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Hundreds of new bacterial species and viruses found on our skin microbiome by EMBL-EBI researchers



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Hundreds of new bacterial species and viruses have been identified in the human skin microbiome.

The discovery, involving researchers at EMBL’s European Bioinformatics Institute (EMBL-EBI) in Hinxton, could aid our understanding of medical conditions, including acne and eczema.

An illustration of the skin microbiome. Picture: Karen Arnott, EMBL-EBI (54157287)
An illustration of the skin microbiome. Picture: Karen Arnott, EMBL-EBI (54157287)

Microbiomes are communities of micro-organisms found everywhere from soil to the oceans, and our bodies. There is growing interest in the human gut microbiome, but much less is known about the skin microbiome, which is believed to play an important role in skin health and disease.

Working with colleagues at the National Institutes of Health, researchers at EMBL-EBI sequenced the genomes of microorganisms detected within 594 samples taken from various skin surfaces of 12 healthy volunteers, primarily from North America, although the study will be expanded to other populations.

They combined a traditional laboratory cultivation approach with metagenomic sequencing to create the Skin Microbial Genome Collection (SMGC) – a collection of reference genomes for the human skin microbiome.

Sara Kashaf, PhD student at the NIH and EMBL-EBI, said: “We discovered thousands of viral sequences including many jumbo phages – very big viruses that infect bacteria – most commonly on the surface of the hands and feet of our volunteers.

“These areas of the body have highly diverse microbiomes, which makes sense because we’re constantly using our hands to touch new things in our environment. Our future work will aim to understand what these different microbes are doing within these communities.”

The collection includes 174 previously unknown bacterial species, four new eukaryotes and 20 new jumbo phages – which are viruses with a genome larger than 200 kilobases, or three to five times larger than an average virus.

The research expands the catalogue of known skin bacteria by 26 per cent.

Rob Finn, group leader at EMBL-EBI, said: “In addition to the bacteria and viruses that we normally recover in metagenomics, we also found 12 genomes from single-celled eukaryotes – fungi, like yeast – from the human skin.

“Some of these genomes were already known, such as Malassezia globosa, which has been associated with the healthy skin mycobiome but has also been associated with conditions such as dandruff.

“ Using the same methods that recovered eight known genomes gives us confidence in the four novel eukaryotes that we found.

“Looking at the patterns of these novel eukaryotes revealed that one of them was very common across the volunteers, and may be found on many of us.”

The study, published in Nature Microbiology, involved included those at the NIH National Human Genome Research Institute and the NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases.

Julie Segre, senior investigator at the NHGRI, said: “This work is a major step toward obtaining a complete genomic blueprint of the skin microbiome. We hope these data will support future investigations improving our understanding of skin health and disease.”

The data will be made freely accessible soon as a new genome catalog in the MGnify data resource, where researchers can find microbiome datasets, including for the human gut.


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