The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers
Open accessAbstract
Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
Amplification of complex gene libraries by emulsion PCR
Williams, R., Peisajovich, S. G., Miller, O. J., Magdassi, S., Tawfik, D. S., & Griffiths, A. D. (2006) · Nature Methods · doi:10.1038/nmeth896 · Cited by 358
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Larsson, D. G. J., & Flach, C.-F. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00649-x · Cited by 3,164
An omics-based framework for assessing the health risk of antimicrobial resistance genes
Zhang, A.-N., Gaston, J. M., Dai, C. L., Zhao, S., Poyet, M., Groussin, M., Yin, X., Li, L.-G., van Loosdrecht, M. C. M., Topp, E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25096-3 · Cited by 939
Self-citationMetal Resistance and Its Association With Antibiotic Resistance
Pal, C., Asiani, K., Arya, S., Rensing, C., Stekel, D. J., Larsson, D. G. J., & Hobman, J. L. (2017) · Advances in Microbial Physiology · doi:10.1016/bs.ampbs.2017.02.001 · Cited by 438
Horizontal transfer of antibiotic resistance genes in the human gut microbiome
McInnes, R. S., McCallum, G. E., Lamberte, L. E., & van Schaik, W. (2020) · Current Opinion in Microbiology · doi:10.1016/j.mib.2020.02.002 · Cited by 401
Zhu, Y., Li, J., Lin, X., Huang, X., & Hoffmann, M. R. (2021) · ACS Applied Bio Materials · doi:10.1021/acsabm.0c01615 · Cited by 18
Metadata
- Authors
- Spencer, S. J., Tamminen, M. V., Preheim, S. P., Guo, M. T., Briggs, A. W., Brito, I. L., A Weitz, D., Pitkänen, L. K., Vigneault, F., Virta, M. P. J., & Alm, E. J.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-09-22
- Volume
- 10
- Issue
- 2
- Pages
- 427-436
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W2335822530
- Cited by
- 233
- References
- 4
- FWCI
- 6.82
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Spencer, S. J., Tamminen, M. V., Preheim, S. P., Guo, M. T., Briggs, A. W., Brito, I. L., A Weitz, D., Pitkänen, L. K., Vigneault, F., Virta, M. P. J., & Alm, E. J. (2016). Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. The ISME Journal. https://doi.org/10.1038/ismej.2015.124
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