The DOI matches its Crossref record; 93 of the 93 references it cites were found in a registry or an index.
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics
Open accessAbstract
Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea; however, while ’omics can be used to infer physiological or ecological roles for species in a community, most of these hypothetical roles remain unvalidated. Here, we report an approach to capture specific microorganisms from complex communities into pure cultures using genome-informed antibody engineering. We apply our reverse genomics approach to isolate and sequence single cells and to cultivate three different species-level lineages of human oral Saccharibacteria (TM7). Using our pure cultures, we show that all three Saccharibacteria species are epibionts of diverse Actinobacteria. We also isolate and cultivate human oral SR1 bacteria, which are members of a lineage of previously uncultured bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life. Microbial ‘dark matter’ is brought into culture using reverse genomics.
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1 retracted
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RetractedQIIME allows analysis of high-throughput community sequencing data
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Cutadapt removes adapter sequences from high-throughput sequencing reads
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
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The oral microbiome: diversity, biogeography and human health
Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S., & He, X. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00963-6 · Cited by 661
Challenges in exploring and manipulating the human skin microbiome
Boxberger, M., Cenizo, V., Cassir, N., & La Scola, B. (2021) · Microbiome · doi:10.1186/s40168-021-01062-5 · Cited by 247
Beresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194
Unifying the known and unknown microbial coding sequence space
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2022) · eLife · doi:10.7554/elife.67667 · Cited by 134
Wang, Y., Gallagher, L. A., Andrade, P. A., Liu, A., Humphreys, I. R., Turkarslan, S., Cutler, K. J., Arrieta-Ortiz, M. L., Li, Y., Radey, M. C., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.017 · Cited by 108
Metadata
- Authors
- Cross, K. L., Campbell, J. H., Balachandran, M., Campbell, A. G., Cooper, C. J., Griffen, A., Heaton, M., Joshi, S., Klingeman, D., Leys, E., Yang, Z., Parks, J. M., & Podar, M.
- Venue
- Nature Biotechnology
- Published
- 2019-09-30
- Volume
- 37
- Issue
- 11
- Pages
- 1314-1321
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2976566477
- Cited by
- 375
- References
- 93
- FWCI
- 12.39
- Type
- journal article
- Language
- en
- Open access
- green
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- Cross, K. L., Campbell, J. H., Balachandran, M., Campbell, A. G., Cooper, C. J., Griffen, A., Heaton, M., Joshi, S., Klingeman, D., Leys, E., Yang, Z., Parks, J. M., & Podar, M. (2019). Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nature Biotechnology. https://doi.org/10.1038/s41587-019-0260-6
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