The Human Microbiota: How Microbial Communities Affect Health and Disease

Unraveling the mysteries of the human microbiome Addressing the latest findings on the microbes that colonize epithelial surfaces in the human body, The Human Microbiota presents a comprehensive review of the microbial diversity found in humans and the role it plays in human health. After an introduction to the pivotal research efforts at the Human Microbiome Project, the book presents cutting-edge methods for studying the human microbiome and links particular microbial communities to various conditions and diseases. It explains in detail how to use animal models, cultivate microbes, and manipulate existing microbiota. Advice on the design of microbiome studies as well as the strengths and weaknesses of different methods is also included. A group of pioneers in microbial ecology contribute authoritative, state-of-the-art chapters on: Characterization and analysis techniques as well as mathematical approaches for describing microbial communities The different microbial populations found in the gut, the respiratory tract, the mouth, and the genital tract Lessons learned from animal models about microbial communities and immune response to the microbiota Novel approaches to cultivating human microbes in the laboratory, including their challenges and benefits The use of prebiotics, probiotics, and synbiotics to enhance human health The Human Microbiota is an invaluable resource for microbiologists, microbial ecologists, physicians, infectious disease specialists, and anyone wishing to learn about the latest tools in molecular biology and what they reveal about this exciting, rapidly evolving field.

PREFACE vii CONTRIBUTORS xi 1 THE NIH HUMAN MICROBIOME PROJECT 1 Lita M. Proctor, Shaila Chhibba, Jean McEwen, Jane Peterson, Chris Wellington, Carl Baker, Maria Giovanni, Pamela McInnes, and R. Dwayne Lunsford 2 METHODS FOR CHARACTERIZING MICROBIAL COMMUNITIES ASSOCIATED WITH THE HUMAN BODY 51 Christine Bassis, Vincent Young, and Thomas Schmidt 3 PHYLOARRAYS 75 Eoin L. Brodie and Susan V. Lynch 4 MATHEMATICAL APPROACHES FOR DESCRIBING MICROBIAL POPULATIONS: PRACTICE AND THEORY FOR EXTRAPOLATION OF RICH ENVIRONMENTS 85 Manuel E. Lladser and Rob Knight 5 TENSION AT THE BORDER: HOW HOST GENETICS AND THE ENTERIC MICROBIOTA CONSPIRE TO PROMOTE CROHN’S DISEASE 105 Daniel N. Frank and Ellen Li 6 THE HUMAN AIRWAY MICROBIOME 119 Edith T. Zemanick and J. Kirk Harris 7 MICROBIOTA OF THE MOUTH: A BLESSING OR A CURSE? 135 Angela H. Nobbs, David Dymock, and Howard F. Jenkinson 8 MICROBIOTA OF THE GENITOURINARY TRACT 167 Laura K. Sycuro and David N. Fredricks 9 FUNCTIONAL STRUCTURE OF INTESTINAL MICROBIOTA IN HEALTH AND DISEASE 211 Alexander Swidsinski and Vera Loening–Baucke 10 FROM FLY TO HUMAN: UNDERSTANDING HOW COMMENSAL MICROORGANISMS INFLUENCE HOST IMMUNITY AND HEALTH 255 June L. Round 11 INSIGHTS INTO THE HUMAN MICROBIOME FROM ANIMAL MODELS 273 Bethany A. Rader and Karen Guillemin 12 TO GROW OR NOT TO GROW: ISOLATION AND CULTIVATION PROCEDURES IN THE GENOMIC AGE 289 Karsten Zengler 13 NEW APPROACHES TO CULTIVATION OF HUMAN MICROBIOTA 303 Slava S. Epstein, Maria Sizova, and Amanda Hazen 14 MANIPULATING THE INDIGENOUS MICROBIOTA IN HUMANS: PREBIOTICS, PROBIOTICS, AND SYNBIOTICS 315 George T. Macfarlane and Sandra Macfarlane INDEX 339

“Having said that, I’m sure the book will be of interest to all those studying the effects of micro–organisms on the human body.”  ( Microbiology Today , 30 August 2013)