title: A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.
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.
authors: Serena
authors: S
authors: Dollive
authors: Gregory L
authors: GL
authors: Peterfreund
authors: Scott
authors: S
authors: Sherrill-Mix
authors: Kyle
authors: K
authors: Bittinger
authors: Rohini
authors: R
authors: Sinha
authors: Christian
authors: C
authors: Hoffmann
authors: Christopher S
authors: CS
authors: Nabel
authors: David A
authors: DA
authors: Hill
authors: David
authors: D
authors: Artis
authors: Michael A
authors: MA
authors: Bachman
authors: Rebecca
authors: R
authors: Custers-Allen
authors: Stephanie
authors: S
authors: Grunberg
authors: Gary D
authors: GD
authors: Wu
authors: James D
authors: JD
authors: Lewis
authors: Frederic D
authors: FD
authors: Bushman
mesh_terms: D056890:Eukaryota / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D005243:Feces / Q000382:microbiology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota; D012313:RNA / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods; D012984:Software
chemical_list: C034477:RNA primers; D012337:RNA, Ribosomal, 18S; D012313:RNA