IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-14677-3.html
   My bibliography  Save this article

A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

Author

Listed:
  • Bing Ma

    (University of Maryland School of Medicine
    University of Maryland School of Medicine)

  • Michael T. France

    (University of Maryland School of Medicine
    University of Maryland School of Medicine)

  • Jonathan Crabtree

    (University of Maryland School of Medicine)

  • Johanna B. Holm

    (University of Maryland School of Medicine
    University of Maryland School of Medicine)

  • Michael S. Humphrys

    (University of Maryland School of Medicine)

  • Rebecca M. Brotman

    (University of Maryland School of Medicine
    University of Maryland School of Medicine)

  • Jacques Ravel

    (University of Maryland School of Medicine
    University of Maryland School of Medicine)

Abstract

Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. In this study, we assemble a comprehensive human vaginal non-redundant gene catalog (VIRGO) that includes 0.95 million non-redundant genes. The gene catalog is functionally and taxonomically annotated. We also construct a vaginal orthologous groups (VOG) from VIRGO. The gene-centric design of VIRGO and VOG provides an easily accessible tool to comprehensively characterize the structure and function of vaginal metagenome and metatranscriptome datasets. To highlight the utility of VIRGO, we analyze 1,507 additional vaginal metagenomes, and identify a high degree of intraspecies diversity within and across vaginal microbiota. VIRGO offers a convenient reference database and toolkit that will facilitate a more in-depth understanding of the role of vaginal microorganisms in women’s health and reproductive outcomes.

Suggested Citation

  • Bing Ma & Michael T. France & Jonathan Crabtree & Johanna B. Holm & Michael S. Humphrys & Rebecca M. Brotman & Jacques Ravel, 2020. "A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-14677-3
    DOI: 10.1038/s41467-020-14677-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-14677-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-14677-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-14677-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.