The answer to one of medicine’s most urgent challenges — the search for new antibiotics and other antimicrobials — may be hiding in an unexpected place: the bacteria living on our own skin.
From head to toe, the human body is crawling with good microbes — bustling communities of bacteria, fungi, and viruses that exist all across our skin. Together, these communities make up a vast microbial metropolis called the skin microbiome, which acts as a protective barrier that helps shield us from other, more dangerous microbes.
In a new study out of McMaster University, researchers have shed light on how the skin microbiome protects human health, and their findings suggest that our own skin could be an untapped reservoir of new antibiotics and other new antimicrobial chemicals.
Published today in the journal Nature Communications, the new study involved more than 30 volunteers who were swabbed at eight different body sites representing distinct microenvironments, including the neck, outer nose, nostrils, back, arms, forearms, belly button, and toes.
Together, the swabs pulled in 968 unique strains of bacteria — including four previously undiscovered species — to help establish the largest and most diverse collection of skin-associated microbes ever assembled.
Lindsay Kalan, an associate professor in McMaster’s Department of Biochemistry and Biomedical Sciences and principal investigator on the new study, estimates that the new library — dubbed the Epithelial Isolate Collection, or “EPIC” — represents 95 per cent of the entire human skin microbiome.
Kalan says that the ambitious research project, which was featured by Nature Communications as an Editor’s Highlight, was inspired by a growing body of evidence that suggests microbes play a critical role in protecting animal health, pointing to recent discoveries made by McMaster researchers Cameron Currie and Jianping Xu. Currie discovered that leaf-cutting ants harbour symbiotic bacteria to defend their food source from infection, and Xu discovered that the bacteria found on bat wings may prevent a highly fatal fungal disease called white-nose syndrome.
“We looked at the human microbiome the same way,” says Kalan, associate director of McMaster’s Michael G. DeGroote Institute for Infectious Disease Research. “We isolated samples from the gut, the nose, the mouth, and the skin, and found that the skin microbiome exerted a remarkable amount of antimicrobial activity.”
Kalan’s group validated its early findings by systematically exposing the new library of skin-associated bacteria to a broad panel of more than 20 human pathogens, ranging from bacteria like E. coli and S. aureus to fungi like Cryptococcus and multidrug-resistant C. auris. These experiments revealed that many members of the skin microbiome produced an array of antimicrobial chemicals capable of warding off invaders.
Researchers then zeroed in on the four new species of bacteria uncovered by their skin swabs, and found that three of them produced chemicals that were especially effective at deterring disease-causing fungi.
“These new species of bacteria are what we’re calling ‘fungal specialists,’” Kalan says. “They can inhibit several different kinds of pathogenic fungi, including those that are otherwise drug-resistant.”
The team’s next challenge was determining whether these newly discovered microbes were producing new chemistry, or if they were recycling previously discovered molecules produced by other known bacteria.
“What we found was a tremendous amount of novelty,” Kalan says.
In fact, across all of the skin bacteria studied, researchers found that only four per cent of the gene clusters traditionally responsible for antimicrobial production had been previously characterized, suggesting the remaining 96 per cent could encode potentially new molecules.
“This work shows that the human skin microbiome is a rich source of new molecules, many of which could have important clinical applications,” says Kalan. “This new collection of skin-associated bacteria presents us with a huge opportunity to explore a ton of new chemistry.”
Kalan’s team is now working to better understand the medicinal potential of the most intriguing new molecules, while also exploring whether or not the producing bacteria themselves could one day be harnessed as skin probiotics.
This work was supported in part by the National Institutes of Health, the Weston Family Foundation, and the Canada Research Chairs Program.