Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

ISME Journal

Volumn 6, Issue 7, 2012, Pages 1440-1444

  Soergel, David A W ^a   Dey, Neelendu ^b,d,e   Knight, Rob ^c   Brenner, Steven E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e WASHINGTON UNIVERSITY   (United States)

Author keywords

16S ribosomal RNA; bacteria; classification; phylogeny; sequencing; taxonomy

Indexed keywords

BACTERIAL RNA; PRIMER DNA; RNA 16S;

BACTERIOLOGY; BACTERIUM; DATABASE; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; TAXONOMY;

ARTICLE; BACTERIUM IDENTIFICATION; GASTROINTESTINAL TRACT; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METAGENOME; METHODOLOGY; MICROBIOLOGY;

BACTERIAL TYPING TECHNIQUES; DNA PRIMERS; GASTROINTESTINAL TRACT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS);

EID: 84862631902     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.208     Document Type: Article

References (18)

1. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL et al. (2004). Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554. (Pubitemid 38998626)
2. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ et al. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA 108(Suppl 1): 4516-4522.
3. Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP et al. (2010). Comparison of two nextgeneration sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38: E200.
4. Desantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072. (Pubitemid 44078840)
5. Degnan PH, Ochman H. (2012). Illumina-based analysis of microbial community diversity. The ISME J 6: 183-194.
6. Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
7. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT et al. (2010). Meeting report: The terabase metagenomics workshop and the vision of an Earth Microbiome Project. Stand Genomic Sci 3: 243-248.
8. Hamp TJ, Jones WJ, Fodor AA. (2009). Effects of experimental choices and analysis noise on surveys of the 00rare biosphere00. Appl Environ Microbiol 75: 3263-3270.
9. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: E1000255.
10. Jonasson J, Olofsson M, Monstein HJ. (2002). Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 110: 263-272. (Pubitemid 34454607)
11. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M et al. (2009). Metagenomic study of the oral microbiota by Illumina high-Throughput sequencing. J Microbiol Methods 79: 266-271.
12. Liu CH, Lee SM, Vanlare JM, Kasper DL, Mazmanian SK. (2008). Regulation of surface architecture by symbiotic bacteria mediates host colonization. Proc. Natl. Acad. Sci. USA 105: 3951-3956. (Pubitemid 351723505)
13. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A et al. (2011). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J; e-pub ahead of print 1 December 2011; doi:10.1038/ismej.2011.139.
14. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR et al. (2006). Microbial diversity in the deep sea and the underexplored 00rare biosphere00. Proc. Natl. Acad. Sci. USA 103: 12115-12120. (Pubitemid 44215820)
15. Stahl DA, Lane DJ, Olsen GJ, Pace NR. (1984). Analysis of hydrothermal vent-Associated symbionts by ribosomal RNA sequences. Science 224: 409-411.
16. Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM et al. (2007). Bacterial flora-Typing with targeted, chip-based pyrosequencing. BMC Microbiol 7: 108.
17. 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. (Pubitemid 47326658)
18. Wu D, Hartman A,Ward N, Eisen JA. (2008). An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One 3: E2566.