Julie Segre is touring the microbial landscape of our body’s biggest organ, the skin. In anticipation of a $115 million, 5-year effort by the U.S. National Institutes of Health (NIH), she’s traveling from head to toe, conducting a census of some of the trillions of bacteria that live within and upon human skin. Although their project is just getting off the ground, Segre, a geneticist at the National Human Genome Research Institute (NHGRI) in Bethesda, Maryland, and her colleagues have already uncovered a surprising diversity and distribution among skin bacteria. And a few oddities have emerged, too: Microbes known mostly from soils like healthy human skin, living in harmony with us; and the space between our toes is a bacterial desert compared to the nose and belly button.
Segre’s work on what bacteria live where “is cool stuff,” says Steven Salzberg, a bio-informaticist at the University of Maryland, College Park. “We need to increase our own and the public’s awareness of the diversity and quantity of bacterial species on our own skin. The more people are aware, the more we can do to control infection.”
Bacteria and other microbes that colonize our skin and other tissues outnumber the human body’s cells 10 to 1, forming dynamic communities that influence our ability to develop, fight infection, and digest nutrients. “We’re an amalgamation of the human and microbial genomes,” says Segre. Recognizing this, NIH last year designated the Human Microbiome Project as one of its two Roadmap initiatives (Science, 2 June 2006, p. 1355). Researchers will sequence the genomes of about 600 bacteria identified as human inhabitants and get a handle on the 99% of bacteria that defy culturing but thrive in the skin, nose, gut, mouth, or vagina. “You have to understand what is the normal flora in the healthy skin to understand the impact of flora on disease,” says Kevin Cooper, a dermatologist at Case Western Reserve University in Cleveland, Ohio.
As a first step, Segre, NHGRI postdoctoral fellow Elizabeth Grice, and their colleagues have studied five healthy volunteers, swabbing the insides of their right and left elbows. The site chosen isn’t as unusual as it sounds; people with eczema often develop symptoms there. To survey the full thickness of skin, the researchers also used a scalpel to scrape off the top cel ls. And to reach even deeper, they took small “punches” of skin, a procedure akin to removing a mole.
From all the samples, Grice, Segre, and colleagues pulled out 5300 16S ribosomal RNA genes, which vary from microbe to microbe. After lumping together the most similar 16S genes, they came up with 113 kinds of bacteria and identified these dermal residents by matching the 16S genes to those of known bacteria. (Segre described the results at a recent meeting at Cold Spring Harbor Laboratory, and they are being published online 23 May in Genome Research.) “That’s a lot of diversity, a lot of different organisms,” says Martin Blaser, a microbiologist at New York University, who has done a similar survey of microbes living on the forearm, also finding a lot of diversity.
Yet just 10 bacteria accounted for more than 90% of the sequences. Almost 60% of the 16S genes came from Pseudomonas, Gram-negative bacteria that flourish in soil, water, and decomposing organic debris. The next most common one, accounting for 20%, was another Gram-negative soil and water bug, Janthinobacterium. Neither had been considered skin microbes before this census. Although there were some differences among the volunteers in the microbes present, their elbows did share a common core set of microbes, the group reports.
The three sampling methods yielded slightly different results, with “punches” revealing a surprising number of bacteria under the skin–1 million bacteria per square centimeter compared with 10,000 from the scrapes. “I would have thought under the skin there would be fewer,” says Salzberg.
Segre and her team have also begun sampling 20 other skin sites, including behind the ear and the armpit, from the bodies of volunteers. Skin varies in acidity, temperature, moisture, oil accumulation, and “different environments select for different microbes,” says Blaser. Bacteriawise, reports Segre, “no subsite is identical.”
Some researchers suspect that shifts in the makeup of skin microbial communities activate the immune system to cause diseases such as eczema. “If you know what the [healthy] flora is, then one strategy is to recolonize the area with the right flora,” says Cooper.
Science 23 May 2008:
Vol. 320. no. 5879, p. 1001
DOI: 10.1126/science.320.5879.1001