201. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.
- Author
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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, and Bushman FD
- Subjects
- Eukaryota genetics, Feces microbiology, High-Throughput Nucleotide Sequencing, Humans, RNA genetics, Single-Cell Analysis methods, Software, Eukaryota classification, Eukaryota isolation & purification, Microbiota, RNA, Ribosomal, 18S genetics, Sequence Analysis, RNA methods
- 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 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.
- Published
- 2012
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