Introduction

Eukaryotic microorganisms are important but understudied components of the human microbiome. Here we present a pipeline for analysis of deep sequencing data on single cell eukaryotes. We designed a new 18S rRNA gene-specific PCR primer set and compared a published rRNA gene internal transcribed spacer (ITS) gene primer set. Amplicons were tested against 24 specimens from defined eukaryotes and eight well-characterized human stool samples. A software pipeline https://sourceforge.net/projects/brocc/ was developed for taxonomic attribution, validated against simulated data, and tested on pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.

Publications

  1. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.
    Cite this
    Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD, 2012-07-01 - Genome biology

Credits

  1. Serena Dollive
    Developer

  2. Gregory L Peterfreund
    Developer

  3. Scott Sherrill-Mix
    Developer

  4. Kyle Bittinger
    Developer

  5. Rohini Sinha
    Developer

  6. Christian Hoffmann
    Developer

  7. Christopher S Nabel
    Developer

  8. David A Hill
    Developer

  9. David Artis
    Developer

  10. Michael A Bachman
    Developer

  11. Rebecca Custers-Allen
    Developer

  12. Stephanie Grunberg
    Developer

  13. Gary D Wu
    Developer

  14. James D Lewis
    Developer

  15. Frederic D Bushman
    Investigator

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Summary
AccessionBT004204
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByFrederic D Bushman