Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads

Applied and Environmental Microbiology

Volumn 77, Issue 11, 2011, Pages 3846-3852

  Bartram, Andrea K ^a   Lynch, Michael D J ^b   Stearns, Jennifer C ^a   Moreno Hagelsieb, Gabriel ^b   Neufeld, Josh D ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b WILFRID LAURIER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; 16S RRNA GENE SEQUENCE; 454-PYROSEQUENCING; ARCTIC TUNDRA; BACTERIAL COMMUNITY; BACTERIAL ISOLATES; FLOW CELLS; ILLUMINA; MICROBIAL COMMUNITIES; RELATIVE ABUNDANCE; REPRODUCIBILITIES; TAXONOMIC DIVERSITY;

BACTERIOLOGY; DATA REDUCTION; MICROORGANISMS; QUALITY CONTROL; RNA; SOILS;

GENES;

RNA 16S;

ARCTIC ENVIRONMENT; COMPUTER SIMULATION; DATA SET; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; HOST-PARASITE INTERACTION; IDENTIFICATION METHOD; MICROBIAL COMMUNITY; RELATIVE ABUNDANCE; RNA; SAMPLING; SOIL MICROORGANISM; SPECIES DIVERSITY; TAXONOMY; TUNDRA;

ARTICLE; BIOLOGY; DNA SEQUENCE; EVALUATION; GENETICS; METAGENOMICS; METHODOLOGY; REPRODUCIBILITY; RNA GENE;

COMPUTATIONAL BIOLOGY; GENES, RRNA; METAGENOMICS; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS);

EID: 79958265126     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02772-10     Document Type: Article

References (34)

1. Andersson, A. F., et al. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3:1-8.
2. Caporaso, J. G., et al. 2010. QIIME allows analysis of high-throughput community sequence data. Nat. Methods 7:335-336.
3. Caporaso, J. G., et al. 15 March 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U. S. A. 108:4516-4522.
4. Claesson, M. J., et al. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 38:e200.
5. Cole, J. R., et al. 2008. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
6. Curtis, T. P., et al. 2006. What is the extent of prokaryotic diversity? Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:2023-2037.
7. Frank, D. N. 2009. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 10:362.
8. Gloor, G. B., et al. 2010. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One 5:e15406.
9. Good, I. J. 1952. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264.
10. Hamady, M., J. J. Walker, J. K. Harris, N. J. Gold, and R. Knight. 2008. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5:235-237.
11. Huber, J. A., et al. 2007. Microbial population structures in the deep marine biosphere. Science 318:97-100.
12. Hummelen, R., et al. 2010. Deep sequencing of the vaginal microbiota of women with HIV. PLoS One 5:e12078.
13. Huse, S. M., D. M. Welch, H. G. Morrison, and M. L. Sogin. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12:1889-1898.
14. Huse, S. M., et al. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255.
15. Kuczynski, J., et al. 2010. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat. Methods 7:813-819.
16. Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12:118-123.
17. Kysela, D. T., C. Palacios, and M. L. Sogin. 2005. Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition. Environ. Microbiol. 7:356-364.
18. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. Wiley and Sons Ltd., Chichester, United Kingdom.
19. Lauber, C. L., M. Hamady, R. Knight, and N. Fierer. 2009. Pyrosequencingbased assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75:5111-5120.
20. Lazarevic, V., et al. 2009. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 79:266-271.
21. Li, W., and A. Godzik. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
22. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
23. Neufeld, J. D., J. Li, and W. W. Mohn. 2008. Scratching the surface of the rare biosphere with ribosomal sequence tag primers. FEMS Microbiol. Lett. 283:146-153.
24. Neufeld, J. D., and W. W. Mohn. 2005. Assessment of microbial phylogenetic diversity based on environmental nucleic acids, p. 219-260. In E. Stackebrandt (ed.), Molecular identification, systematics, and population structure of prokaryotes. Springer-Verlag, Heidelberg, Germany.
25. Neufeld, J. D., and W. W. Mohn. 2005. Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl. Environ. Microbiol. 71:5710-5718.
26. Neufeld, J. D., Z. Yu, W. Lam, and W. W. Mohn. 2004. Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ. Microbiol. 6:131-144.
27. Olsen, G. J., D. J. Lane, S. J. Giovannoni, and N. R. Pace. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
28. Pedrós-Alió, C. 2007. Dipping into the rare biosphere. Science 315:192-193.
29. Rousk, J., et al. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4:1340-1351.
30. Shendure, J., and J. Hanlee. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
31. Sogin, M. L., et al. 2006. Microbial diversity in the deep sea and underexplored "rare biosphere." Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
32. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
33. Yu, Z., M. Yu, and M. Morrison. 2006. Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterization of bacterial diversity and community composition. Environ. Microbiol. 8:603-611.
34. Zhou, H. W., et al. 21 October 2010. BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J. 5:741-749.