Development and application of a T-RFLP data analysis method using correlation coefficient matrices

Yoshio Nakano, Toru Takeshita, Noriaki Kamio, Susumu Shiota, Yukie Shibata, Masaki Yasui, Yoshihisa Yamashita

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Environmental microbiology studies commonly use terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes, for example, to analyze changes in community structure in relation to changing physicochemical and biological conditions over space and time. Although T-RFLP is most useful for comparing samples from different environments, a large number of samples makes effective analysis difficult using the Web-based tools that are currently available. To resolve this dilemma, we used a new approach for calculating data from multiple T-RFLP samples by estimating terminal fragment combinations, then applying a correlation analysis using two different fluorescent dyes generated simultaneously from all samples. This calculation was based on the expectation that the proportions of two terminal fragments from one full-length polymerase chain reaction fragment would be nearly the same in each analysis. Using this program, the oral microflora in 73 human saliva samples were analyzed, and 24 bacterial groups, with peak areas of at least 0.5% and correlation coefficients of 0.55 or greater, were identified from the T-RFs within 40 s.

Original languageEnglish
Pages (from-to)501-505
Number of pages5
JournalJournal of Microbiological Methods
Volume75
Issue number3
DOIs
Publication statusPublished - Dec 1 2008

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Restriction Fragment Length Polymorphisms
Environmental Microbiology
Fluorescent Dyes
rRNA Genes
Saliva
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)

Cite this

Development and application of a T-RFLP data analysis method using correlation coefficient matrices. / Nakano, Yoshio; Takeshita, Toru; Kamio, Noriaki; Shiota, Susumu; Shibata, Yukie; Yasui, Masaki; Yamashita, Yoshihisa.

In: Journal of Microbiological Methods, Vol. 75, No. 3, 01.12.2008, p. 501-505.

Research output: Contribution to journalArticle

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