A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples
Open accessAbstract
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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Diet has been associated with other gut microbes, including archaea, fungi, and bacteriophage.
“Diet has also been associated with other types of microbes in the gut, such as archaea, fungi, and bacteriophage (Figure 2)45-47.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [45]
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MethodDiet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease
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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
- ORCID
- Venue
- Genome biology
- Published
- 2012-07-03
- Volume
- 13
- Issue
- 7
- Pages
- R60-R60
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4053730
- 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
- gold
- doi.org
- 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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