Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform

Applied and Environmental Microbiology

Volumn 79, Issue 17, 2013, Pages 5112-5120

  Kozich, James J ^a   Westcott, Sarah L ^a   Baxter, Nielson T ^a   Highlander, Sarah K ^b   Schloss, Patrick D ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON SEQUENCES; CLONE LIBRARY; MICROBIAL COMMUNITIES; MICROBIAL ECOLOGY; NEXT-GENERATION SEQUENCING; ORDERS OF MAGNITUDE; OVERLAPPING REGIONS; SEQUENCING VARIABLES;

GENES;

RNA;

BIOTECHNOLOGY; COST-BENEFIT ANALYSIS; ERROR ANALYSIS; FECES; GENETIC ANALYSIS; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PIPELINE; RNA; SOIL MICROORGANISM;

EID: 84884251320     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01043-13     Document Type: Article

References (28)

1. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376.
2. The Human Microbiome Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
3. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci. U. S. A. 103:12115-12120.
4. Junemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D. 2012. Bacterial community shift in treated periodontitis patients revealed by Ion Torrent 16S rRNA gene amplicon sequencing. PLoS One 7:e41606. doi:10.1371/journal.pone.0041606.
5. Fichot EB, Norman RS. 2013. Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Microbiome 1:10.
6. Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R, Reid G. 2010. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One 5:e15406. doi:10.1371/journal.pone.0015406.
7. Huse SM, Welch DM, Morrison HG, Sogin ML. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12:1889-1898.
8. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12:118-123.
9. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38. doi:10 .1186/1471-2105-12-38.
10. Schloss PD, Gevers D, Westcott SL. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6:e27310. doi:10.1371/journal.pone.0027310.
11. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
12. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
13. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6:1621-1624.
14. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U. S. A. 108(Suppl. 1):4516-4522.
15. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. 2012. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J. 6:1273-1276.
16. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10:57-59.
17. Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. 2012. PANDAseq: paired-end assembler for Illumina sequences. BMC Bioinformatics 13:31. doi:10.1186/1471-2105-13-31.
18. Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF. 2012. Stabilization of the murine gut microbiome following weaning. Gut Microbes 3:383-393.
19. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
20. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21:494-504.
21. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117-1123.
22. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
23. Schloss PD. 2010. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA genebased studies. PLoS Comput. Biol. 6:e1000844. doi:10.1371/journal.pcbi .1000844.
24. Schloss PD. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One 4:e8230. doi:10.1371/journal.pone .0008230.
25. Schloss PD. 2013. Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J. 7:457-460.
26. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
27. Schloss PD, Westcott SL. 2011. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl. Environ. Microbiol. 77:3219-3226.
28. Yue JC, Clayton MK. 2005. A similarity measure based on species proportions. Commun. Stat. Theory Methods 34:2123-2131.