The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Illumina-based analysis of microbial community diversity
Open accessAbstract
Microbes commonly exist in milieus of varying complexity and diversity. Although cultivation-based techniques have been unable to accurately capture the true diversity within microbial communities, these deficiencies have been overcome by applying molecular approaches that target the universally conserved 16S ribosomal RNA gene. The recent application of 454 pyrosequencing to simultaneously sequence thousands of 16S rDNA sequences (pyrotags) has revolutionized the characterization of complex microbial communities. To date, studies based on 454 pyrotags have dominated the field, but sequencing platforms that generate many more sequence reads at much lower costs have been developed. Here, we use the Illumina sequencing platform to design a strategy for 16S amplicon analysis (iTags), and assess its generality, practicality and potential complications. We fabricated and sequenced paired-end libraries of amplified hyper-variable 16S rDNA fragments from sets of samples that varied in their contents, ranging from a single bacterium to highly complex communities. We adopted an approach that allowed us to evaluate several potential sources of errors, including sequencing artifacts, amplification biases, non-corresponding paired-end reads and mistakes in taxonomic classification. By considering each source of error, we delineate ways to make biologically relevant and robust conclusions from the millions of sequencing reads that can be readily generated by this technology.
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Cites
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747
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
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
Pyrosequencing analysis of the oral microflora of healthy adults
Keijser, B. J. F., Zaura, E., Huse, S. M., van der Vossen, J. M. B. M., Schuren, F. H. J., Montijn, R. C., ten Cate, J. M., & Crielaard, W. (2008) · Journal of Dental Research · doi:10.1177/154405910808701104 · Cited by 669 · cited 2×
“…barcodes): 967F 50-XXX CAACGCGAAGAACCTTACC-30 and 1046R 50-XXX CGACAGCCATGCANCACCT-30 (Short 1 V6 (S1V6); 98 bp in Escherichia coli) (Sogin et al., 2006), and 917F 50-XXX GAATTGACGGGGRCCCGC-30 and 1061R 50-XXX CACGRCACGAGCTGACGAC-30 (Long V6 (LV6); 163 bp in E. coli) (Keijser et al., 2008).”
MethodMicrobiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
Gloor, G. B., Hummelen, R., Macklaim, J. M., Dickson, R. J., Fernandes, A. D., MacPhee, R., & Reid, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015406 · Cited by 330
Unlocking short read sequencing for metagenomics
Rodrigue, S., Materna, A. C., Timberlake, S. C., Blackburn, M. C., Malmstrom, R. R., Alm, E. J., & Chisholm, S. W. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011840 · Cited by 168
Cited by
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt593 · Cited by 4,497
Inferring Correlation Networks from Genomic Survey Data
Friedman, J., & Alm, E. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002687 · Cited by 2,706
PANDAseq: paired-end assembler for Illumina sequences
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., & Neufeld, J. D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-31 · Cited by 2,132
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, D. M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3601 · Cited by 819
The Microbiome Quality Control Project Consortium, Sinha, R., Abu-Ali, G., Vogtmann, E., Fodor, A. A., Ren, B., Amir, A., Schwager, E., Crabtree, J., Ma, S., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3981 · Cited by 587
Metadata
- Authors
- Degnan, P. H., & Ochman, H.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-06-16
- Volume
- 6
- Issue
- 1
- Pages
- 183-194
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W1966689073
- Cited by
- 421
- References
- 6
- FWCI
- 18.33
- Type
- journal article
- Language
- en
- Open access
- green
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