Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations

Frontiers in Bioengineering and Biotechnology

Volumn 3, Issue SEP, 2015, Pages

  García López, Rodrigo ^a,b,c   Vázquez Castellanos, Jorge Francisco ^a,b,c   Moya, Andrés ^a,b,c  

^a Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana FISABIO Salud Publica   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

Author keywords

Assembler; Diversity; OTU; Viral metagenomics

Indexed keywords

CLASSIFICATION (OF INFORMATION); DECISION TREES; GENES; LIBRARIES; POPULATION STATISTICS; SHOVELS;

ASSEMBLER; DIVERSITY; GENERALIZED LINEAR MODEL; HIGH-THROUGHPUT SEQUENCING; METAGENOMIC LIBRARIES; METAGENOMICS; OPERATIONAL TAXONOMIC UNITS; SPECIES DISTRIBUTIONS;

POPULATION DISTRIBUTION;

EID: 85012028042     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2015.00141     Document Type: Article

References (39)

1. Abeles, S. R., and Pride, D. T. (2014). Molecular bases and role of viruses in the human microbiome. J. Mol. Biol. 426, 3892-3906. doi:10.1016/j.jmb.2014.07.002
2. Aguirre de Cárcer, D., Angly, F. E., and Alcamí, A. (2014). Evaluation of viral genome assembly and diversity estimation in deep metagenomes. BMC Genomics 15:989. doi:10.1186/1471-2164-15-989
3. Anthony, S. J., Epstein, J. H., Murray, K. A., Navarrete-Macias, I., Zambrana-Torrelio, C. M., Solovyov, A., et al. (2013). A strategy to estimate unknown viral diversity in mammals. MBio 4, e598-e513. doi:10.1128/mBio.00598-13
4. Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., and Gordon, J. I. (2005). Host-bacterial mutualism in the human intestine. Science 307, 1915-1920. doi:10.1126/science.1104816
5. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi:10.1089/cmb.2012.0021
6. Boisvert, S., Raymond, F., Godzaridis, E., Laviolette, F., and Corbeil, J. (2012). Ray meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13, R122. doi:10.1186/gb-2012-13-12-r122
7. Chao, A. (1987). Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791. doi:10.2307/2531532
8. Chevreux, B., Wetter, T., and Suhai, S. (1999). Genome sequence assembly using trace signals and additional sequence information. Computer science and biology. Proc. German Conf. Bioinf. 99, 45-56.
9. CLC Bio. (2012). White Paper De Novo Assembly in CLC Assembly 4.0 ClC Bio 2012 [Internet]. 14. Available from: http://www.clcbio.com/files/whitepapers/whitepaper-denovo-ssembly-4.pdf
10. Dutilh, B. E., Cassman, N., McNair, K., Sanchez, S. E., Silva, G. G., Boling, L., et al. (2014). A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498. doi:10.1038/ncomms5498
11. Eren, A. M., Morrison, H. G., Huse, S. M., and Sogin, M. L. (2014). DRISEE overestimates errors in metagenomic sequencing data. Brief. Bioinformatics 15, 783-787. doi:10.1093/bib/bbt010
12. Felts, B., Nulton, J., Mahaffy, J., and Rohwer, F. (2005). PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6:41. doi:10.1186/1471-2105-6-41
13. Hill, M. O. (1973). Diversity and evenness: a unifying notation and its consequences. Ecology 54, 427-473. doi:10.2307/1934352
14. Hughes, J. B., Hellmann, J. J., Ricketts, T. H., and Bohannan, B. J. (2001). Counting the uncontable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67, 4399-4406. doi:10.1093/nar/gks678
15. Johnson, S., Trost, B., Long, J. R., Pittet, V., and Kusalik, A. (2014). A better sequence-read simulator program for metagenomics. BMC Bioinformatics 15(Suppl. 9):S14. doi:10.1186/1471-2105-15-S9-S14
16. Keegan, K. P., Trimble, W. L., Wilkening, J., Wilke, A., Harrison, T., D'Souza, M., et al. (2012). A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput. Biol. 8:e1002541. doi:10.1371/journal.pcbi.1002541
17. Kim, K. H., and Bae, J. W. (2011). Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl. Environ. Microbiol. 77, 7663-7668. doi:10.1128/AEM.00289-11
18. Langmead, B., and Salzberg, S. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359. doi:10.1038/nmeth.1923.Lauber
19. Lauber, C., and Gorbalenya, A. E. (2012). Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses. J. Virol. 86, 3905-3915. doi:10.1128/JVI.07174-11
20. Li, D., Liu, C. M., Luo, R., Sadakane, K., and Lam, T. W. (2015). MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674-1676. doi:10.1093/bioinformatics/btv033
21. Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., et al. (2010). De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272. doi:10.1101/gr.097261.109
22. Li, Z., Chen, Y., Mu, D., Yuan, J., Shi, Y., Zhang, H., et al. (2012). Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph. Brief. Funct. Genomics 11, 25-37. doi:10.1093/bfgp/elr035
23. Marine, R., McCarren, C., Vorrasane, V., Nasko, D., Crowgey, E., Polson, S. W., et al. (2014). Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome 2, 3. doi:10.1186/2049-2618-2-3
24. Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., et al. (2011). The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625. doi:10.1101/gr.122705.111
25. Namiki, T., Hachiya, T., Tanaka, H., and Sakakibara, Y. (2012). MetaVelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40, e155. doi:10.1093/nar/gks678
26. NIH HMP Working Group. (2009). The NIH Human Microbiome Project. Genome Res. 19, 2317-2323. doi:10.1101/gr.096651.109
27. Peng, Y., Leung, H. C., Yiu, S. M., and Chin, F. Y. (2011). Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27, i94-i101. doi:10.1093/bioinformatics/btr216
28. Pérez-Brocal, V., García-López, R., Vázquez-Castellanos, J. F., Nos, P., Beltrán, B., Latorre, A., et al. (2013). Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach. Clin. Transl. Gastroenterol. 4, e36. doi:10.1038/ctg.2013.9
29. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi:10.1038/nature08821
30. Reyes, A., Haynes, M., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F., et al. (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338. doi:10.1038/nature09199
31. Robles-Sikisaka, R., Ly, M., Boehm, T., Naidu, M., Salzman, J., and Pride, D. T. (2013). Association between living environment and human oral viral ecology. ISME J. 7, 1710-1724. doi:10.1038/ismej.2013.63
32. Rosario, K., and Breitbart, M. (2011). Exploring the viral world through metagenomics. Curr. Opin. Virol. 1, 289-297. doi:10.1016/j.coviro.2011.06.004
33. Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864. doi:10.1093/bioinformatics/btr026
34. Smits, S. L., Bodewes, R., Ruiz-Gonzalez, A., Baumgärtner, W., Koopmans, M. P., Osterhaus, A. D., et al. (2014). Assembly of viral genomes from metagenomes. Front. Microbiol. 5:714. doi:10.3389/fmicb.2014.00714
35. Trifonov, V., and Rabadan, R. (2010). Frequency analysis techniques for identification of viral genetic data. MBio 1, e00156-10. doi:10.1128/mBio.00156-10
36. Vázquez-Castellanos, J. F., García-López, R., Pérez-Brocal, V., Pignatelli, M., and Moya, A. (2014). Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. BMC Genomics 18:37. doi:10.1186/1471-2164-15-37
37. Wen, L., Ley, R. E., Volchkov, P. Y., Stranges, P. B., Avanesyan, L., Stonebraker, A. C., et al. (2008). Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455, 1109-1113. doi:10.1038/nature07336
38. Zerbino, D. R., and Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829. doi:10.1101/gr.074492.107
39. Zou, N., Ditty, S., Li, B., and Lo, S. C. (2003). Random priming PCR strategy to amplify and clone trace amounts of DNA. Biotechniques 35, 758-760.