Extracting Metagenomic DNA
  - Amplifying Metagenomic DNA
  - Billions of Amplification Products
  - High-Throughput DNA Sequencing
- 4.4 The 鈥淥mics鈥�
  - Metatranscriptomics
  - Metaproteomics
  - Metabolomics
  - Spatial Omics
CHAPTER 5 Analyzing Microbiome Data
- 5.1 The Data Analysis Pipeline
  - The Raw Data
  - Garbage In, Garbage Out
- 5.2 Reconstruction of Genes and Genomes
  - Locating Open Reading Frames
  - Predicting Sequence Functions
- 5.3 Microbiome Data Analysis
  - Online Data Analysis Package Programs
  - Operational Taxonomic Units (OTUs)
  - Assigning Taxonomic Identities
  - Species Accumulation Curves
- 5.4 Species Diversity Measures
  - Alpha Diversity
  - Alpha Diversity Indices
  - Faith鈥檚 Phylogenetic Diversity Metric
  - Beta Diversity
  - Bray-Curtis Dissimilarity Metric
  - Unique Fraction Metric
- 5.5 Visualizing Diversity Estimates
  - Principal Component Analysis
CHAPTER 6 Applying Microbiome Analysis
- 6.1 The Scientific Primary Literature
- 6.2 Dissecting a Research Article
  - Abstract
  - Introduction
  - Results
  - Methods
  - Data Analysis
  - Discussion
- 6.3 Introduction to Qiita
  - The Basics
  - Diving Deeper into Qiita
  - Qiita-Based Taxonomic Distribution Analysis
  - Qiita-Based Alpha Diversity Analysis
  - Qiita-Based PCA Analysis
- 6.4 Beyond Qiita
CHAPTER 7 Mother鈥檚 First Gift
- 7.1 The Microbiome of the Female Reproductive Tract
  - Vaginal Community State Types
  - Primary Functions of the Vaginal Microbiome Types
  - Dysbiosis of the Vaginal Microbiome Types
- 7.2 The Mother鈥檚 Microbiome during Pregnancy
  - What We Can Learn from the Mouse about a Mother鈥檚 Microbiome during Pregnancy
  - Immune Interactions between the Developing Fetus and the Maternal Microbiome
  - The Maternal Impact on Development of the Fetal Immune System
- 7.3 The Birthing Process and the Newborn Microbiome
  - Vaginal Delivery
  - Cesarean Section
- 7.4 The Infant鈥檚 Core Microbiome
  - Structuring the Infant鈥檚 Core Microbiome
  - Wave after Wave of Microbial Colonization
- 7.5 Beyond the Gut Microbiome
  - The Newborn鈥檚 Skin Microbiome
- 7.6 The Wonder of Mother鈥檚 Milk
  - The Composition of Breast Milk
- 7.7 Transitioning to Solid Foods
- 7.8 Environmental Impacts on the Infant鈥檚 Microbiome
- 7.9 Health Impacts of a Newborn鈥檚 Dysbiotic Microbiome
  - Antibiotics
  - Box 7.1 RESEARCH IN ACTION Antibiotics and the Newborn Gut鈥擫ong-Term Impacts on Microbiome Development
  - Malnutrition
  - Allergic Diseases
  - Obesity
  - Diabetes
- 7.10 Microbiome-Based Therapies
  - Probiotics
  - Vaginal Microbiome Transplant
  - Fecal Microbiota Transplant
  - Oral Probiotics
  - Oral Prebiotics
CHAPTER 8 The Microbiome and the Brain
- 8.1 The Nervous System
- 8.2 The Maternal Microbiome and Neural Development
  - Box 8.1 RESEARCH IN ACTION Maternal Microbiota鈥擲haping the Fetal Brain鈥檚 Biochemistry
  - Formation of the Blood-Brain Barrier
- 8.3 The Microbiota-Gut-Brain Axis
  - MGBA Communication via the Endocrine Pathway
  - MGBA Communication via the Neural Pathway
  - MGBA Communication via the Immune Pathway
  - MGBA Communication via Autophagy
- 8.4 Gut Microbiota and Neuropsychiatric Disorders
  - Depression
  - Autism Spectrum Disorder
  - Parkinson鈥檚 Disease
- 8.5 Gut Microbiome-Based Therapies
  - Probiotic Therapies
  - Prebiotic Therapies
- 8.6 The Evolved Dependence of Our Microbiota
CHAPTER 9 The Microbiome and Immunity
- 9.1 Components and Activation of the Immune System
  - Primary Components of the Immune System
  - Activating the Immune System
  - Box 9.1 Components of the Innate and Adaptive Immune Systems
- 9.2 The Gut Microbiome and Immune Response
- 9.3 The Mucosal Firewall Influences Immune Function
- 9.4 Immune System and Extra-Intestinal Microbiome Cross Talk
  - Skin
  - Lung
  - Liver
- 9.5 Influence of the Maternal Microbiota during Fetal Development
  - Immune Cells in Fetal Development
  - Distinguishing Self from Non-Self
  - Maternal Inflammation and Infection and the Fetus
- 9.6 Influence of the Maternal and Fetal Microbiota during the Infant Years
  - Breast Milk
  - Immunoglobulin A
- 9.7 Immune Diseases and Dysbiosis of the Gut Microbiome
  - Rheumatoid Arthritis
  - Cardiometabolic Disease
  - Cancer
CHAPTER 10 Microbiome Dysbiosis
- 10.1 Defining Eubiosis and Dysbiosis
  - The Eubiotic Microbiome
  - The Dysbiotic Microbiome
  - More Is Not Necessarily Better
- 10.2 An Ecological Perspective on the Microbiome-Host Relationships
  - Ecological Interactions between the Gut and Its Microbiome
  - The Microbial Leash Metaphor
  - Host Control of Microbiomes in Small versus Large Intestines
  - Host Control of a Microbiome-Based Disease
  - Microbial Control of the Gut Microbiota
  - Dysbiosis, the Cause or Consequence of Disease?
- 10.3 A Framework for Assessing Microbiota-Disease Associations
  - Polymicrobial Synergy and Dysbiosis
  - Polymicrobial Synergy in Gum Disease
  - Box 10.1 A Microbiome-Based Model of Periodontal Disease
  - Box 10.2 RESEARCH IN ACTION Breaking the Single-Species Myth in Periodontal Disease
  - Shared Dysbiosis
  - Is the Term Dysbiosis Still Useful?
  - Koch鈥檚 Postulates Applied to Microbiome-Health Associations
  - Box 10.3 A Comparison of the Original and Ecological Koch鈥檚 Postulates
CHAPTER 11 The Microbiome and Obesity
- 11.1 The Obesity Epidemic
  - Losing Weight Is Hard to Do
- 11.2 The Microbiome of Obesity
  - Obese versus Lean Gut Microbiomes
  - Microbial Guilds at Work in Obesity
  - Not Just Your Gut Microbes
- 11.3 Metabolic Markers of Weight Loss
  - Rendering Bile Acids Impotent
  - Triggers of Fat Storage
  - Mediating Low-Grade Inflammation
- 11.4 The Gut Microbiome and Weight Loss
  - Box 11.1 RESEARCH IN ACTION Microbiome Predictors鈥擝iomarkers for Weight Loss Success
- 11.5 Diet-Based Approaches
  - Phytochemicals
  - Fermented Foods
  - Probiotics
  - Prebiotics
  - Fecal Microbiota Transplantation
CHAPTER 12 Allergic Diseases and the Microbiome
- 12.1 The Allergic Response
  - The Allergic Cascade
- 12.2 A Critical Window of Immune Training to Prevent Allergic Disease
- 12.3 Epigenetic Changes and Allergic Disease
- 12.4 Impact of the Maternal Microbiome on Allergic Reactions
- 12.5 The Impact of the Environment in Allergic Disease
  - The Response of Gut Microbes to Environmental Triggers of Allergic Disease
  - The Farm Effect
  - The Atopic March
- 12.6 The Old Friends and Biodiversity Hypotheses
- 12.7 The Role of Antibiotics in Allergic Disease
- 12.8 The Impact of the Microbiome on Allergic Disease
  - Asthma
  - Atopic Dermatitis
  - Food Allergy
- 12.9 Microbiome-Based Therapeutics for Allergic Diseases
  - Oral Immunotherapy
  - Synbiotics
  - Fecal Microbiota Transplantation
  - Faecalibacterium, Lachnospira, Veillonella, and Rothia
  - Inulin
- 12.10 A Circle of Causality
CHAPTER 13 Our Evolving Microbiome
- 13.1 Where Did Our Microbiome Come From?
  - Our Closest Living Relatives
  - Looking to Our Evolutionary Siblings
  - Coprolites
  - Dental Plaque
  - Oral Microbiome
  - Box 13.1 Expansion of the Human Brain May Have Been Triggered by a Starch-Rich Diet
  - Microbes from the Middle Ages
  - Bacteriophages
- 13.2 The Industrialization of Our Microbiome
  - The Hygiene Hypothesis
  - The Disappearing-Microbiota Hypothesis
  - Antibiotics
  - Diet
  - The Consequences of the Missing Microbiota
  - Recolonizing a Vacated Niche
- 13.3 The Microbiome and the Missing-Heritability Problem
  - Box 13.2 RESEARCH IN ACTION Lactose Digestion and the Microbiome鈥擜n Evolutionary Link
- 13.4 Reacquiring Our Ancient Microbiota
CHAPTER 14 The Microbiome of the Built Environment
- 14.1 What Is the Built Environment?
  - The Earliest Human-Built Environments
  - The Earliest Homes Appear
- 14.2 What Is the Microbiome of the Built Environment?
  - Health Impacts of the MoBE
  - Controlling the MoBE
  - Physical Factors Influence the MoBE
  - Early Studies of the MoBE
  - Human Microbial Clouds
- 14.3 Microbiology of the Built Environment
  - Constituents of the MoBE
  - The Skin and Oral Microbiomes Contribute Most to the MoBE
  - The Virome
  - Plant Microbiomes
- 14.4 BE Factors That Influence the MoBE
  - Humidity and Mold
  - Ventilation and Microbial Spread
  - Light Influences Which Microbes Survive
  - Indoor Plumbing
  - Cleaning Practices Impact the MoBE
- 14.5 The Impact of the MoBE on Health
  - Sick Building Syndrome
  - The Farm Effect
  - Box 14.1 RESEARCH IN ACTION The Amish Advantage鈥擧ow Dust Exposure Reduces Asthma Risk
- 14.6 Tracking Microbes in the Built Environment
  - Tracking Hospital Pathogens
  - The Neonatal Intensive Care Unit
  - The Hospital MoBE
  - The Hospital Resistome
- 14.7 Microbial Metabolomics and the BE
  - Metabolites in the BE
  - Volatile Organic Compounds and the BE
- 14.8 The Future MoBE
  - COVID-19 and the MoBE
  - Build Back Better
  - The Rewilding Hypothesis
  - Nature-Based Solutions
CHAPTER 15 Taking Charge of Your Microbiome
- 15.1 Is Your Gut Microbiome Healthy?
- 15.2 Seeking Professional Advice
  - Consulting a Medical Professional
  - Gut Microbiome Index
  - Box 15.1 RESEARCH IN ACTION Gut Microbiome Health Index鈥擜 Predictor of Disease Probability
  - Consulting a Naturopath
- 15.3 The DIY Approach
  - Assessing Stool Quality
  - Assessing Gut Transit Time
  - Assessing Gut Microbiome Composition
- 15.4 Defining a Healthy Microbiome
  - Fiber-Fermenting Bacteria
- 15.5 The Healthy Plate
- 15.6 Microbiome-Based Therapeutics
  - Probiotics
  - Prebiotics
  - Synbiotics
- 15.7 Microbiome Recovery Following Antibiotic Use
- 15.8 Let Food Be Thy Medicine
Glossary
References
Index

“This is truly a useful introductory text, as it explains things without becoming too overbearing on a particular subject.”—Jack Gilbert, University of California, San Diego

“I do want to congratulate the author, as I have never read anything so well written about the experimental process. I wish I could share it with my students today! Margaret Riley has made it all so easy to understand. It is well organized, clearly laid out in relevant sections, and reads beautifully.”—Sara Flood, Utah Valley University

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