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Biogeography and individuality shape function in the human skin metagenome

Author

Listed:
  • Julia Oh

    (Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA)

  • Allyson L. Byrd

    (Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA)

  • Clay Deming

    (Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA)

  • Sean Conlan

    (Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA)

  • Heidi H. Kong

    (Dermatology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA)

  • Julia A. Segre

    (Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA)

Abstract

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.

Suggested Citation

  • Julia Oh & Allyson L. Byrd & Clay Deming & Sean Conlan & Heidi H. Kong & Julia A. Segre, 2014. "Biogeography and individuality shape function in the human skin metagenome," Nature, Nature, vol. 514(7520), pages 59-64, October.
    • Handle: RePEc:nat:nature:v:514:y:2014:i:7520:d:10.1038_nature13786
    DOI: 10.1038/nature13786
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    Cited by:

    1. Manoshi S. Datta & Idan Yelin & Ori Hochwald & Imad Kassis & Liron Borenstein-Levin & Amir Kugelman & Roy Kishony, 2021. "Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    2. Lucas Moitinho-Silva & Frauke Degenhardt & Elke Rodriguez & Hila Emmert & Simonas Juzenas & Lena Möbus & Florian Uellendahl-Werth & Nicole Sander & Hansjörg Baurecht & Lukas Tittmann & Wolfgang Lieb &, 2022. "Host genetic factors related to innate immunity, environmental sensing and cellular functions are associated with human skin microbiota," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Mohammed Y. Refai & Aala A. Abulfaraj & Israa J. Hakeem & Nehad A. Shaer & Mashael D. Alqahtani & Maryam M. Alomran & Nahaa M. Alotaibi & Hana S. Sonbol & Abdulrahman M. Alhashimi & Nouf S. Al-Abbas &, 2023. "Rhizobiome Signature and Its Alteration Due to Watering in the Wild Plant Moringa oleifera," Sustainability, MDPI, vol. 15(3), pages 1-25, February.
    4. Edoardo Pasolli & Duy Tin Truong & Faizan Malik & Levi Waldron & Nicola Segata, 2016. "Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-26, July.
    5. Christopher Ruis & Aaron Weimann & Gerry Tonkin-Hill & Arun Prasad Pandurangan & Marta Matuszewska & Gemma G. R. Murray & Roger C. Lévesque & Tom L. Blundell & R. Andres Floto & Julian Parkhill, 2023. "Mutational spectra are associated with bacterial niche," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    6. Mohammed Ashrafi & Yun Xu & Howbeer Muhamadali & Iain White & Maxim Wilkinson & Katherine Hollywood & Mohamed Baguneid & Royston Goodacre & Ardeshir Bayat, 2020. "A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study," PLOS ONE, Public Library of Science, vol. 15(2), pages 1-26, February.
    7. Manal A. Tashkandi & Rewaa S. Jalal & Lina Baz & Mohammed Y. Refai & Ashwag Shami & Ruba Abdulrahman Ashy & Haneen W. Abuauf & Fatimah M. Alshehrei & Fawzia A. Alshubaily & Aminah A. Barqawi & Sahar A, 2022. "Functional Interpretation of Cross-Talking Pathways with Emphasis on Amino Acid Metabolism in Rhizosphere Microbiome of the Wild Plant Moringa oleifera," Agriculture, MDPI, vol. 12(11), pages 1-22, October.
    8. Kumar P Mainali & Sharon Bewick & Peter Thielen & Thomas Mehoke & Florian P Breitwieser & Shishir Paudel & Arjun Adhikari & Joshua Wolfe & Eric V Slud & David Karig & William F Fagan, 2017. "Statistical analysis of co-occurrence patterns in microbial presence-absence datasets," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-21, November.

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