Using molecular techniques that detect all known types of microbes and borrowing statistical techniques from field ecology and population genetics, Paul Eckburg, MD, a postdoctoral scholar in infectious diseases and geographic medicine, conducted the most extensive study to date surveying the inhabitants of the lower digestive tract. In the three healthy subjects he studied, he found 395 unique bacterial species.
"The intestinal flora is critical to human physiology and a wide spectrum of disease, but the first step in studying this ecosystem is to figure out who is there and how the community census varies in time and space," said Eckburg, the lead author of the study published in this week's online edition of Science Express. "But even with this large sequencing project, which produced orders of magnitude more sequence data than had been generated in the past, we are not completely there yet. This is just the tip of the iceberg."
Eckburg works with David Relman, MD, associate professor of medicine (infectious diseases and geographic medicine) and of microbiology and immunology. Relman's lab at the Veteran Affairs Palo Alto Heath Care System specializes in microbial pathogen discovery and human microbial ecology, and in appreciating the roles played by microbes in human health and disease.
The paper by Eckburg and Relman is intended as the first of several studies looking at how microbial communities vary according to host, diet, geography, disease and other variables.
To distinguish individual bacteria among the hundreds of types in the samples, Eckburg took advantage of a technique that compares the genetic sequence of a molecule shared by bacteria and archaea. The molecule, 16S rRNA,