The Human Microbiota

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 CROHNâS 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