High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions

Nucleic Acids Research

Volumn 41, Issue 22, 2013, Pages

  Amir, Amnon ^a   Zeisel, Amit ^a   Zuk, Or ^b,c   Elgart, Michael ^a   Stern, Shay ^a   Shamir, Ohad ^d   Turnbaugh, Peter J ^e   Soen, Yoav ^a   Shental, Noam ^f  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d MICROSOFT RESEARCH   (United Kingdom)

^e HARVARD UNIVERSITY   (United States)

^f OPEN UNIVERSITY OF ISRAEL   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BACTERIUM DETECTION; DROSOPHILA; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE INTERACTION; GENOME ANALYSIS; HUMAN; INTERMETHOD COMPARISON; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MICROBIAL GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PYROSEQUENCING; RNA GENE; RNA SEQUENCE; RNA STRUCTURE; SALIVA ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL MODEL; UNINDEXED SEQUENCE;

ACETOBACTER; ANIMALS; BACTERIA; DROSOPHILA MELANOGASTER; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, STATISTICAL; PHYLOGENY; RNA, RIBOSOMAL, 16S; SALIVA; SEQUENCE ANALYSIS, DNA; WOLBACHIA;

EID: 84890360058     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1070     Document Type: Article

References (39)

1. Whitman, W.B., Coleman, D.C. and Wiebe, W.J. (1998) Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA, 95, 6578-6583.
2. Curtis, T.P., Sloan, W.T. and Scannell, J.W. (2002) Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA, 99, 10494-10499.
3. Rappe, M.S. and Giovannoni, S.J. (2003) The uncultured microbial majority. Annu. Rev. Microbiol., 57, 369-394.
4. Oliver, J.D. (2005) The viable but nonculturable state in bacteria. J. Microbiol., 43, 93-100.
5. DeSantis, T.Z., Dubosarskiy, I., Murray, S.R. and Andersen, G.L. (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics, 19, 1461-1468.
6. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J. and Glockner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res., 35, 7188-7196.
7. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, D141-D145.
8. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.-J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
9. Bennett, S.T., Barnes, C., Cox, A., Davies, L. and Brown, C. (2005) Toward the 1, 000 dollars human genome. Pharmacogenomics, 6, 373-382.
10. Hamady, M., Walker, J.J., Harris, J.K., Gold, N.J. and Knight, R. (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods, 5, 235-237.
11. Hamady, M. and Knight, R. (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res., 19, 1141-1152.
12. The Human Microbiome Project Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
13. 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) Moving pictures of the human microbiome. Genome Biol., 12, R50.
14. Wang, Q., Garrity, G.M., Tiedje, J.M. and Cole, J.R. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microb., 73, 5261-5267.
15. Kuczynski, J., Lauber, C.L., Walters, W.A., Parfrey, L.W., Clemente, J.C., Gevers, D. and Knight, R. (2012) Experimental and analytical tools for studying the human microbiome. Nat. Rev. Genet., 13, 47-58.
16. Schleifer, K.H. (2009) Classification of Bacteria and Archaea: past, present and future. Syst. Appl. Microbiol., 32, 533-542.
17. Fox, G.E., Wisotzkey, J.D. and Jurtshuk, P. (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol., 42, 166-170.
18. Miller, C.S., Baker, B.J., Thomas, B.C., Singer, S.W. and Banfield, J.F. (2011) EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol., 12, R44.
19. Fan, L., McElroy, K. and Thomas, T. (2012) Reconstruction of ribosomal RNA genes from metagenomic data. PLoS One, 7, e39948.
20. Ong, S.H., Kukkillaya, V.U., Wilm, A., Lay, C., Ho, E.X.P., Low, L., Hibberd, M.L. and Nagarajan, N. (2013) Species identification and profiling of complex microbial communities using shotgun illumina sequencing of 16S rRNA amplicon sequences. PLoS One, 8, e60811.
21. Sharpton, T.J., Riesenfeld, S.J., Kembel, S.W., Ladau, J., O'Dwyer, J.P., Green, J.L., Eisen, J.A. and Pollard, K.S. (2011) PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput. Biol., 7, e1001061.
22. Lozupone, C. and Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol., 71, 8228-8235.
23. Zuk, O., Amir, A., Zeisel, A., Shamir, O. and Shental, N. (2013) Accurate profiling of microbial communities from massively parallel sequencing using convex optimization. In: Kurland, O., Lewenstein, M. and Porat, E. (eds), SPIRE 2013. Jerusalem, Israel, pp. 279-297.
24. Wang, Y. and Qian, P.Y. (2009) Conservative fagments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLos One, 4, e7401.
25. Weisburg, W.G., Barns, S.M., Pelletier, D.A. and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol., 173, 697-703.
26. Grant, M. and Boyd, S. (2008) Graph implementations for nonsmooth convex programs. In: Blondel, V., Boyd, S. and Kimura, H. (eds), Recent Advances in Learning and Control. Lecture Notes in Control and Information Sciences, Zurich, pp.95-110.
27. Lozupone, C.A., Hamady, M., Kelley, S.T. and Knight, R. (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol., 73, 1576-1585.
28. Fukuyama, J., McMurdie, P.J., Dethlefsen, L., Relman, D.A. and Holmes, S. (2012) Comparisons of distance methods for combining covariates and abundances in microbiome studies. Pac. Symp. Biocomput., 2012, 213-224.
29. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., Fierer, N. and Knight, R. (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA, 108, 4516-4522.
30. Marcais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27, 764-770.
31. Stern, S., Fridmann-Sirkis, Y., Braun, E. and Soen, Y. (2012) Epigenetically heritable alteration of fly development in response to toxic challenge. Cell Rep., 1, 528-542.
32. Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A. et al. (2008) The metagenomics RAST server- A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386.
33. Faith, J.J., McNulty, N.P., Rey, F.E. and Gordon, J.I. (2011) Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science, 333, 101-104.
34. Walker, A.W., Ince, J., Duncan, S.H., Webster, L.M., Holtrop, G., Ze, X.L., Brown, D., Stares, M.D., Scott, P., Bergerat, A. et al. (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J., 5, 220-230.
35. Chandler, J.A., Lang, J.M., Bhatnagar, S., Eisen, J.A. and Kopp, A. (2011) Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genet., 7, e1002272.
36. Maiden, M.C., Bygraves, J.A., Feil, E., Morelli, G., Russell, J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D.A. et al. (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl Acad. Sci. USA, 95, 3140-3145.
37. Jolley, K.A., Bliss, C.M., Bennett, J.S., Bratcher, H.B., Brehony, C., Colles, F.M., Wimalarathna, H., Harrison, O.B., Sheppard, S.K., Cody, A.J. et al. (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology, 158, 1005-1015.
38. Kao, W.-C., Stevens, K. and Song, Y.S. (2009) BayesCall: a modelbased base-calling algorithm for high-throughput short-read sequencing. Genome Res., 19, 1884-1895.
39. Kao, W.-C. and Song, Y.S. (2011) naiveBayesCall: an efficient model-based base-calling algorithm for high-throughput sequencing. J. Comput. Biol., 18, 365-377.