NIH researchers find thousands of new microorganisms living on human skin

Researchers have now identified and catalogued more species that reside on the human skin than has ever been possible, largely due to advances in bioinformatics and laboratory techniques. Some of these previously unknown species are the most abundant on human skin. The results appear in a new catalog, the Skin Microbial Genome Collection (SMGC), published today in Nature Microbiology.

Investigators at the National Human Genome Research Institute (NHGRI), European Bioinformatics Institute and the National Institute of Arthritis and Musculoskeletal and Skin Diseases participated in the collaborative study.

According to researchers, the new catalog is remarkable in its breadth, bringing to light an incredibly complex map of species that make up the skin microbiome. It also opens the door for scientists to figure out the root causes of various skin diseases. 

“The organisms that make up the skin microbiome have an enormous impact on our health, and changes in the microbiome can contribute to several skin diseases,” said Julie Segre, Ph.D., head of the Microbial Genomics Section at NHGRI. “The resource we've created will support research that explores skin health and seeks to understand the cause of these disorders. ”The skin is the human body’s largest organ. It is covered with bacteria, fungi, viruses and other types of organisms. Collectively, these species make up the skin’s community of micro-organisms called the microbiome.

Historically, scientists have encountered many challenges to figuring out exactly what microorganisms live on the skin. One of the most useful techniques to study the skin microbiome is to grow each skin microorganism separately in a laboratory. But many of the microorganisms cannot be grown in such a setting because their natural environments cannot be reproduced in a laboratory.

The organisms that make up the skin microbiome have an enormous impact on our health, and changes in the microbiome can contribute to several skin diseases. The skin is the human body’s largest organ. It is covered with bacteria, fungi, viruses and other types of organisms. Collectively, these species make up the skin’s community of micro-organisms called the microbiome.

Another way to study these microbes is to take skin samples and perform genomic analyses to identify which microorganisms make up the sample.

“A microbe has a smaller, less complex genome than a human. But in any given skin sample, it’s as if genomic pieces of each microbe are thrown in with hundreds of different pieces in one box,” said Segre. “Putting the pieces together for each microbe is the hard part.”

This means that the databases that scientists use to compare the microbiomes of skin samples are not complete.

While growing and using genomics to assemble bacteria each have their limitations, the researchers set out to create a more comprehensive reference catalogue of the skin microbiome by combining the two scientific practices.

In the first step, the researchers took skin swabs from 14 parts of the body from 12 healthy volunteers. From these samples, they grew several bacterial species that are known to live on human skin, under multiple laboratory conditions.

In the second step, the researchers accessed previously sequenced and identifiable microbial samples that spanned 19 body sites from a dozen healthy volunteers. These samples were taken over five years, to understand how skin microbiome changes over time.

These previously acquired skin samples had been sequenced using shotgun metagenomic sequencing, a technique that randomly samples many short sequences of DNA. In this case, the researchers used skin samples that included microorganisms residing on the skin. The short, randomly chosen sequences were fed into an algorithm, which eventually helped to create a whole sequence.

From these complex datasets, researchers gained a fuller view of the microorganisms that live on human skin.

The authors identified 174 novel bacterial species in the skin microbiome, for a total of 622 bacterial species catalogued in the SMGC.

The newly identified species represented a 26% increase in the knowledge of skin bacterial diversity. The researchers recognized that some of the most a­­bundant and prevalent microbes on the skin are novel. The researchers also identified three new fungal species and the first examples of jumbo viruses that specifically infect bacteria living on the skin.

Knowledge of these genomes, along with fungi and viral genomes, will now enable researchers who use the SMGC resource to identify roughly 85% of the microorganisms present in a skin sample.

“Our future goals are to isolate some of these newly identified species and understand how they help shape the skin microbial community and its functions,” said Sara Saheb Kashaf, first author of the study and an M.D./Ph.D. candidate through the National Institutes of Health Oxford-Cambridge Scholars Program.