Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome

Stephen Nayfach, Katherine S. Pollard
doi: https://doi.org/10.1101/009001
Stephen Nayfach
1Integrative Program in Quantitative Biology, University of California San Francisco, CA 94158
2Gladstone Institutes, University of California San Francisco, CA 94158
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katherine S. Pollard
1Integrative Program in Quantitative Biology, University of California San Francisco, CA 94158
2Gladstone Institutes, University of California San Francisco, CA 94158
3Institute for Human Genetics, University of California San Francisco, CA 94158
4Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94158
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: stephen.nayfach-battilana@ucsf.edu kpollard@gladstone.ucsf.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Average genome size (AGS) is an important, yet often overlooked property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate AGS from short-read metagenomics data and applied our tool to over 1,300 human microbiome samples. We found that AGS differs significantly within and between body sites and tracks with major functional and taxonomic differences. For example, in the gut, AGS ranges from 2.5 to 5.8 megabases and is positively correlated with the abundance of Bacteroides and polysaccharide metabolism. Furthermore, we found that AGS variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.

  • List of Abbreviations

    AGS
    average genome size of a microbial community
    CV
    coefficient of variation
    Mb
    megabase
    CPU
    central processing unit
    NCBI
    National Center for Biotechnology Institute
    HMP
    Human Microbiome Project
    T2D
    type-2 diabetes metagenomics sequencing project
    MetaHIT
    Metagenomics of the Human Intestinal Tract
    OTU
    operational taxonomic unit
    KEGG
    Kyoto Encyclopedia of Genes and Genomes
    KO
    KEGG Orthology Group
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
    Back to top
    PreviousNext
    Posted September 11, 2014.
    Download PDF

    Supplementary Material

    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome
    Stephen Nayfach, Katherine S. Pollard
    bioRxiv 009001; doi: https://doi.org/10.1101/009001
    Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
    Citation Tools
    Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome
    Stephen Nayfach, Katherine S. Pollard
    bioRxiv 009001; doi: https://doi.org/10.1101/009001

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (4113)
    • Biochemistry (8815)
    • Bioengineering (6518)
    • Bioinformatics (23459)
    • Biophysics (11789)
    • Cancer Biology (9207)
    • Cell Biology (13322)
    • Clinical Trials (138)
    • Developmental Biology (7436)
    • Ecology (11409)
    • Epidemiology (2066)
    • Evolutionary Biology (15149)
    • Genetics (10436)
    • Genomics (14043)
    • Immunology (9171)
    • Microbiology (22153)
    • Molecular Biology (8812)
    • Neuroscience (47566)
    • Paleontology (350)
    • Pathology (1428)
    • Pharmacology and Toxicology (2491)
    • Physiology (3730)
    • Plant Biology (8079)
    • Scientific Communication and Education (1437)
    • Synthetic Biology (2220)
    • Systems Biology (6037)
    • Zoology (1253)