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

doi:10.1016/j.mimet.2008.08.002

Cited by 13 publications

(6 citation statements)

References 16 publications

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“…The diversity of the bacterial community was evaluated by the number of TRFs and the Shannon diversity index of T-RFLP profiles. The bacterial candidates corresponding to the TRFs with significantly more or fewer subjects in one cluster than in the other clusters were selected using BP-TRFMA (24). The correlation threshold in BP-TRFMA was set at 0.13, which corresponds to a significant correlation coefficient in this sample size.…”

Section: Methodsmentioning

confidence: 99%

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva

Takeshita

Suzuki

Nakano

et al. 2010

Appl Environ Microbiol

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Oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. In this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (T-RFLP) profiles using hierarchical cluster analysis, and the patterns of the microbial community composition of those exhibiting higher and lower malodor were explored. Four types of bacterial community compositions were detected (clusters I, II, III, and IV). Two parameters for measuring oral malodor intensity (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) were noticeably lower in cluster I than in the other clusters. Using multivariate analysis, the differences in the levels of oral malodor were significant after adjustment for potential confounding factors such as total bacterial count, mean periodontal pocket depth, and tongue coating score (P < 0.001). Among the four clusters with different proportions of indigenous members, the T-RFLP profiles of cluster I were implicated as the bacterial populations with higher proportions of Streptococcus, Granulicatella, Rothia, and Treponema species than those of the other clusters. These results clearly correlate the global composition of indigenous bacterial populations with the severity of oral malodor.

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Section: Methodsmentioning

confidence: 99%

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva

Takeshita

Suzuki

Nakano

et al. 2010

Appl Environ Microbiol

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“…The T-RFs which showed a more than 10% peak level for all of three enzymes were selected to predict the genus of the microorganisms based on a database 41) . To confirm these findings, a qualitative PCR analysis was carried out using genus-and species-specific primers.…”

Section: Qualitative Pcrmentioning

confidence: 99%

“…When the signal data for three degradation enzymes was matched, the accuracy of the estimation might have been increased, and the database 41) of bacterial species might have better correspond to the T-RFLP pattern. Therefore, a principal component analysis of the T-RFLP profiles was performed for the three enzymes (date not shown).…”

Section: Qualitative Analyses Of Biofilms On the Samplesmentioning

confidence: 99%

“…The qualitative PCR analysis using the genus-or species-specific primers was carried out to confirm whether the species narrowed down from the database 41) truly corresponded to the T-RF of the five alloys and resin. The results of the PCR analysis for the five alloys and the resin sample showed that several microorganisms associated with aspiration pneumonia, including genera of Actinomyces, Fusobacterium, Haemophilus, Mycoplasma and Peptostreptococcus (Table 2), existed in the biofilms formed on the five alloys and resin.…”

Section: Qualitative Analyses Of Biofilms On the Samplesmentioning

confidence: 99%

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An analysis of the biofilms adhered to framework alloys using in vitro denture plaque models

et al. 2014

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The purpose of this study was to perform a quantitative and qualitative evaluation of the biofilms formed on framework alloys in vitro. The biofilms formed by unfiltered fresh human saliva or Streptococcus mutans and/or Candida albicans on commercially pure titanium and gold-copper-platinum demonstrated higher amounts than other alloy and resin samples. In contrast, the silverpalladium-copper-gold showed a significantly decreased level of biofilm formation. Although the adhesion level of Streptococcus mutans on cobalt-chromium was high, that of Candida albicans was less extensive. A T-RFLP analysis and qualitative PCR of the microbes in the biofilms were performed. In a cluster analysis of all T-RFLP profiles, the cobalt-chromium pattern was integrated into one cluster. On qualitative PCR, the existence of microorganisms related to caries, preriodontitis and aspiration pneumonia was observed. Our results showed that the biofilm formation on each framework alloy was different in terms of both the quantity and quality.

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“…T-RFLP analysis is a method to study complex microbial communities based on variation in the 16S rRNA gene (Osborn et al, 2001). It was used to determine the pattern of the bacteria from various environments (Nakano et al, 2008) and bacterial dynamics in response to environmental changes (Osborn et al, 2001). Some of the advantages of this method are low cost and able to analyze hundred of samples per day (Zhang et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Bacterial Diversity of the Deep Sea of Sangihe Talaud, Sulawesi

Patantis¹,

Chasanah²,

Zilda³

et al. 2013

Squalen Bull. Marine Fisheries Postharvest Biotech.

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Deep sea is an extreme environment characterized by cold temperature, high pressure, lack of light and nutrients. Microorganisms live in these habitat are unique microorganisms and known to have tremendous source of potential agents for biotechnology processes. Indonesia as an archipelagic country has a vast deep ocean. This study aims to see the diversity of bacteria in Sangihe Talaud Deep Sea, Sulawesi. Analysis of bacterial diversity was carried out by cultured and uncultured method. Terminal Restriction Fragment Length Polymorphism (T-RFLP) technique was used for uncultured analysis of the microorganisms biodiversity, while cultured one was done by plating the samples of water onto Zobell media. The results showed that, there were 21 isolates obtained by cultured method. The identification which based on 16S rDNA by PCR method showed the genus of Pseudomonas, Pseudoalteromonas, Alteromonas, Vibrio, Shewanella and Uncultured bacterium were identified. However, 14 classes of bacteria were obtained by using TRFLP method i.e Acetobacteraceae class, Actinobacteria, α-proteobacteria, -proteobacteria, δ-proteobacteria, γ-proteobacteria, Bacili, Bacteroidetes, Chlorobi, Chroococcales, Clostridia, Erysipelotrichi, Synergistia, and Zetaproteobacteria. There were also unclassified bacteria and uncultured bacterium found in the samples.

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

Cited by 13 publications

References 16 publications

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva

An analysis of the biofilms adhered to framework alloys using in vitro denture plaque models

Bacterial Diversity of the Deep Sea of Sangihe Talaud, Sulawesi

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