Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes

DNA Research

Volumn 21, Issue 2, 2014, Pages 217-227

  Mori, Hiroshi ^a   Maruyama, Fumito ^b   Kato, Hiromi ^c   Toyoda, Atsushi ^d   Dozono, Ayumi ^a   Ohtsubo, Yoshiyuki ^c   Nagata, Yuji ^c   Fujiyama, Asao ^d,e   Tsuda, Masataka ^c   Kurokawa, Ken ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^c TOHOKU UNIVERSITY   (Japan)

^d NATIONAL INSTITUTE OF GENETICS   (Japan)

^e NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

16S rRNA; Microbial community; Non degenerate primer; Primer design

Indexed keywords

RIBOSOME RNA; RNA 16S; PRIMER DNA;

AMPLICON; ARCHAEAL GENE; ARTICLE; BACTERIAL GENE; CELL ORGANELLE; EUKARYOTIC CELL; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE SEQUENCE; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; PROKARYOTIC CELL; PYROSEQUENCING; SEQUENCE ANALYSIS; SOIL MICROFLORA; SPECIES COMPARISON; ARCHAEON; BACTERIA; CHEMISTRY; CLASSIFICATION; EUKARYOTE; GENETICS; MICROBIOLOGY; RNA GENE;

ARCHAEA; BACTERIA; DNA PRIMERS; EUKARYOTA; GENES, RRNA; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

EID: 84899117846     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst052     Document Type: Article

References (42)

1. Hamady, M and Knight, R. 2009, Microbial community profiling for human microbiome projects: Tools, techniques, and challenges, Genome Res., 19, 1141-52
2. Rappe, M.S and Giovannoni, S.J. 2003, The uncultured microbial majority, Annu. Rev. Microbiol., 57, 369-94
3. Hamady, M.,Walker, J.J., Harris, J.K.,Gold, N.J.andKnight, R. 2008, Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex, Nat. Methods, 5, 235-7
4. Mori, H.,Maruyama, F.andKurokawa, K.2010,VITCOMIC: Visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences, BMC Bioinformatics, 11, 332
5. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., et al. 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480-4
6. Margulies, M., Egholm, M., Altman, W.E., et al. 2005, Genome sequencing in microfabricated high-Density picolitre reactors, Nature, 437, 376-80
7. Kuczynski, J., Lauber, C.L., Walters, W.A., et al. 2012, Experimental and analytical tools for studying the human microbiome, Nat. Rev. Genet., 13, 47-58
8. Liu, Z., Lozupone, C., Hamady, M., Bushman, F.D and Knight, R. 2007, Short pyrosequencing reads suffice for accurate microbial community analysis, Nucleic Acids Res., 35, e120
9. Wang, Y and Qian, P.Y. 2009, Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomalDNA amplicons in metagenomic studies, PLoS ONE, 4, e7401
10. Baker, G.C., Smith, J.J and Cowan, D.A. 2003, Review and re-Analysis of domain-specific 16S primers, J. Microbiol. Methods, 55, 541-55
11. Kim, S.W., Suda, W., Kim, S., et al. 2013, Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-Throughput pyrosequencing, DNA Res., 20, 241-53
12. Huse, S.M., Dethlefsen, L., Huber, J.A., Mark, W.D., Relman, D.A and Sogin, M.L. 2008, Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing, PLoS Genet., 4, e1000255
13. Auguet, J.C., Barberan, A and Casamayor, E.O. 2010, Global ecological patterns in uncultured Archaea, ISME J., 4, 182-90
14. Swan, B.K., Ehrhardt, C.J., Reifel, K.M., Moreno, L.I and Valentine, D.L. 2010, Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea, Appl. Environ. Microbiol., 76, 757-68
15. Bates, S.T., Berg-Lyons, D., Caporaso, J.G., Walters, W.A., Knight, R and Fierer, N. 2011, Examining the global distribution of dominant archaeal populations in soil, ISME J., 5, 908-17
16. Walters, W.A., Caporaso, J.G., Lauber, C.L., Berg-Lyons, D., Fierer, N and Knight, R. 2011, PrimerProspector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers, Bioinformatics, 27, 1159-61
17. Klindworth, A., Pruesse, E., Schweer, T., et al. 2012, Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencingbased diversity studies, Nucleic Acids Res., 41, e1
18. Huys, G., Vanhoutte, T., Joossens, M., et al. 2008, Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: Possible consequences for population fingerprinting of complex microbial communities, Curr. Microbiol., 56, 553-7
19. Prosdocimi, E.M.,Novati, S., Bruno, R., et al. 2013, Errors in ribosomal sequence datasets generated using PCRcoupled panbacterial' pyrosequencing, and the establishment of an improved approach, Mol. Cell Probes, 27, 65-7
20. Galkiewicz, J.P and Kellogg, C.A. 2008, Cross-kingdom amplification using bacteria-specific primers: Complications for studies of coral microbial ecology, Appl. Environ. Microbiol., 74, 7828-31
21. The Human Microbiome Project Consortium. 2012, A framework for human microbiome research, Nature, 486, 215-21
22. Kumar, P.S., Brooker, M.R., Dowd, S.E and Camerlengo, T. 2011, Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing, PLoS ONE, 6, e20956
23. de Lillo, A.,Ashley, F.P., Palmer, R.M., et al.2006,Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets, Oral Microbiol. Immunol., 21, 61-8
24. Bennett, S. 2004, Solexa Ltd, Pharmacogenomics, 5, 433-8
25. Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T and Ussery, D.W. 2007, RNAmmer: Consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 35, 3100-8
26. Yarza, P., Richter, M., Peplies, J., et al. 2008, The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains, Syst. Appl. Microbiol., 31, 241-50
27. Acinas, S.G.,Marcelino, L.A., Klepac-Ceraj, V and Polz, M.F. 2004, Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons, J. Bacteriol., 186, 2629-35
28. Katoh, K and Toh, H.2008,Improved accuracy ofmultiple ncRNA alignment by incorporating structural information into a MAFFT-based framework, BMC Bioinformatics, 9, 212
29. Cole, J.R., Wang, Q., Cardenas, E., et al. 2009, The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, D141-5
30. Cannone, J.J., Subramanian, S., Schnare, M.N., et al. 2002, ThecomparativeRNAweb(CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs, BMC Bioinformatics, 3, 2
31. Claesson, M.J., Wang, Q., O'Sullivan, O., et al. 2010, Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions, Nucleic Acids Res., 38, e200
32. Wang, Y., Shimodaira, J., Miyasaka, T., et al. 2008, Detection of bphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method of RNA preparation from soil, Biosci. Biotechnol. Biochem., 72, 694-701
33. Schloss, P.D., Westcott, S.L., Ryabin, T., et al. 2009, Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 75, 7537-41
34. Altschul, S.F., Gish, W., Miller, W., Myers, E.W and Lipman, D.J. 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403-10
35. Itoh, T., Suzuki, K and Nakase, T. 1998, Occurrence of introns in the 16S rRNA genes of members of the genus Thermoproteus, Arch. Microbiol., 170, 155-61
36. Mao, D.P., Zhou, Q., Chen, C.Y and Quan, Z.X. 2012, Coverage evaluation of universal bacterial primers using the metagenomic datasets, BMC Microbiol., 12, 66
37. Frank, J.A., Reich, C.I., Sharma, S., Weisbaum, J.S., Wilson, B.A and Olsen, G.J. 2008, Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes, Appl. Environ. Microbiol., 74, 2461-70
38. Schneider, T.D and Stephens, R.M. 1990, Sequence logos: A new way to display consensus sequences, Nucleic Acids Res., 18, 6097-100
39. King, G.M., Judd, C., Kuske, C.R and Smith, C. 2012, Analysis of stomach and gut microbiomes of the eastern oyster (Crassostrea virginica) from coastal Louisiana, PLoS ONE, 7, e51475
40. Gribaldo, S and Brochier-Armanet, C. 2006, The origin and evolution of Archaea: A state of the art, Philos. Trans. R. Soc. Lond. B Biol. Sci., 361, 1007-22
41. Hamp T.J., Jones, W.J and Fodor, A.A. 2009, Effects of experimental choices and analysis noise on surveys of the rare biosphere, Appl. Environ.Microbiol., 75, 3263-70
42. Yooseph, S., Nealson, K.H., Rusch, D.B., et al. 2010, Genomic and functional adaptation in surface ocean planktonic prokaryotes, Nature, 468, 60-6