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The human microbiome is the term used to describe the distinct microbial communities that inhabit different host environments on the body’s skin and mucosal surfaces. Historically, microbiologists referred to microbial populations routinely found on and in the body as normal flora. The term microbiome also encompasses all of the genetic material associated with these normal constituents. As you will read below, the genetic capabilities of any given normal flora organism can have profound and important impacts on the interactions that the microbe has with the host. The establishment of the human microbiome is initiated immediately after birth and is a necessary and normal part of human development.

Until relatively recently, our understanding of the organisms that compose the human microbiome relied on cultivation to isolate organisms in pure culture. This approach is limited in its usefulness for several reasons. First, the vast majority of microbes associated with humans cannot be cultivated ex vivo. Second, the ability to culture a microbe does not yield any information on the relative abundance of that organism in the niche under investigation. Finally, growing an organism out of its environment in pure culture gives little, if any, information on the complexity and interdependence of the microbial communities in that niche.

The development of sophisticated molecular techniques over the past decade (see Chapter 9 for more detail) has revealed enormous numbers of bacteria, yeasts, and protozoa that are associated with the human microbiome, many of which were previously unknown. Current estimates suggest that there is an approximately equal number of prokaryotic cells on and in the human body as there are human cells, most of which are gut-associated. This remarkable statistic is even more notable considering that the average adult gut is home to ~1000 bacterial species, each of which contains ~2000 genes, cataloging a total of 2,000,000 gut-associated microbial genes. This is 100 times more than the ~20,000 genes encoded in the entire human genome.

Variation in the abundance and complexity of the microbiome constituents is observed within an individual over time and certainly between individuals. However, longitudinal characterization of the human gut microbiome has shown that within the first few years of life, our microbial communities mature and become relatively stable and unique to each individual unless perturbed, such as by antibiotic treatment.

Once established, members of the microbiome are considered permanent residents of the associated body sites, such as the skin, oropharynx, colon, and vagina (Tables 6–1 and 6–2). These microbes are often referred to as commensals, which are organisms that derive benefit from another host but do not damage that host.

Table 6–1Summary of the Members of Normal Flora and Their Anatomic Locations

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