Cited by 147Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity StudiesGut microbiota and health

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

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Dollive, Serena, Peterfreund, Gregory L, Sherrill-Mix, Scott, Bittinger, Kyle, Sinha, Rohini, Hoffmann, Christian, Nabel, Christopher S, Hill, David A +7 more·2012·Genome biology

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.

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Authors
Dollive, S., Peterfreund, G. L., Sherrill-Mix, S., Bittinger, K., Sinha, R., Hoffmann, C., Nabel, C. S., Hill, D. A., Artis, D., Bachman, M. A., Custers-Allen, R., Grunberg, S., Wu, G. D., Lewis, J. D., & Bushman, F. D.
Affiliations
  • University of Pennsylvania (US)
  • University of Michigan (US)
Corresponding author
Bushman, Frederic D
Venue
Genome biology
Published
2012-07-03
Volume
13
Issue
7
Pages
R60-R60
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
OpenAlex
W2166559909
Cited by
147
References
44
Citations by year
2026: 5 · 2025: 6 · 2024: 8 · 2023: 9 · 2022: 17 · 2021: 7 · 2020: 5 · 2019: 10 · 2018: 17 · 2017: 24 · 2016: 9 · 2015: 11 · 2014: 10 · 2013: 8 · 2012: 1
FWCI
3.85
Type
journal article
Language
en
Open access
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Howard Hughes Medical Institute
  • Pennsylvania Department of Health
  • University of Pennsylvania (UL1 RR024134)
  • Crohn's and Colitis Foundation (268761)
  • National Institutes of Health (DK050306)
  • National Institute of Allergy and Infectious Diseases (AI083480, T32AI055400, AI087990, T32AI060516, R01AI039368, R21AI087990, AI39368, R21AI083480, U01AI095608)
  • National Institute of Diabetes and Digestive and Kidney Diseases (K24DK078228, UH2DK083981, P30DK050306)
  • National Center for Research Resources (UL1RR024134, S10RR024525)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
protists, human microbiome, 18S rRNA, ITS gene, primer design, taxonomic assignment, fecal samples, bioinformatics pipeline
MeSH terms
Feces, Humans, RNA, RNA, Ribosomal, 18S, Software, Sequence Analysis, RNA, Eukaryota, Single-Cell Analysis, High-Throughput Nucleotide Sequencing, Microbiota

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