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Metagenomics Uncovers New Information About Skin Microbes

NEW YORK (GenomeWeb News) – A new metagenomic study by National Institutes of Health researchers has revealed the diverse microorganisms residing on human skin — and lays the foundation for larger studies of the skin microbiome. 
In a paper published online today in Genome Research, NIH scientists used 16S rRNA sequences to survey the microbes on five people’s inner elbows. They identified a common microbiome as well as microorganisms that varied between individuals’ right and left elbows and from person to person. The study, part of the NIH’s Human Microbiome Project, also compared three different sampling methods — an analysis that will inform future projects cataloguing microbial diversity on and within human skin.
The Human Microbiome Project, part of the NIH Roadmap for Medical Research, is intended to explore the role of microorganisms in both health and disease, NIH researcher Julie Segre, the paper’s senior author, told GenomeWeb Daily News. By cataloguing the beneficial or harmless microorganisms found on human skin, it may be possible to better understand the changes in the microbial community that are associated with disease states, she said.
Traditionally, studies of skin microbes have depended on culturing bugs in the lab and then identifying them. While that approach is useful, researchers say it misses a great deal of the real microbial diversity on the skin and elsewhere, because some microbes can’t be cultured in the lab or require very specific growth conditions.
“You can imagine that what is cultured off of the skin is not exactly representative of what is there,” lead author Elizabeth Grice, a post-doctoral fellow in Segre’s lab, told GenomeWeb Daily News, noting that culturing conditions are biased towards certain species.
To get around that problem, the team took a metagenomic approach, extracting DNA from uncultured microbes. They used conserved primers to amplify 16S rRNA from microbes found on both inner elbows of five individuals using three different sampling methods — swabs, scrapes, or punch biopsies. Overall, the three sampling methods gave very similar results, although more bacterial cells were collected by scraping and punch biopsy than by swabbing.
The researchers sequenced roughly 200 clones from each library using an ABI 3730x1 sequencer. After tossing out chimeric sequences, they performed phylogenetic analysis on nearly 5,400 sequences and classified the bugs in 113 phylotypes or “operational taxonomic units” containing organisms whose sequences were at least 97 percent similar.
About half of the OTUs and some 90 percent of the total sequences represented bacteria in the Proteobacteria group. The majority of these — some 59 percent — belonged to the genus Pseudomonas, although the researchers also found Janthinobacterium, Serratia, and Stenotrophomonas.
“It was actually quite surprising that Proteobacteria was the dominant bacteria,” Segre noted, since culturing studies suggested Staphylococcus epidermidis would be prevalent. As it turned out, S. epidermidis and Propionibacterium acnes — another bug that was thought to be quite common on skin — actually represented less than five percent of the microbes detected.
The researchers also found sequences from the Actinobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Cyanobacteria divisions and from a group of microorganisms that was nearly 94 percent similar to an unknown organism found in agricultural soil samples.
These results overlapped, to a certain extent, with the findings of a 2007 metagenomics paper on forearm microbes published by New York University researchers in the Proceedings of the National Academy of Sciences. But Segre’s team found a distinct microbiome on the inner elbow skin.
Segre suspects the disparate results reflect real differences in the microbial communities at the two skin sites. “The microbiome — the bacterial species and their diversity — are really quite different,” she said, suggesting there is great microbial diversity between skin on different parts of the body.
For the most part, the variation between the five individuals was similar to that detected when the researchers compared the microbial communities on each person’s left inner elbow with their right. But there was an exception: one individual was colonized by Staphylococcus, a bug previously shown to colonize some five to ten percent of healthy adults without causing clinical symptoms.
Eventually, the researchers hope to tease apart the gene-environment interactions influencing microbial diversity, Segre explained. To begin doing this, they compared the microbes found on human skin with those found on mouse ear skin, an area of the mouse that’s “probably most like human skin,” Grice said. Indeed, the microbiome of mouse ear skin appeared to be remarkably similar to that of the human inner elbow.
In the future, Segre said, the information gained from these early experiments will be applied to help culture and eventually sequence reference genomes for skin microbes. Investigators participating in the Human Microbiome Project also plan to do larger studies, surveying 250 individuals to catalogue the microbes at five sub-sites: the gut, mouth, nose, skin, and vagina. 

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