The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index.
Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples
Open accessAbstract
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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“A database of background microorganisms commonly detected in mNGS data and arising from normal flora or laboratory contamination101,104 typically needs to be maintained for accurate mNGS analyses.”
From Clinical metagenomics (2019) · cites this paper as [104]
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129
Comprehensive molecular characterization of human colon and rectal cancer
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11252 · Cited by 8,499
Comprehensive genomic characterization of squamous cell lung cancers
The Cancer Genome Atlas Research Network (2012) · Nature · doi:10.1038/nature11404 · Cited by 3,994
Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
Feng, H., Shuda, M., Chang, Y., & Moore, P. S. (2008) · Science · doi:10.1126/science.1152586 · Cited by 3,208
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
Castellarin, M., Warren, R. L., Freeman, J. D., Dreolini, L., Krzywinski, M., Strauss, J., Barnes, R., Watson, P., Allen-Vercoe, E., Moore, R. A., et al. (2012) · Genome Research · doi:10.1101/gr.126516.111 · Cited by 2,043
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., et al. (2012) · Genome Research · doi:10.1101/gr.126573.111 · Cited by 1,960
Transcriptome and genome sequencing uncovers functional variation in humans
The Geuvadis Consortium, Lappalainen, T., Sammeth, M., Friedländer, M. R., ‘t Hoen, P. A. C., Monlong, J., Rivas, M. A., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., et al. (2013) · Nature · doi:10.1038/nature12531 · Cited by 1,888
Integrative analysis of environmental sequences using MEGAN4Preprint
Huson, D. H., Mitra, S., Ruscheweyh, H., Weber, N., & Schuster, S. C. (2011) · Genome Research · doi:10.1101/gr.120618.111 · Cited by 1,559
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
Pruitt, K. D., Tatusova, T., Brown, G. R., & Maglott, D. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1079 · Cited by 1,149 · cited 1×
“28 searches against the Human RefSeq RNA database and then to the NCBI nucleotide (nt) database to identify reads corresponding to known exogenous organisms [19,20].”
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Items 101–182 of 182
Perlejewski, K., Bukowska‐Ośko, I., Rydzanicz, M., Dzieciątkowski, T., Zakrzewska‐Pniewska, B., Podlecka‐Piętowska, A., Filipiak, A., Barć, K., Cortés, K. C., Pawełczyk, A., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0240601 · Cited by 10
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Akter, S., Nakao, R., Imasato, Y., Alam, M. Z., & Katakura, K. (2018) · Genomics · doi:10.1016/j.ygeno.2018.05.020 · Cited by 10
Wang, X., Gao, Y., Cheng, Z., Chen, C., Han, M., Yang, P., Xiong, G., & Ning, K. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01560 · Cited by 10
Yuan, L., Zhu, Q., Chen, Q., Lai, L. M., Liu, P., & Liu, Y. (2023) · Laboratory Medicine · doi:10.1093/labmed/lmad046 · Cited by 9
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Hernandez, A. M., & Ryan, J. F. (2018) · PeerJ · doi:10.7717/peerj.5067 · Cited by 9
Lai, Z.-L., Su, Y.-D., Lin, H.-H., Wang, S.-Y., Lin, Y., Liang, S., Chen, W.-C., & Hsueh, P. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.03119-24 · Cited by 8
Hamelin, B., Hosch, S., Neidhöfer, C., Ruf, M., Haslbauer, J. D., Field, C. M., Schläpfer, P., Manzo, M., Neumayr, A. L. C., Kuenzli, E., et al. (2025) · Laboratory Investigation · doi:10.1016/j.labinv.2025.104254 · Cited by 8
Lin, B.-W., Hong, J.-C., Jiang, Z.-J., Zhang, W., Fan, Q.-C., & Yao, X.-P. (2024) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001818 · Cited by 9
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Charalampous, T., Kay, G. L., & O’Grady, J. (2019) · European Respiratory Society eBooks · doi:10.1183/2312508x.10015618 · Cited by 8
Lah, E. F. C., Ahamad, M., Apanaskevich, D. A., Md‐Zain, B. M., & Yaakop, S. (2023) · Journal of Medical Entomology · doi:10.1093/jme/tjad044 · Cited by 8
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Sajantila, A. (2014) · Investigative Genetics · doi:10.1186/s13323-014-0017-4 · Cited by 8
Boruah, A. P., Kroopnick, A., Thakkar, R., Wapniarski, A. E., Kim, C. F., Dugue, R., Harrigan, E., Lipkin, W. I., Mishra, N., & Thakur, K. T. (2023) · Journal of NeuroVirology · doi:10.1007/s13365-023-01172-w · Cited by 7
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Yuan, Z., Ye, X., Zhu, L., Zhang, N., An, Z., & Zheng, W. J. (2020) · Cancer Medicine · doi:10.1002/cam4.3325 · Cited by 7
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Zhao, S., Du, X., Zhang, Y., Bai, J., Lu, M., Li, X., Ma, J., Sheng, H., Fu, X., Guan, Y., et al. (2025) · BMC Cancer · doi:10.1186/s12885-025-14186-w · Cited by 5
Spirina, E., Kuleshov, K. V., Yunusova, A. K., Vishnivetskaya, T. A., & Rivkina, E. (2019) · Microbiology Resource Announcements · doi:10.1128/mra.00889-19 · Cited by 5
Metagenomics in Microbiomic Studies
Laurence, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816664-2.00007-4 · Cited by 5
Wang, C., Xia, Y., Liu, Y., Kang, C., Lu, N., Tian, D., Lu, H., Han, F., Xu, J. C., & Yomo, T. (2022) · Applied Sciences · doi:10.3390/app12126209 · Cited by 5
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Orosz, F. (2017) · Journal of Bacteriology & Parasitology · doi:10.4172/2155-9597.1000317 · Cited by 5
Metagenomic Next-Generation Sequencing for Pathogen Detection and Identification
Miller, S. A., & Chiu, C. Y. (2018) · Springer eBooks · doi:10.1007/978-3-319-95111-9_25 · Cited by 5
Urinary Microbiome Research Has Not Established a Conclusive Influence: Revisiting Koch’s Postulates
Werneburg, G. T., & Southgate, J. (2024) · European Urology Focus · doi:10.1016/j.euf.2024.07.005 · Cited by 4
Álvarez-Carretero, S., & dos Reis, M. (2020) · Springer eBooks · doi:10.1007/978-3-030-60181-2_13 · Cited by 4
Jiang, T., Buchkovich, M. L., & Motsinger‐Reif, A. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/531558 · Cited by 4
Lee, H., Lee, Y., Hong, S., & Park, J. (2023) · Current Genomics · doi:10.2174/0113892029258657231010065320 · Cited by 3
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Strong, M. J., Lin, Z. N., & Flemington, E. K. (2014) · mBio · doi:10.1128/mbio.01989-14 · Cited by 3
Self-citationChen, J., Yan, X., Sun, Y., Ren, Z., Yan, G., Wang, G., Liu, Y., Zhao, Z., Liu, Y., Tu, C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.03.482774 · Cited by 3
Granata, I., Sangiovanni, M., & Guarracino, M. R. (2016) · Springer eBooks · doi:10.1007/978-3-319-45723-9_11 · Cited by 2
Mortezaei, Z. (2022) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2022.101054 · Cited by 2
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Lopes, A. L. K., Kriegová, E., Lukeš, J., Krieger, M. A., & Ludwig, A. (2021) · PLoS ONE · doi:10.1371/journal.pone.0251133 · Cited by 2
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Filkins, L., & Schlaberg, R. (2021) · Springer eBooks · doi:10.1007/978-3-030-62155-1_7 · Cited by 2
Jiang, T., Buchkovich, M. L., & Motsinger‐Reif, A. A. (2021) · Research Square · doi:10.21203/rs.3.rs-858518/v1 · Cited by 2
Fan, S., Wang, X., Hu, Y., Shi, J., Zou, Y., Zhao, W., Qiao, X., Wang, C., Chin, J. H., Liu, L., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/658047 · Cited by 2
Oki, H., Niwa, R., Somboonthum, P., Motooka, D., Onda, Y., Nakata, J., Nakajima, H., Oka, Y., Sugiyama, H., Yoshii, Y., et al. (2024) · Access Microbiology · doi:10.1099/acmi.0.000779.v3 · Cited by 1
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Jo, Y., Choi, H., & Cho, W. K. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00926 · Cited by 1
Mangul, S., Yang, H. T., & Zaitlen, N. (2018) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3233547.3233726 · Cited by 1
Jo, Y., Choi, H., Kim, S.-M., Lee, B. C., & Cho, W. K. (2020) · Journal of Applied Biological Chemistry · doi:10.3839/jabc.2020.026 · Cited by 1
Mahmoudi, M., Albalawi, M., Stanley, C., Berry, J. D., & Aljewari, H. (2026) · Preprints.org · doi:10.20944/preprints202603.1630.v1 · Cited by 1
Mazzitelli, J.-Y. (2017) · theses.fr (ABES) · doi:10.70675/784ebd4dz5c57z4210z9224zf2e92f10b404 · Cited by 1
Maretty, L., Sibbesen, J. A., & Krogh, A. (2014)
Genome-Wide Scanning of Gene Expression
Park, S.-J. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20132-5
Hidden Treasures in Contemporary RNA Sequencing
Mangul, S., Yang, H. T., Eskin, E., & Zaitlen, N. (2019) · SpringerBriefs in computer science · doi:10.1007/978-3-030-13973-5_1
Hu, L., Wang, J., Huang, Z., Yang, Z., Huang, T., Wang, Y., Chen, M., Li, Y., & Zhou, H. (2021) · Research Square · doi:10.21203/rs.3.rs-473231/v1
Faculty Opinions recommendation of Plasmid DNA contaminant in molecular reagents.
Galperin, M. Y. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735053070.793556365
Zheng, N. Q., Guo, P., Chen, X., He, H., Li, Y., Li, L., & Cai, W. (2019) · doi:10.21203/rs.2.19687/v1
Otter, J. A. (2015) · Journal of Hospital Infection · doi:10.1016/j.jhin.2015.02.011
Genome-Wide Scanning of Gene Expression
Park, S., & Nakai, K. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00217-7
Why is next-generation sequencing essential in modern virology?
Lefèvre, C., & Irigoyen, N. (2024) · Journal of General Virology · doi:10.1099/jgv.0.002050
Smith, J., Ajithkumar, P., Wilkinson, E. J., Dutta, A., Vasantharajan, S. S., Yee, A., Gimenez, G., Subramaniam, R. M., Lau, M., Zarrabi, A. D., et al. (2024) · Data · doi:10.3390/data9120150
Validation and Quality Control of Next‐Generation Sequencing Assays
Schlaberg, R. (2025) · Wiley eBooks · doi:10.1002/9781683674597.ch23
Marcelino, V. R., Clausen, P. T. L. C., Buchmann, J. P., Wille, M., Iredell, J. R., Meyer, W., Lund, O., Sorrell, T. C., & Holmes, E. C. (2020) · Figshare · doi:10.6084/m9.figshare.12211688
Moragues-Solanas, L., Le-Viet, T., McSorley, E., Halford, C. M., Lockhart, D. S., Aydin, A., Kay, G. L., Elumogo, N., Mullen, W. H., O’Grady, J., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25347035
Marcelino, V. R., Clausen, P. T. L. C., Buchmann, J. P., Wille, M., Iredell, J. R., Meyer, W., Lund, O., Sorrell, T. C., & Holmes, E. C. (2020) · Figshare · doi:10.6084/m9.figshare.12211673
Marcelino, V. R., Clausen, P. T. L. C., Buchmann, J. P., Wille, M., Iredell, J. R., Meyer, W., Lund, O., Sorrell, T. C., & Holmes, E. C. (2020) · Figshare · doi:10.6084/m9.figshare.12211724
Fan, S., Wang, X., Hu, Y., Shi, J., 邹月丽, Zhao, W., Qiao, X., Wang, C., Chin, J. H., Liu, L., et al. (2019) · doi:10.21203/rs.2.17334/v1
Moragues-Solanas, L., Le-Viet, T., McSorley, E., Halford, C. M., Lockhart, D. S., Aydin, A., Kay, G. L., Elumogo, N., Mullen, W. H., O’Grady, J., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25347255
Regulation of mRNA translation during the inflammatory response in murine macrophages
Blin, J. (2020) · theses.fr (ABES) · doi:10.70675/9eed69d2z2c72z4b4dz8603zdc632396f487
Lee, D., Norton, N., & Dale, A. P. (2026) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0000000000001208
Stentoft, E., Olausson, J., Rudbeck, E., Studahl, M., & Jakobsson, H. E. (2026) · PLoS ONE · doi:10.1371/journal.pone.0358189
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Burnwal, S., Sadekar, S. S., & Madhusudhan, M. S. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7549384
Rethinking the tumor microbiome: Methodological challenges and a framework for rigorous research
Zhu, L., Deng, Z., Mou, W., Deng, G., Lu, H., Xu, L., Lin, S., Huang, H., Wu, K., Liang, Q., et al. (2026) · mLife · doi:10.1002/mlf2.70107
Metadata
- 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.
- 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
- 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
- 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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