CORE: A phylogenetically-curated 16S rDNA database of the core oral microbiome

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Griffen, Ann L ^a   Beall, Clifford J ^a   Firestone, Noah D ^a   Gross, Erin L ^a   DiFranco, James M ^a   Hardman, Jori H ^b   Vriesendorp, Bastienne ^a,c   Faust, Russell A ^a,d   Janies, Daniel A ^b   Leys, Eugene J ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

^c EDUARDO MONDLANE UNIVERSITY   (Mozambique)

^d ST JOHN HEALTH SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RIBOSOME DNA;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI; GENETIC DATABASE; GENETIC DISTANCE; GENUS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; MICROBIOME; MOUTH FLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; TAXONOMY; GENETICS; HUMAN; METAGENOME; MICROBIOLOGY; MOUTH;

BACTERIA (MICROORGANISMS);

DNA, RIBOSOMAL; HUMANS; METAGENOME; MOUTH; PHYLOGENY;

EID: 79955530922     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019051     Document Type: Article

References (34)

1. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
2. Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
3. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7: 335-336.
4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
5. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
6. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, et al. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Research 33: D294-D296.
7. 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.
8. Armougom F, Raoult D, (2009) Exploring Microbial Diversity Using 16S rRNA High-Throughput Methods. J Comput Sci Syst Biol 2: 069-092.
9. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ, (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-7736.
10. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ, (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-5741.
11. Hugenholtz P, Huber T, (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic and Evolutionary Microbiology 53: 289-293.
12. Lozupone CA, Knight R, (2008) Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 32: 557-578.
13. Aas JA, Griffen AL, Dardis SR, Lee AM, Olsen I, et al. (2008) Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol 46: 1407-1417.
14. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE, (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721-5732.
15. Kazor CE, Mitchell PM, Lee AM, Stokes LN, Loesche WJ, et al. (2003) Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J Clin Microbiol 41: 558-563.
16. de Lillo A, Booth V, Kyriacou L, Weightman AJ, Wade WG, (2004) Culture-independent identification of periodontitis-associated Porphyromonas and Tannerella populations by targeted molecular analysis. J Clin Microbiol 42: 5523-5527.
17. Dymock D, Weightman AJ, Scully C, Wade WG, (1996) Molecular analysis of microflora associated with dentoalveolar abscesses. J Clin Microbiol 34: 537-542.
18. Kumar PS, Griffen AL, Moeschberger ML, Leys EJ, (2005) Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. J Clin Microbiology 43: 3944-3955.
19. Kumar PS, Leys EJ, Bryk JM, Martinez FJ, Moeschberger ML, et al. (2006) Changes in periodontal health status are associated with bacterial community shifts as assessed by quantitative 16S cloning and sequencing. J Clin Microbiol 44: 3665-3673.
20. Munson MA, Banerjee A, Watson TF, Wade WG, (2004) Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 42: 3023-3029.
21. Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, et al. (2001) Bacterial diversity in human subgingival plaque. J Bacteriol 183: 3770-3783.
22. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
23. Maddison WP, Maddison DR, (2009) Mesquite: a modular system for evolutionary analysis. Version 2.6.
24. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
25. Stamatakis A, Hoover P, Rougemont J, (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57: 758-771.
26. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, et al. (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8: 460.
27. Letunic I, Bork P, (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128.
28. Hillis DM, Bull JJ, (1993) An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis. Systematic Biology 42.
29. Shannon CE, (1948) A Mathematical Theory of Communication. Bell System Technical Journal 27: 379-423, 623-656.
30. Zmasek CM, Eddy SR, (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384.
31. Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, et al. (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) 2010: baq013.
32. Chakravorty S, Helb D, Burday M, Connell N, Alland D, (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69: 330-339.
33. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, et al. (2010) The Human Oral Microbiome. J Bacteriol.
34. Schloss PD, Handelsman J, (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.