Fundamentals of Microbiome Science provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. Resident microbes in healthy animals – including humans – can dictate many traits of the animal host. This animal microbiome is a second immune system conferring protection against pathogens; it can structure host metabolism in animals as diverse as reef corals and hibernating mammals; and it may influence animal behaviour, from social recognition to emotional states. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet, and have contributed to animal diversification over long evolutionary timescales.
Drawing on concepts and data across a broad range of disciplines and systems, Angela Douglas provides a conceptual framework for understanding these animal-microbe interactions while shedding critical light on the scientific challenges that lie ahead. Douglas explains why microbiome science demands creative and interdisciplinary thinking – the capacity to combine microbiology with animal physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.
An essential introduction to a cutting-edge field that is revolutionizing the life sciences, Fundamentals of Microbiome Science explains why microbiome science presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for many medical conditions and new strategies for pest control.
1 Introduction: Animals in a Microbial World 1
1.1 What Is An Animal? 1
1.2 Terminology: Dismantling the Tower of Babel 3
1.3 The Microbiology of Animals 5
1.4 Scope of this Book 9
2 The Ancient Roots of the Animal Microbiomes 12
2.1 Introduction 12
2.2 The Social Life of Bacteria 13
2.3 The Multiorganismal Origins of Eukaryotes 20
2.4 The Ubiquity of Microbial Associations in Eukaryotes 23
2.5 The Animal Condition 29
2.6 Summary 36
3 The Microbiome and Human Health 38
3.1 Introduction 38
3.2 The Biogeography of the Human Microbiome 39
3.3 How to Study Microbiota Effects on Human Health 45
3.4 The Microbiota and Human Disease 55
3.5 The Mass Extinction Event Within? 60
3.6 Summary 64
4 Defining the Rules of Engagement: The Microbiome and the Animal Immune System 66
4.1 Introduction 66
4.2 Immune Effectors and the Regulation of the Microbiota 68
4.3 The Effects of the Microbiota on Animal Immune Function 76
4.4 Symbiont-Mediated Protection: Microbiota as the Second Immune System 84
4.5 Summary 91
5 Microbial Drivers of Animal Behavior 93
5.1 Introduction 93
5.2 Microbes and Animal Feeding Behavior 95
5.3 Microbial Arbiters of Mental Well-Being 102
5.4 Microbes and Animal Communication 112
5.5 Summary 118
6 The Inner Ecosystem of Animals 121
6.1 Introduction 121
6.2 The Abundance and Distribution of Animal-Associated Microorganisms 123
6.3 Ecological Processes Shaping Microbial Communities in Animals 127
6.4 Functions of the Inner Ecosystem 137
6.5 Summary 150
7 Evolutionary Processes and Consequences 152
7.1 Introduction 152
7.2 Costs and Benefits 153
7.3 Evolutionary Specialization and Its Consequences 164
7.4 Symbiosis as the Evolutionary Engine of Diversification 173
7.5 Summary 189
8 The Animal Reimagined 191
8.1 Introduction 191
8.2 The Scope of the Animal 192
8.3 The Determinants of Animal Phenotype 197
8.4 The Animal in the Anthropocene 200
"Douglas has an encyclopedic knowledge of microbial systems, their ecology, and their metabolic functions with which she explains complex physiological mechanisms and identifies important research gaps [...] Overall, reading this book is a most satisfying intellectual feast."
– Fernando Vega, Science
"[Provides] an excellent and comprehensive account of microbiome science that will be valuable to both experts and students in the field."
– Martin Kaltenpoth, The Quarterly Review of Biology
"Highly recommended. Angela Douglas has produced a book of great scholarship, clarity, and intelligence – and with the loving touch of a biologist. Douglas has much to teach students and experts alike."
– Martin J. Blaser, author of Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues
"This ambitious book surveys animal-microbe associations and reimagines the animal as a multi-organismal being. Douglas nicely balances conceptual points and detailed examples, making the text both accessible to anyone with a basic background in biology and interesting to specialists in symbiosis and microbiome science. Fundamentals of Microbiome Science is a very enjoyable read."
– David Berry, University of Vienna
"A very significant contribution to the emerging field of animal-bacteria symbiosis. I am not aware of any other book that covers this topic so exhaustively and in such an integrated, up-to-date, and comprehensive manner."
– François Leulier, Centre National de la Recherche Scientifique, Paris