Rapid identification of high-confidence taxonomic assignments for metagenomic data

Nucleic Acids Research

Volumn 40, Issue 14, 2012, Pages

  MacDonald, Norman J ^a   Parks, Donovan H ^a   Beiko, Robert G ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

ACCURACY; ACIDOBACTERIA; ARTICLE; BACTERIUM IDENTIFICATION; BACTEROIDETES; CLASSIFICATION ALGORITHM; DNA SEQUENCE; GENOME ANALYSIS; INTERMETHOD COMPARISON; INTESTINE FLORA; METAGENOME; METAGENOMICS; MICROBIOME; NONHUMAN; ONLINE ANALYSIS; PHYLUM; PRIORITY JOURNAL; PROTEOBACTERIA; RAPID IDENTIFICATION TAXONOMIC ASSIGNMENT; RUMEN MICROORGANISM; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; TAXONOMIC IDENTIFICATION;

ALGORITHMS; ANIMALS; CATTLE; CLASSIFICATION; HUMANS; ICE COVER; METAGENOME; METAGENOMICS; RUMEN; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; STOMACH;

EID: 84864945803     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks335     Document Type: Article

References (41)

1. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W. et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-73.
2. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P. et al. (2009) A core gut microbiome in obese and lean twins. Nature, 22, 480-484.
3. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., Solovyev, V.V., Rubin, E.M., Rokhsar, D.S. and Banfield, J.F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428, 37-43. (Pubitemid 38332350)
4. Garća Mart́n, H., Ivanova, N., Kunin, V., Warnecke, F., Barry, K.W., McHardy, A.C., Yeates, C., He, S., Salamov, A.A., Szeto, E. et al. (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol., 24, 1263-1269. (Pubitemid 44564773)
5. Hess, M., Sczyrba, A., Egan, R., Kim, T.W., Chokhawala, H., Schroth, G., Luo, S., Clark, D.S., Chen, F. and Zhang, T. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 331, 463-467.
6. Case, R.J., Boucher, Y., Dahllö , I., Holmströ m, C., Doolittle, W.F. and Kjelleberg, S. (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol., 73, 278-288. (Pubitemid 46079960)
7. Liu, B., Gibbons, T., Ghodsi, M. and Pop, M. (2010) MetaPhyler: taxonomic proEling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 18-21 December 2010, pp. 23-28.
8. Crosby, L.D. and Criddle, C.S. (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques, 34, 790-794.
9. Forney, L.J., Zhou, X. and Brown, C.J. (2004) Molecular microbial ecology: land of the one-eyed king. Curr. Opin. Microbiol., 7, 210-220. (Pubitemid 38758061)
10. Manichanh, C., Chapple, C.E., Frangeul, L., Gloux, K., Guigo, R. and Dore, J. (2008) A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res., 36, 5180-5188.
11. Green Tringe, S., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C. et al. (2005) Comparative metagenomics of microbial communities. Science, 308, 554-557. (Pubitemid 40570586)
12. Gilbert, J.A., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P. and Joint, I. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One, 3, e3042.
13. Perry, S.C. and Beiko, R.G. (2010) Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. Genome Biol. Evol., 2, 117-131.
14. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
15. Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A. and Stoye, J. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res., 36, 2230-2239. (Pubitemid 351566997)
16. Schreiber, F., Gumrich, P., Daniel, R. and Meincke, P. (2010) Treephyler: fast taxonomic profiling of metagenomes. Bioinformatics, 26, 960-961.
17. Zhang, Y. and Sun, Y. (2012) MetaDomain: a profile HMM-based protein domain classification tool for short sequences. Pac. Sym. Biocomput., 17, 271-282.
18. Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K. and Nattkemper, T.W. (2009) TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbour approach. BMC Bioinformatics, 10, 56.
19. Patil, K.R., Haider, P., Pope, P.B., Turnbaugh, P.J., Morrison, M., Scheffer, T. and McHardy, A.C. (2011) Taxonomic metagenome sequence assignment with structured output models. Nat. Methods, 8, 191-192.
20. Parks, D.H., MacDonald, N.J. and Beiko, R.G. (2011) Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics, 12, 328.
21. Rosen, G., Garbarine, E., Diamantino, C., Polikar, R. and Sokhansanj, B. (2008) Metagenome fragment classification using n-mer frequency profiles. Adv. Bioinformatics, 2008, 1-12.
22. Sandberg, R., Winberg, G., Brä nden, C.I., Kaske, A., Ernberg, I. and Cö ster, J. (2001) Capturing whole-genome characteristics in short sequences using a näve Bayesian classifier. Genome Res., 11, 1401-1409.
23. Brady, A. and Salzberg, S.L. (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat. Methods, 6, 673-676.
24. Nalbantoglu, O.U., Way, S.F., Hinrichs, S.H. and Sayood, K. (2011) RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles. BMC Bioinformatics, 12, 41.
25. 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 rDNA analysis. Nucleic Acids Res., 37, D141-D145.
26. Huson, D.H., Auch, A.F., Qi, J. and Schuster, S.C. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386. (Pubitemid 46376747)
27. McHardy, A.C. and Rigoutsos, I. (2007) What's in the mix: phylogenetic classification of metagenome sequence samples. Curr. Opin. Microbiol., 10, 499-503. (Pubitemid 350052685)
28. Simon, C., Wiezer, A., Strittmatter, A.W. and Daniel, R. (2009) Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol., 75, 7519-7526.
29. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M. et al. (2010) Enterotypes of the human gut microbiome. Nature, 473, 174-180.
30. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
31. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65. (Pubitemid 46056171)
32. Arumugam, M., Harrington, E.D., Foerstner, K.U., Raes, J. and Bork, P. (2010) SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics, 26, 2977-2978.
33. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75, 7537-7541.
34. Price, M.N., Dehal, P.S. and Arkin, A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
35. Baldi, P., Brunak, S., Chauvin, Y., Andersen, C.A. and Nielsen, H. (2000) Assessing the accuracy of prediction algorithms for classifications: an overview. Bioinformatics, 16, 412-424. (Pubitemid 30487963)
36. Goldman, B.S., Nierman, W.C., Kaiser, D., Slater, S.C., Durkin, A.S., Eisen, J.A., Ronning, C.M., Barbazuk, W.B., Blanchard, M., Field, C. et al. (2006) Evolution of sensory complexity recorded in a myxobacterial genome. Proc. Natl Acad. Sci. USA, 103, 15200-15205. (Pubitemid 44583188)
37. Thomas, S.H., Wagner, R.D., Arakaki, A.K., Skolnick, J., Kirby, J.R., Shimkets, L.J., Sanford, R.A. and Lö ffler, F.E. (2008) The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS One, 3, e2103.
38. Gori, F., Folino, G., Jetten, M.S.M. and Marchioni, E. (2011) MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. Bioinformatics, 27, l196-203.
39. Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R. and Federhen, S. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
40. Legendre, P. and Legendre, L. (1998) Numerical Ecology, 2nd edn. Elsevier, Amsterdam.
41. Parks, D.H. and Beiko, R.G. (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721.