The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
Open accessAbstract
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina data sets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as one nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
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UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
The Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Moving pictures of the human microbiome
Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., et al. (2011) · Genome Biology · doi:10.1186/gb-2011-12-5-r50 · Cited by 1,138
Cited by
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Callahan, B. J., McMurdie, P. J., & Holmes, S. P. (2017) · The ISME Journal · doi:10.1038/ismej.2017.119 · Cited by 3,300
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730
Self-citationCharacterization of the gut microbiome using 16S or shotgun metagenomics
Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., Perry, T., Kao, D., Mason, A. L., Madsen, K. L., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00459 · Cited by 942
Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research
Vorholt, J. A., Vogel, C., Carlström, C. I., & Müller, D. B. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.07.004 · Cited by 685
Metadata
- Authors
- Tikhonov, M., Leach, R. W., & Wingreen, N. S.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-07-11
- Volume
- 9
- Issue
- 1
- Pages
- 68-80
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W1983047294
- Cited by
- 203
- References
- 9
- FWCI
- 7.91
- Type
- journal article
- Language
- en
- Open access
- green
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