The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
Open accessAbstract
Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.
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Cites
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks808 · Cited by 8,850
Vandeputte, D., Falony, G., Vieira-Silva, S., Tito, R. Y., Joossens, M., & Raes, J. (2016) · Gut · doi:10.1136/gutjnl-2015-309618 · Cited by 1,028
Dynamics and associations of microbial community types across the human body
Ding, T., & Schloss, P. D. (2014) · Nature · doi:10.1038/nature13178 · Cited by 885
Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome
Yuan, S., Cohen, D. B., Ravel, J., Abdo, Z., & Forney, L. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033865 · Cited by 511
Henderson, G., Cox, F., Kittelmann, S., Miri, V. H., Zethof, M., Noel, S. J., Waghorn, G. C., & Janssen, P. H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074787 · Cited by 328
Wesolowska-Andersen, A., Bahl, M. I., Carvalho, V., Kristiansen, K., Sicheritz-Pontén, T., Gupta, R., & Licht, T. R. (2014) · Microbiome · doi:10.1186/2049-2618-2-19 · Cited by 277
Cited by
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S. K., Kjeldgaard, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08853-3 · Cited by 1,199
Self-citationMunk, P., Knudsen, B. E., Lukjancenko, O., Duarte, A. S. R., Van Gompel, L., Luiken, R. E. C., Smit, L. A. M., Schmitt, H., Garcia, A. D., Hansen, R. B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0192-9 · Cited by 355
Self-citationGenomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Munk, P., Brinch, C., Møller, F. D., Petersen, T. N., Hendriksen, R. S., Seyfarth, A. M., Kjeldgaard, J. S., Svendsen, C. A., van Bunnik, B., Berglund, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34312-7 · Cited by 304
Self-citationLiguori, K., Keenum, I., Davis, B. C., Calarco, J., Milligan, E., Harwood, V. J., & Pruden, A. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.1c08918 · Cited by 294
Gut microbial changes of patients with psychotic and affective disorders: A systematic review
Vindegaard, N., Speyer, H., Nordentoft, M., Rasmussen, S., & Benros, M. E. (2021) · Schizophrenia Research · doi:10.1016/j.schres.2019.12.014 · Cited by 66
Metadata
- Authors
- Knudsen, B. E., Bergmark, L., Munk, P., Lukjancenko, O., Priemé, A., Aarestrup, F. M., & Pamp, S. J.
- Venue
- mSystems
- Publisher
- American Society for Microbiology
- Published
- 2016-10-25
- Volume
- 1
- Issue
- 5
- ISSN
- 2379-5077 (ISSN-L)
- OpenAlex
- W2951947140
- Cited by
- 248
- References
- 7
- FWCI
- 6.17
- Type
- journal article
- Language
- en
- Open access
- gold
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- Knudsen, B. E., Bergmark, L., Munk, P., Lukjancenko, O., Priemé, A., Aarestrup, F. M., & Pamp, S. J. (2016). Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition. mSystems. https://doi.org/10.1128/msystems.00095-16
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
