The DOI matches its Crossref record; 105 of the 105 references it cites were found in a registry or an index.
Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory
Open accessAbstract
Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of ('difficult-to-culture') microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform ('MYcrobiota') is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.
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Cites
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Cited by
Gut microbiome and amyotrophic lateral sclerosis: a systematic review of current evidence
Sun, J., Huang, T., Debelius, J. W., & Fang, F. (2021) · Journal of Internal Medicine · doi:10.1111/joim.13336 · Cited by 43
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“, selecting different analysis tools can result in different outcomes, hence consistency of analysis tools is key (107, 108).”
BackgroundBioinformatic Methodologies in Assessing Gut Microbiota
Fox, J. D., Sims, A., Ross, M., Bettag, J., Wilder, A., Natrop, D., Borsotti, A., Kolli, S., Mehta, S., Verma, H., et al. (2024) · Microbiology Research · doi:10.3390/microbiolres15040170 · Cited by 15
Metadata
- Authors
- Boers, S. A., Jansen, R., & Hays, J. P.
- Venue
- European Journal of Clinical Microbiology & Infectious Diseases
- Published
- 2019-03-05
- Volume
- 38
- Issue
- 6
- Pages
- 1059-1070
- ISSN
- 0934-9723 (ISSN-L)
- 1435-4373
- OpenAlex
- W2918200658
- Cited by
- 283
- References
- 105
- FWCI
- 17.43
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Boers, S. A., Jansen, R., & Hays, J. P. (2019). Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory. European Journal of Clinical Microbiology & Infectious Diseases. https://doi.org/10.1007/s10096-019-03520-3
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