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US scientists map genes of microbes in healthy individuals

New Ecosystem of Microbes Model

Scientists say this new reference database of microbes in healthy humans will change the way doctors think about infections, moving from a model of one germ causing disease, to thinking about factors that alter the healthy ecosystem of microbes living in people.

Prior to this study, scientists would culture microbes in lab dishes, but many of the microbes that live in humans are difficult to culture this way, and so far, only a few hundred d species have been isolated in the human body.

Instead of trying to grow cultures, researchers sampled as many as 18 different sites targeting five main body areas, including the airways, the skin, the mouth, the digestive tract and the vagina.

These samples were donated from 242 healthy people ranging in age from 18 to 40 living near Houston or St. Louis.

The researchers then purified all of the DNA in the sample, sequenced the genes and used high-powered computer programs to analyze the data and identify which microbes were present in different areas of the body and in what amounts.

“The beauty of this approach is it identifies everything that is there, giving us complete views of the microbiome at a given body site, like an explorer mapping the coastline of a newly discovered continent for the very first time,” Green said.

Onward to Distinguishing Good and Bad

George Weinstock, associate director of the Genome Institute at Washington University, who helped lead the study, said knowing which microbes live in which “ecological niches” in healthy humans will allow researchers to better target diseases that are thought to have a microbial link, such as Chron's disease and obesity. And it will help doctors understand why dangerous pathogens living in people sometimes turn deadly.

“One of the questions we asked is how many of these organisms are novel,” Weinstock said in a telephone interview.

The good news, he said, is that most of the microbes identified in the study have been seen before, but about 5 to 10 percent of the microbes identified are newly discovered.

Now that researchers have what Weinstock calls the “parts list” for what microbes reside in healthy people, scientists will begin the process of understanding how the microbiome and human cells interact, and how this affects human health.

“There is a very active and extensive dialog going on between all of those microbial cells and all of our human cells,” Weinstock said. “Our bodies somehow know which microbes are OK to have.

The next stage, he said, is trying to figure out how the body establishes the good guys from the bad.

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