Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition

Applied and Environmental Microbiology

Volumn 75, Issue 9, 2009, Pages 2889-2898

  Schellenberg, John ^a   Links, Matthew G ^b   Hill, Janet E ^c   Dumonceaux, Tim J ^b,d   Peters, Geoffrey A ^d   Tyler, Shaun ^d   Ball, T Blake ^a   Severini, Alberto ^a,d   Plummer, Francis A ^a,d  

^a UNIVERSITY OF MANITOBA   (Canada)

^b SASKATOON RESEARCH CENTRE   (Canada)

^c UNIVERSITY OF SASKATCHEWAN   (Canada)

^d Public Health Agency of Canada   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; AMPLICONS; CHAPERONIN; CLONE LIBRARY; DATA SETS; DI-DEOXY SEQUENCING; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY COMPOSITION; MICROBIAL COMMUNITY STRUCTURES; MICROBIOTA; MOLECULAR TARGETS; OPERATIONAL TAXONOMIC UNITS; PROTEIN-ENCODING GENES; PYROSEQUENCING; RELATIVE ABUNDANCE; TAXONOMIC COMPOSITION; TAXONOMIC RICHNESS;

AMPLIFICATION; BIODIVERSITY; CLONING; GENE ENCODING;

TARGETS;

CHAPERONIN; RNA 16S;

COMMUNITY COMPOSITION; COMPARATIVE STUDY; DATA SET; GENE EXPRESSION; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PROTEIN; RNA; TAXONOMY;

ACTINOBACTERIA; AMINO ACID SEQUENCE; AMPLICON; ARTICLE; BACTERIAL GROWTH; BACTEROIDETES; DNA LIBRARY; FIRMICUTES; GENE AMPLIFICATION; GENE TARGETING; GENETIC CODE; LACTOBACILLALES; MICROBIAL COMMUNITY; NUCLEOTIDE SEQUENCE; PYROSEQUENCING; TAXONOMY; VAGINA FLORA; VAGINITIS; BACTERIUM; BIODIVERSITY; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION; FEMALE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; VAGINA;

BACTERIA (MICROORGANISMS);

BACTERIA; BIODIVERSITY; CHAPERONIN 60; FEMALE; HUMANS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; VAGINA;

EID: 65549089957     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01640-08     Document Type: Article

References (37)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Chou, H. H., and M. H. Holmes. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17:1093-1104.
3. Dethlefsen, L., M. McFall-Ngai, and D. A. Relman. 2007. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449:811-818.
4. Dumonceaux, T. J., J. E. Hill, S. M. Hemmingsen, and A. G. Van Kessel. 2006. Characterization of intestinal microbiota and response to dietary vir- giniamycin supplementation in the broiler chicken. Appl. Environ. Micro- biol. 72:2815-2823.
5. Edwards, R. A., B. Rodriguez-Brito, L. Wegley, M. Haynes, M. Breitbart, D. M. Peterson, M. O. Saar, S. Alexander, E. C. Alexander, Jr., and F. Rohwer. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57. 2898 SCHELLENBERG ET AL. A PPL.E NVIRON.M ICROBIOL.
6. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
7. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
8. Fredricks, D. N., T. L. Fiedler, K. K. Thomas, B. B. Oakley, and J. M. Marrazzo. 2007. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis. J. Clin. Microbiol. 45:3270-3276.
9. Goh, S. H., S. Potter, J. O. Wood, S. M. Hemmingsen, R. P. Reynolds, and A. W. Chow. 1996. HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. J. Clin. Microbiol. 34:818-823.
10. Hay, P. 2005. Life in the littoral zone: lactobacilli losing the plot. Sex. Transm. Infect. 81:100-102.
11. Hill, J. E., S. H. Goh, D. M. Money, M. Doyle, A. Li, W. L. Crosby, M. Links, A. Leung, D. Chan, and S. M. Hemmingsen. 2005. Characterization of vaginal microflora of healthy, nonpregnant women by chaperonin-60 se- quence-based methods. Am. J. Obstet. Gynecol. 193:682-692.
12. Hill, J. E., A. Paccagnella, K. Law, P. L. Melito, D. L. Woodward, L. Price, A. H. Leung, L. K. Ng, S. M. Hemmingsen, and S. H. Goh. 2006. Identifi- cation of Campylobacter spp. and discrimination from Helicobacter and Ar- cobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J. Med. Microbiol. 55:393-399.
13. Hill, J. E., S. L. Penny, K. G. Crowell, S. H. Goh, and S. M. Hemmingsen. 2004. cpnDB: a chaperonin sequence database. Genome Res. 14:1669-1675.
14. Hill, J. E., J. R. Town, and S. M. Hemmingsen. 2005. Improved template representation in cpn60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers. Environ. Microbiol. 8:741-746.
15. Hughes, J. B., and B. J. Bohannan. 2004. Application of ecological diversity statistics in microbial ecology, p. 1321-1344. In G. A. Kowalchuck, F. J. de Bruijn, I. M. Head, A. D. Akkermans, and J. D. van Elsas (ed.), Molecular microbial ecology manual, 2nd ed. Kluwer Academic Publishing, London, England.
16. Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
17. Hyman, R. W., M. Fukushima, L. Diamond, J. Kumm, L. C. Giudice, and R. W. Davis. 2005. Microbes on the human vaginal epithelium. Proc. Natl. Acad. Sci. USA 102:7952-7957.
18. Kimani, J., R. Kaul, N. J. Nagelkerke, M. Luo, K. S. MacDonald, E. Ngugi, K. R. Fowke, B. T. Ball, A. Kariri, J. Ndinya-Achola, and F. A. Plummer. 2008. Reduced rates of HIV acquisition during unprotected sex by Kenyan female sex workers predating population declines in HIV prevalence. AIDS 22:131-137.
19. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
20. Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, M. S. Braverman, Y. J. Chen, Z. Chen, S. B. Dewell, L. Du, J. M. Fierro, X. V. Gomes, B. C. Godwin, W. He, S. Helgesen, C. H. Ho, G. P. Irzyk, S. C. Jando, M. L. Alenquer, T. P. Jarvie, K. B. Jirage, J. B. Kim, J. R. Knight, J. R. Lanza, J. H. Leamon, S. M. Lefkowitz, M. Lei, J. Li, K. L. Lohman, H. Lu, V. B. Makhijani, K. E. McDade, M. P. McKenna, E. W. Myers, E. Nickerson, J. R. Nobile, R. Plant, B. P. Puc, M. T. Ronan, G. T. Roth, G. J. Sarkis, J. F. Simons, J. W. Simpson, M. Srinivasan, K. R. Tartaro, A. Tomasz, K. A. Vogt, G. A. Volkmer, S. H. Wang, Y. Wang, M. P. Weiner, P. Yu, R. F. Begley, and J. M. Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
21. Money, D. 2005. The laboratory diagnosis of bacterial vaginosis. Can. J. In- fect. Dis. Med. Microbiol. 16:77-79.
22. Morris, M., A. Nicoll, I. Simms, J. Wilson, and M. Catchpole. 2001. Bacterial vaginosis: a public health review. Br. J. Obstet. Gynecol. 108:439-450.
23. Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
24. Nugent, R. P., M. A. Krohn, and S. L. Hillier. 1991. Reliability of diagnosing bacterial vaginosis is improved by a standardized method of Gram stain interpretation. J. Clin. Microbiol. 29:297-301.
25. Oakley, B. B., T. L. Fiedler, J. M. Marrazzo, and D. N. Fredricks. 2008. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Appl. Environ. Microbiol. 74:4898-4909.
26. Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: the European Molec- ular Biology Open Software Suite. Trends Genet. 16:276-277.
27. Schellenberg, J., T. Blake Ball, M. Lane, M. Cheang, and F. Plummer. 2008. Flow cytometric quantification of bacteria in vaginal swab samples self- collected by adolescents attending a gynecology clinic. J. Microbiol. Methods 73:216-226.
28. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
29. Smith, T. F., and M. S. Waterman. 1981. Identification of common molec- ular subsequences. J. Mol. Biol. 147:195-197.
30. Spear, G. T., M. Sikaroodi, M. R. Zariffard, A. L. Landay, A. L. French, and P. M. Gillevet. 2008. Comparison of the diversity of the vaginal microbiota in HIV-infected and HIV-uninfected women with or without bacterial vagino- sis. J. Infect. Dis. 198:1131-1140.
31. Stajich, J. E., D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz, C. Dagdi- gian, G. Fuellen, J. G. Gilbert, I. Korf, H. Lapp, H. Lehvaslaiho, C. Matsalla, C. J. Mungall, B. I. Osborne, M. R. Pocock, P. Schattner, M. Senger, L. D. Stein, E. Stupka, M. D. Wilkinson, and E. Birney. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12:1611-1618.
32. Sundquist, A., S. Bigdeli, R. Jalili, M. L. Druzin, S. Waller, K. M. Pullen, Y. Y. El-Sayed, M. M. Taslimi, S. Batzoglou, and M. Ronaghi. 2007. Bacte- rial flora-typing with targeted, chip-based pyrosequencing. BMC Microbiol. 7:108.
33. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
34. Turnbaugh, P. J., R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight, and J. I. Gordon. 2007. The human microbiome project. Nature 449:804-810.
35. Verhelst, R., H. Verstraelen, G. Claeys, G. Verschraegen, J. Delanghe, L. Van Simaey, C. De Ganck, M. Temmerman, and M. Vaneechoutte. 2004. Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gard- nerella vaginalis, and bacterial vaginosis. BMC Microbiol. 4:16.
36. Verstraelen, H., R. Verhelst, G. Claeys, M. Temmerman, and M. Vaneechoutte. 2004. Culture-independent analysis of vaginal microflora: the unrecognized association of Atopobium vaginae with bacterial vaginosis. Am. J. Obstet. Gynecol. 191:1130-1132.
37. Wilson, J. 2004. Managing recurrent bacterial vaginosis. Sex. Transm. Infect. 80:8-11.