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a tool kit for quantifying eukaryotic rrna gene sequences from human microbiome samples量化的工具真核核糖体rna基因序列从人类微生物组样本
Dollive et al. Genome Biology 2012, 13:R60
/2012/13/7/R60
METHOD Open Access
A tool kit for quantifying eukaryotic rRNA gene
sequences from human microbiome samples
1 1 1 1 1 1
Serena Dollive , Gregory L Peterfreund , Scott Sherrill-Mix , Kyle Bittinger , Rohini Sinha , Christian Hoffmann ,
1 1,2,3 1,2,3 4,5 1
Christopher S Nabel , David A Hill , David Artis , Michael A Bachman , Rebecca Custers-Allen ,
1 6 7 1*
Stephanie Grunberg , Gary D Wu , James D Lewis and Frederic D Bushman
Abstract
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 /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.
Background Many diseases are mediated by infections of single cell
The human microbiome consists of bacteria, archaea, eukaryotes [1-3], including infections of the gut [4], skin
viruses and
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