Cited by 186Genomics and Phylogenetic StudiesGut microbiota and healthMicrobial Community Ecology and Physiology

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Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

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Strong, Michael J., Xu, Guorong, Morici, Lisa, Splinter Bon-Durant, Sandra, Baddoo, Melody, Lin, Zhen, Fewell, Claire, Taylor, Christopher M., Flemington, Erik K.·2014·PLoS Pathogens

DOI 10.1371/journal.ppat.1004437PMC PMC4239086

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Abstract

The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.

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Authors: Strong, M. J., Xu, G., Morici, L., Splinter Bon-Durant, S., Baddoo, M., Lin, Z., Fewell, C., Taylor, C. M., & Flemington, E. K.
Affiliations: Tulane University (US)
University of California San Diego (US)
Louisiana State University (US)
Corresponding author: Flemington, Erik K.
ORCID: Strong, Michael J.
Morici, Lisa
Baddoo, Melody
Lin, Zhen
Taylor, Christopher M.
Flemington, Erik K.
Venue: PLoS Pathogens
Publisher: Public Library of Science (PLoS)
Published: 2014-11-20
Volume: 10
Issue: 11
Pages: e1004437
ISSN: 1553-7366 (ISSN-L)
1553-7374
DOI: 10.1371/journal.ppat.1004437
PMC: PMC4239086
OpenAlex: W1974764034
Cited by: 186
References: 33
Citations by year: 2026: 3 · 2025: 5 · 2024: 15 · 2023: 6 · 2022: 14 · 2021: 12 · 2020: 23 · 2019: 30 · 2018: 25 · 2017: 13 · 2016: 27 · 2015: 9 · 2014: 4
FWCI: 7.24
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS Pathogens (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Figshare (submittedVersion, cc-by)
Funders: National Institutes of Health
National Cancer Institute (R01CA138268, F30CA177267)
National Institute of General Medical Sciences (P20GM103518, U54GM104940)
National Institute of Allergy and Infectious Diseases (R01AI101046, R01AI106676)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: microbial contamination, next-generation sequencing, RNA-seq, bacterial contamination, clinical samples, environmental contamination, pathogen discovery, pathogen diagnosis, sequencing protocols, microbial signatures
MeSH terms: Equipment Contamination, Humans, Infections, Databases, Nucleic Acid, High-Throughput Nucleotide Sequencing

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Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

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