Biogeography and individuality shape function in the human skin metagenome

Abstract

SummaryThe varied topography of human skin offers a unique opportunity to study how the body’s microenvironments influence the functional and taxonomic composition of microbial communities. Phylogenetic marker gene-based studies have identified many bacteria and fungi that colonize distinct skin niches. Here, metagenomic analyses of diverse body sites in healthy humans demonstrate that local biogeography and strong individuality define the skin microbiome. We developed a relational analysis of bacterial, fungal, and viral communities, which showed not only site-specificity but also individual signatures. We further identified strain-level variation of dominant species as heterogeneous and multiphyletic. Reference-free analyses captured the uncharacterized metagenome through the development of a multi-kingdom gene catalog, which was used to uncover genetic signatures of species lacking reference genomes. This work is foundational for human disease studies investigating inter-kingdom interactions, metabolic changes, and strain tracking and defines the dual influence of biogeography and individuality on microbial composition and function.

Transplantation of human skin microbiota in models of atopic dermatitis

“…The predominant Gram-negative species identified by our culture methods in HV was Roseomonas mucosa. This and other Gram-negative bacteria grown by our methods were consistent with what has been identified by prior metagenomic analysis (6). However, incomplete genome characterization of organisms such as R. mucosa in current databases, and pooled analysis across individuals, limited species-level identification and determination of species diversity in a given individual in those metagenomic studies.…”

A systematic literature review of the human skin microbiome as biomarker for dermatological drug development

“…swabs, biopsies, tape strips, wound curettes). Interestingly, all have been shown to exhibit a wide variation in biomass yield, microbial profile, human DNA contribution/contamination, sampling depth and discomfort level for the test subject 19, 62, 82, 83, 84, 85, 86, 87. In addition to the sampling method, the selection of sampling sites and sampling frequency are important factors that were not always considered in the included studies.…”

Topical Antimicrobial Treatments Can Elicit Shifts to Resident Skin Bacterial Communities and Reduce Colonization by Staphylococcus aureus Competitors

“…While culture-independent surveys have recently illuminated the complexity of the skin microbiota (15)(16)(17), its necessity for normal function and disease remains unclear. One postulated function includes a role in colonization resistance, whereby members of the commensal microbiota could protect the host from infection by opportunistic and pathogenic skin microorganisms (18).…”