The Human Microbiota – How Microbial Communities Affect Health and Disease

David Fredricks is an expert in infectious diseases and the human indigenous microbiota, with a research focus on the bacterial biota of the human vagina and how changes in the composition of vaginal microbes lead to the syndrome bacterial vaginosis. He has authored more than 32 peer reviewed journal articles, 7 book chapters, and 9 editorials or invited reviews. He has been a peer reviewer for more than a dozen major medical and infectious diseases journals, and has served on several NIH study sections.

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