Getting to Know the Microbiome

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PUBLISHED: 14 MARCH 2016 | ARTICLE NUMBER: 16030 | DOI: 10.1038/NMICROBIOL.2016.30 books & arts Getting to know the microbiome

Welcome to the result of millennia of dynamic co-evolution. Finally, the book discusses how Microbiome: Getting When discussing the methods for studying researchers are going beyond observational to Know the Trillions microorganisms, DeSalle and Perkins studies to establish a mechanistic link of Bacteria In, On begin their account in the 1600s, when between the microbiome and particular Robert Hooke and Antonie van Leeuwenhoek diseases. For instance, they describe the and Around You were first using microscopy to observe importance of research using germ-free by Rob DeSalle and microorganisms (or ‘animicules’ as ‘bubble mice’ (that is, mice raised in sterile Susan Perkins van Leeuwenhoek called them), proceeding environments) to identify phenotypes to a description of how sequence-based caused by a lack of microorganisms. They YALE UNIVERSITY PRESS: ‘culture-independent’ techniques coupled with continue with a discussion of how mouse 2016. 288PP. US$32.50 advances in throughput has catapulted our models have allowed for the establishment knowledge of microbial diversity forward. of causal links between microorganisms Despite the rich history of microbial and complex diseases such as obesity and uman microbiome research is research, the relative infancy of microbiome depression/anxiety. However, this really undergoing a renaissance, driven research is highlighted. Much of the new only scratches the surface of the deluge of Hlargely by advances in technologies research discussed includes observational recent research on this topic — literature such as ‘next generation’ sequencing studies that address fundamental questions: linking the microbiome with a myriad that enable a deeper characterization of what types of microorganisms typically of allergic and autoimmune disorders, microbial populations than has ever been inhabit the diverse habitats our bodies cardio-metabolic diseases and various possible. Also underlying this renaissance provide? How variable is the microbiome cancers are not described, and the various is a paradigm shift in how microorganisms across people, populations, and over time? mechanisms through which the microbiome are viewed: transitioning from a focus on How are human microbiomes acquired can affect health could have benefited from a combatting pathogens to one that appreciates in early life and how do they change more thorough treatment. the importance of a complex interaction throughout life? How are microorganisms Mechanistic understanding is essential between polymicrobial communities and the transferred between people and between for translating rich information on the host that has been evolving over millenia. In local environments? Baseline information complexities of the microbiome into this book, Rob DeSalle and Susan Perkins on human microbiome composition advancements in human health. In a of the American Museum of Natural patterns provides a critical framework for chapter addressing the question ‘What are History provide a guide to understanding understanding the complex interaction our defenses?’, there is a discussion of our the microbiome from an evolutionary between the microbiome and various disease natural defences (our immune system), as perspective, giving an overview of not only states. However, knowing the functional well as human contrived defences such as the current state of understanding in the properties of microbiomes and how they vaccines and antibiotics, and how and why field, but also a history of how we got here. directly influence host biology are ultimately microorganisms can develop resistance. The unique value of the book is the rich the keys to harnessing rich information on However, vaccines and antibiotics are background it provides, including information the microbiome to promote health. both classes of therapeutics that fit neatly on the microorganisms themselves (What The book’s discussion of the role the within the ‘one pathogen one disease’ are the major types? How are they named?), microbiome may play in health highlights paradigm. Some description of new how we interact with microorganisms (How a very important concept: it is not research concerning ‘beneficial bacteria’ as does the immune system function?), and the always straightforward to characterize potential therapeutics is given, but lacks a techniques used to study microorganisms a particular microorganism as ‘good’ or thorough treatment of how the complexity (How do DNA sequences describe microbial ‘bad’ or a particular microbiome state as of interactions between microbiome and communities?), all explored with an ‘healthy’ or ‘unhealthy’. A cited example is host may have the potential to inform ‘next evolutionary/historical perspective. For Helicobacter pylori — a species of bacteria generation’ therapies. instance, DeSalle and Perkins begin with that humans have been living in relative While this book would benefit from the more existential question of ‘What is harmony with for at least 100,000 years, but a deeper exploration of the radical life?’, explaining the history of inquiry that that has been greatly reduced in prevalence advancements in understanding the informed our understanding of how life due to improved hygiene and widespread microbiome’s role in human health, emerged and diverged over time to become antibiotic use. H. pylori has been considered the historical foundation it provides on the complex spectrum of life forms present a pathogen because its colonization of the topic is excellent. Overall, this is a today. When discussing the immune system, the stomach increases the risk for peptic wonderful primer for anyone interested in DeSalle and Perkins first describe microbial- ulcers and gastric cancer, but it turns learning more about the amazing world of resistance mechanisms in plants and move out that H. pylori also protects against unseen life that is teeming on and in our into hydrozoans at the base of the animal gastro-oesophageal reflux disease and linked bodies and all around us. ❐ branch of the tree of life, before ultimately disorders including oesophageal carcinoma. addressing the incredible complexity of the Clearly, even individual microorganisms REVIEWED BY CATHERINE A. LOZUPONE immune system in humans. This progression need to be considered as a part of a complex Catherine A. Lozupone is an assistant professor at illustrates to the reader how our complex system when trying to understand their the University of Colorado, Denver 80045, USA. relationship with microorganisms is the relationship to health. e-mail: [email protected]