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The words well-being and microbes typically are not spoken in the same breath. Microbes have a strong negative connotation in contemporary societies and are viewed in a warlike context. Disease-producing or pathogenic microbes are indeed serious threats to human health and have received justifiable attention from the inception of the field of microbiology. The list of known and notorious pathogens is long. However, most human encounters with microbes are not hostile but benign or even beneficial. Advances in DNA sequencing and computational biology now permit comprehensive description of the composition of and the roles played by the microbial communities (microbiota) associated with the human body.

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Like all animals on the planet, humans have had to adapt to a microbe-dominated biosphere. The number of microbes on Earth is staggering. It has been estimated that 1030 microbes live in the ocean, in surface and subsurface terrestrial ecosystems, and on and inside animals and plants. Microbes, which are defined here as microscopic living organisms that belong to any of the three known domains of life on Earth (Bacteria, Archaea, and Eukarya), inhabit the exposed exterior and interior surfaces of the human body (e.g., the skin, mouth, airways, gastrointestinal tract, and vagina). The uterus traditionally has been thought to be microbe-free, although new evidence may prompt a reevaluation of the idea that this ecosystem is completely sterile throughout gestation. Colonization with microbes begins no later than during parturition; in the ensuing years, microbes come to outnumber human cells by an estimated tenfold in the human body. Therefore, a comprehensive view of humans as a life form entails consideration of the body's microbial and Homo sapiens cells together as a connected network'a coevolved symbiosis ("living together")'in which various body habitats serve as homes to microbial communities. These habitats harbor microbiota composed of members that function as mutualists (both host and microbe benefit from the other's presence), commensals (one partner benefits, and the other is seemingly unaffected), and potential or overt pathogens (one partner benefits, and the other is harmed).

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Human Microbiome Projects

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Human microbiome projects (HMPs) reflect this view of the human body as an amalgamation of human and microbial cells as well as human and microbial genes. These projects represent a confluence of ongoing technical and computational advances in the genome sciences. The newest generation of massively parallel DNA sequencers can be used to document—with unprecedented speed and economy—which microbes compose a microbiota and to characterize a microbiota's gene content (its microbiome). Key terms relevant to HMPs are defined in Table 64-1.

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Table 64-1 Glossary of Terms Used in Discussion of the Human Microbiome 

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