The story of microbes in historical scholarship and in the history of medical research often starts with a discussion of the germ theory of disease and ends with a discussion of antibiotics, or its consequences (antibiotic-resistant bacteria, for example.) The focus of this work is on infectious pathogenic bacteria. However, the vast majority of bacteria that are implicated in the human body are not disease-causing pathogens. In fact, the body is teeming with these bacteria -- there are trillions -- orders of magnitude that show more bacterial cells than human cells. Recently, these nonpathogenic bacteria have achieved a kind of celebrity: the National Institutes of Health began a well-covered large-scale inter-institute initiative to study this collection of microbial fellow travelers -- historically called the normal bacterial flora -- in 2007. This initiative, called the Human Microbiome Project, aims to characterize and begin to better understand the role of the bacterial inhabitants of the body, largely through new genomic techniques. The key technique, metagenomics, takes the genetic material of an environment as its analytical target instead of a sole organism.