Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Skin Microbial Genome Catalogue

Human skin acts as a physical barrier to prevent the invasion of foreign pathogens, while providing a home for commensals. The paucity of reference genomes has limited our ability to interpret skin metagenomic datasets. Here we combine extensive bacterial culturing, deep metagenomic sequencing, pooling of metagenomic datasets, and incorporation of publicly available skin metagenomic datasets to elucidate novel constituents and functions of the human skin microbiome. The resulting Skin Microbial Genome Collection (SMGC) spans 622 prokaryotic species derived from 7,535 metagenome-assembled genomes (MAGs) and 251 isolate genomes. This collection includes 174 novel bacterial species and 12 novel bacterial genera providing an increase of 26% in the skin bacterial diversity. Notably, we detected new and abundant members of an uncultured genus, here named Candidatus Pellibacter. We validated the quality of our bacterial MAGs by comparing them to isolates obtained from the same samples. We also recovered 12 eukaryotic species and thousands of viral sequences including novel clades of jumbo phages prevalent in foot sites. With the ability to now classify a median of 85% of skin metagenomic sequences, the SMGC elucidates a new multi-kingdom map of microbes patterning human skin.