PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Dabdoub, Shareef M ^a   Fellows, Megan L ^a   Paropkari, Akshay D ^a   Mason, Matthew R ^a   Huja, Sarandeep S ^b   Tsigarida, Alexandra A ^c   Kumar, Purnima S ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF KENTUCKY COLLEGE OF DENTISTRY   (United States)

^c UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; PIPELINE; SPECIES; VELOCITY; BACTERIUM; BIODIVERSITY; BIOLOGY; CLASSIFICATION; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROFLORA; PHYLOGENY; SOFTWARE;

RNA 16S;

BACTERIA; BIODIVERSITY; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROBIOTA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOFTWARE;

EID: 84977269708     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep29123     Document Type: Article

References (28)

1. Coenye, T. & Vandamme, P. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol. Lett. 228, 45-49 (2003).
2. Hugenholtz, P., Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774 (1998).
3. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
4. Shchipkova, A., Nagaraja, H. & Kumar, P. Subgingival microbial profles of smokers with periodontitis. J. Dent. Res. 89, 1247-1253 (2010).
5. Tomar, S. L. & Asma, S. Smoking-attributable periodontitis in the United States: fndings from NHANES III. J. Periodontol. 71, 743-751 (2000).
6. Kumar, P. S., Matthews, C. R., Joshi, V., de Jager, M. & Aspiras, M. Tobacco smoking afects bacterial acquisition and colonization in oral bioflms. Infect. Immun. 79, 4730-4738 (2011).
7. Marsh, P. D., Moter, A. & Devine, D. A. Dental plaque bioflms: communities, confict and control. Periodontol. 2000 55, 16-35 (2011).
8. Kumar, P. S., Brooker, M. R., Dowd, S. E. & Camerlengo, T. Target region selection is a critical determinant of community fngerprints generated by 16S pyrosequencing. PLoS One 6, 1-8 (2011).
9. Mason, M. R. et al. The subgingival microbiome of clinically healthy current and never smokers. ISME J. 9, 268-272 (2014).
10. Huja, S. et al. Rice rat an animal model of osteonecrosis of the jaw. J. Dent. Res. 89, 3545 (2010).
11. Chao, A., Hwang, W.-H., Chen, Y. & Kuo, C. Estimating the number of shared species in two communities. Stat. Sinica 10, 227-246 (2000).
12. Mason, M. R., Nagaraja, H. N., Camerlengo, T., Joshi, V. & Kumar, P. S. Deep sequencing identifes ethnicity-specifc bacterial signatures in the oral microbiome. PLoS One 8, 1-7 (2013).
13. Shaw, J. H. & Grifths, D. Relation of protein, carbohydrate, and fat intake to the periodontal syndrome. J. Dent. Res. 40, 614-621 (1961).
14. Dick, D. & Shaw, J. The infectious and transmissible nature of the periodontal syndrome of the rice rat. Arch. Oral Biol. 11, 1095-1108 (1966).
15. Group, M. R. Annual Industry Report. Implant Dentistry 9, 192-194 (2000).
16. Dabdoub, S. M., Tsigarida, A. A. & Kumar, P. S. Patient-specifc analysis of periodontal and peri-implant microbiomes. J. Dent. Res. 92, 168S-175S (2013).
17. Letunic, I. & Bork, P. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128 (2007).
18. Letunic, I. & Bork, P. Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. W475-W478 (2011).
19. Löe, H., Teilade, E. & Jensen, S. B. Experimental gingivitis in man. J. Periodontol. 36, 177-187 (1965).
20. Löe, H. & Silness, J. Periodontal disease in pregnancy I. Prevalence and severity. Acta Odontol. Scand. 21, 533-551 (1963).
21. Lindhe, J. & Meyle, J. Peri-implant diseases: Consensus report of the sixth european workshop on periodontology. J. Clin. Periodontol. 35, 282-285 (2008).
22. Kumar, P. S., Grifen, A. L., Moeschberger, M. L. & Leys, E. J. Identifcation of candidate periodontal pathogens and benefcial species by quantitative 16S clonal analysis. J. Clin. Micro. 43, 3944-3955 (2005).
23. Dowd, S. E., Sun, Y., Wolcott, R. D., Domingo, A. & Carroll, J. A. Bacterial tag-encoded fx amplicon pyrosequencing (btefap) for microbiome studies: bacterial diversity in the ileum of newly weaned salmonella-infected pigs. Foodborne Pathog. Dis. 5, 459-72 (2008).
24. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Bio. 215, 403-410 (1990).
25. DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072 (2006).
26. Chen, T. et al. The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database 2010, doi: 10.1093/database/baq013 (2010).
27. Vázquez-Baeza, Y., Pirrung, M., Gonzalez, A. & Knight, R. EMPeror: a tool for visualizing high-throughput microbial community data. Giga Science 2, 16 (2013).
28. Lima, F. S. et al. Prepartum and postpartum rumen fuid microbiomes: characterization and correlation with production traits in dairy cows. Appl. Environ. Microbiol. 81, 1327-1337 (2015).