Biogeography and individuality shape function in the human skin metagenome

The 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 niche...

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Bibliographic Details
Published in:Nature (London) 2014-10, Vol.514 (7520), p.59-64
Main Authors: Oh, Julia, Byrd, Allyson L, Deming, Clay, Conlan, Sean, Kong, Heidi H, Segre, Julia A
Format: Article
Language:English
Subjects:
Bacteria
Bacteriophages - genetics
Bacteriophages - isolation & purification
Biogeography
Biomass
Female
Fungi
Genes
Genetic aspects
Genetic research
Genome, Bacterial - genetics
Genome, Fungal - genetics
Genome, Viral - genetics
Genomes
Genomics
Healthy Volunteers
Humans
Male
Metabolism
Metagenome - genetics
Microbiological research
Microbiota (Symbiotic organisms)
Phylogenetics
Phylogeny
Physiology
Propionibacterium acnes - genetics
Propionibacterium acnes - isolation & purification
Propionibacterium acnes - virology
Skin
Skin - microbiology
Skin - virology
Staphylococcus epidermidis - genetics
Staphylococcus epidermidis - isolation & purification
Staphylococcus epidermidis - virology
Studies
Symbiosis
Taxonomy
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Summary:The 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 catalogue, 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.
ISSN:0028-0836
1476-4687
DOI:10.1038/nature13786