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Popping the Zit Microbiome

Ashley Yeager

Could the microbes in our pores help explain why some people suffer severe acne? Some researchers believe so. Learn more...

We’ve all had a zit or two, but some people suffer from severe acne, which can be both socially and physically painful. However, the cause of severe acne has remained a mystery and the available treatments are not always effective.

A close-up of a biofilm of P. acnes bacteria and some red blood cells. Soure: Bayston et. al., 2006.

But now, by studying the DNA sequences of microbes from patients with severe acne, scientists think it might come down to which strains of the bacterium Propionibacterium acnes live in the oily depths of a person’s pores.

“In the past, P. acnes was the bad guy,” said Huiying Li, a systems biologist at the University of California, Los Angeles whose research team published a study on P. acnes strains found in human skin yesterday in the Journal of Investigative Dermatology (1).

Previous experiments linked P. acnes with inflamed skin and pimples, but Li and colleagues found that both people with acne and those with clear skin had similar amounts of P. acnes in their pores. The difference between these two populations was the strains of P. acnes they had.

The team had 101 college students—49 acne-suffering students and 52 clear-faced students—use over the counter pore cleansing strips to pull dirt and bacteria from the bridges of their noses. After culturing the bacteria from those samples, the scientists analyzed the metagenome from those microbial communities.

Using bioinformatics, the team further investigated the microbiome of the students' pores, isolating 1000 strains of P. acnes. The researchers then classified the strains into 10 types. Six strain types were more prevalent among the acne prone students, while only one strain type appeared repeatedly in the samples from healthy skin students.

The key was to look at the strains of P. acnes, rather than studying it as a single species, Li said. So far, Li believes that the study has produced the largest number of individual skin microbiomes reported at the strain level. “It’s still very hard looking at the strain level of bacteria, but it’s important because, as our results show, not all strains are bad and not all are good," she said.

To better understand the genetic differences, the team isolated 66 previously unidentified strains—a few from each P. acnes strain type—and ran their DNA through a high-throughput sequencer.

Compared with the genomes of previously sequenced strains of P. acnes, the DNA of two strain types associated with acne had genetic islands that could harbor genes linked to the disfiguring skin disease. In contrast, the DNA of the strains associated with clear skin had genetic components that could block viral infections. This is one possible mechanism by which some P. acnes strains could actually keep skin healthy.

The results don't yet show for certain that the bad strains of P. acnes actually cause acne or explain why some people carry certain P. acnes strains and others don’t. The next steps, however, are to show a connection between the bad bacteria strains and acne and to test whether healthy skin strains can withstand virus attacks.

In the end, the strain level analysis could help dermatologists develop new drugs that kill acne causing strains of P. acnes, Li said.


1. Fitz-Gibbon, S., S. Tomida, B.-H. H. Chiu, L. Nguyen, C. Du, M. Liu, D. Elashoff, M. C. Erfe, A. Loncaric, J. Kim, R. L. Modlin, J. F. Miller, E. Sodergren, N. Craft, G. M. Weinstock, and H. Li. 2013. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. The Journal of investigative dermatology (January).

Keywords:  metagenomics microbiome