The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
Open accessAbstract
Summary: Next‐generation sequencing has dramatically changed the landscape of microbial ecology, large‐scale and in‐depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both I llumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon‐specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine‐tuning experimental and computational parameters used to characterize natural communities.
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Cites
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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
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Mapping the Tree of Life: Progress and Prospects
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Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
Morgan, J. L., Darling, A. E., & Eisen, J. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010209 · Cited by 248
Cited by
metaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496
Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H.-F., Sadakane, K., Yamashita, H., & Lam, T.-W. (2016) · Methods · doi:10.1016/j.ymeth.2016.02.020 · Cited by 2,079
Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D., & Konstantinidis, K. T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093827 · Cited by 684
D’Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., Shakya, M., Podar, M., Quince, C., & Hall, N. (2016) · BMC Genomics · doi:10.1186/s12864-015-2194-9 · Cited by 405
Self-citationIllumina error profiles: resolving fine-scale variation in metagenomic sequencing data
Schirmer, M., D’Amore, R., Ijaz, U. Z., Hall, N., & Quince, C. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0976-y · Cited by 376
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Metadata
- Authors
- Shakya, M., Quince, C., Campbell, J. H., Yang, Z. K., Schadt, C. W., & Podar, M.
- Venue
- Environmental Microbiology
- Publisher
- Wiley
- Published
- 2013-02-06
- Volume
- 15
- Issue
- 6
- Pages
- 1882-1899
- ISSN
- 1462-2912 (ISSN-L)
- 1462-2920
- OpenAlex
- W1905818355
- Cited by
- 214
- References
- 6
- FWCI
- 20.15
- Type
- journal article
- Language
- en
- Open access
- green
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- Shakya, M., Quince, C., Campbell, J. H., Yang, Z. K., Schadt, C. W., & Podar, M. (2013). Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environmental Microbiology. https://doi.org/10.1111/1462-2920.12086
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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