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CHAPTER 3: THE HUMAN MICROBIOME

Jeffrey I. Gordon; Rob Knight

INTRODUCTION

The technologies that allowed us to decipher the human genome have revolutionized our ability to delineate the composition and functions of the microbial communities that colonize our bodies and make up our microbiota. Each body habitat, including the skin, nose, mouth, airways, gastrointestinal tract, and vagina, harbors a distinctive community of microbes. Efforts to understand our microbiota and its collection of microbial genes (our microbiome) are changing our views of “self” and deepening our understanding of many normal physiologic, metabolic, and immunologic features and their interpersonal and intrapersonal variations. In addition, this area of research is beginning to provide new insights into diseases not previously known to have microbial “contributors” and is suggesting new strategies for treatment and prevention. Key terms used in the discussion of the human microbiome are defined in Table 3-1.

TABLE 3-1GLOSSARY OF TERMS USED IN DISCUSSION OF THE HUMAN MICROBIOME
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TABLE 3-1 GLOSSARY OF TERMS USED IN DISCUSSION OF THE HUMAN MICROBIOME
TERM DEFINITION
Culture-independent analysis A type of analysis in which the culture of microbes is not required but rather information is extracted directly from environmental samples
Diversity (alpha and beta) Alpha diversity measures the effective number of species (kinds of organisms) at the level of individual habitats, sites, or samples. Beta diversity measures differences in the number of kinds of organisms across habitats, sites, or samples.
Domains of life The three major branches of life on Earth: the Eukarya (including humans), the Bacteria, and the Archaea
Dysbiosis Any deleterious condition arising from a structural and/or functional aberration in one or more of the host organism’s microbial communities
Gnotobiotics The rearing of animals under sterile (germ-free) conditions. These animals can subsequently be colonized at various stages of the life cycle with defined collections of microbes.
Holobiont The biologic entity consisting of a host and all its internal and external symbionts, their gene repertoires, and their functions
Human microbiome In ecology, biome refers to a habitat and the organisms in it. In this sense, the human microbiome would be defined as the collection of microorganisms associated with the human body. However, the term microbiome is also used to refer to the collective genomes and genes present in members of a given microbiota (see “Microbiota,” below), and the human metagenome is the sum of the human genome and microbial genes (microbiome). A core human microbiome is defined as everything shared in a given body habitat among all or the vast majority of human microbiomes. A core microbiome may include a common set of genomes and genes encoding various protein families and/or metabolic capabilities. Microbial genes that are variably represented in different humans may contribute to distinctive physiologic/metabolic phenotypes.
Metagenomics An emerging field encompassing culture-independent studies of the structures and functions of microbial communities as well as the interactions of these communities with the habitats they occupy. Metagenomics includes (1) shotgun sequencing ...

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