Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing
Tóm tắt
Từ khóa
Tài liệu tham khảo
Colombo AP, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, etal. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol. 2009; 80: 1421–32. [PubMed Abstract] [PubMed CentralFull Text].
Socransky SS, Haffajee AD, Cugini MA, Smith C, Kent RL Jr. Microbial complexes in subgingival plaque. J Clin Periodontol. 1998; 25: 134–44. [PubMed Abstract].
Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, etal. The oral metagenome in health and disease. ISME J. 2012; 6: 46–56. [PubMed Abstract] [PubMed CentralFull Text].
Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, etal. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012; 6: 1176–85. [PubMed Abstract] [PubMed CentralFull Text].
Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, etal. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 2013; 7: 1016–25. [PubMed Abstract].
Diaz PI, Dupuy AK, Abusleme L, Reese B, Obergfell C, Choquette L, etal. Using high throughput sequencing to explore the biodiversity in oral bacterial communities. Mol Oral Microbiol. 2012; 27: 182–201. [PubMed Abstract] [PubMed CentralFull Text].
Diaz PI, Chalmers NI, Rickard AH, Kong C, Milburn CL, Palmer RJ Jr., etal. Molecular characterization of subject-specific oral microflora during initial colonization of enamel. Appl Environ Microbiol. 2006; 72: 2837–48. [PubMed Abstract] [PubMed CentralFull Text].
Morgan JL, Darling AE, Eisen JA. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One. 2010; 5: e10209. [PubMed Abstract] [PubMed CentralFull Text].
Ahn JH, Kim BY, Song J, Weon HY. Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities. J Microbiol. 2012; 50: 1071–4. [PubMed Abstract].
Willner D, Daly J, Whiley D, Grimwood K, Wainwright CE, Hugenholtz P. Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One. 2012; 7: e34605. [PubMed Abstract] [PubMed CentralFull Text].
Momozawa Y, Deffontaine V, Louis E, Medrano JF. Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human. PLoS One. 2011; 6: e16952. [PubMed Abstract] [PubMed CentralFull Text].
Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, etal. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 2010; 10: 206. [PubMed Abstract] [PubMed CentralFull Text].
Hwang C, Ling F, Andersen GL, LeChevallier MW, Liu WT. Evaluation of methods for the extraction of DNA from drinking water distribution system biofilms. Microbes Environ. 2012; 27: 9–18. [PubMed Abstract].
Lazarevic V, Gaia N, Girard M, Francois P, Schrenzel J. Comparison of DNA extraction methods in analysis of salivary bacterial communities. PLoS One. 2013; 8: e67699. [PubMed Abstract] [PubMed CentralFull Text].
Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005; 43: 5721–32. [PubMed Abstract] [PubMed CentralFull Text].
Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, etal. Bacterial diversity in human subgingival plaque. J Bacteriol. 2001; 183: 3770–83. [PubMed Abstract] [PubMed CentralFull Text].
Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, etal. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010; 6: e1000713. [PubMed Abstract] [PubMed CentralFull Text].
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, etal. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75: 7537–41. [PubMed Abstract] [PubMed CentralFull Text].
Schloss PD, Westcott SL. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 2011; 77: 3219–26. [PubMed Abstract] [PubMed CentralFull Text].
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73: 5261–7. [PubMed Abstract] [PubMed CentralFull Text].
Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford). 2010. [PubMed CentralFull Text] baq013.
Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, etal. The human oral microbiome. J Bacteriol. 2010; 192: 5002–17. [PubMed Abstract] [PubMed CentralFull Text].
Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992; 131: 479–91. [PubMed Abstract] [PubMed CentralFull Text].
Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One. 2012; 7: e33865. [PubMed Abstract] [PubMed CentralFull Text].
Dupuy AK, David MS, Li L, Heider TN, Peterson JD, Montano EA. Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery ofMalasseziaas a Prominent Commensal. PLoS One. 2014; 9(3): e90899. [PubMed Abstract] [PubMed CentralFull Text].
Bunge J, 2011, Pac Symp Biocomput, 121