Prediction of Plausible Bacterial Composition Based on Terminal Restriction Fragment Length Polymorphisms using a Monte Carlo Method

Yoshio Nakano, Toru Takeshita, Masaki Yasui, Yoshihisa Yamashita

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

We have developed a new approach for the estimation of bacterial proportional compositions in microbiota based on terminal restriction length polymorphism (T-RFLP) data and a Monte Carlo algorithm. This program estimates proportional compositions by minimizing distances between peak values and the relative abundance of each group, containing several species, estimated from peak areas of capillary electrophoresis for T-RFLP analysis. Oral bacteria in 36 saliva samples obtained from three individuals were analyzed using the program. Upon comparison, the estimated proportional composition obtained from one of the samples matched that from a clone library. Additionally, comparisons among the bacterial proportional compositions of saliva samples obtained from three individuals four times per day for 3 days revealed that the types of microbiota present in each individual did not change within each 24-h time period and were distinguishable from those in other individuals.

Original languageEnglish
Pages (from-to)364-372
Number of pages9
JournalMicrobial Ecology
Volume60
Issue number2
DOIs
Publication statusPublished - 2010

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saliva
Monte Carlo method
restriction fragment length polymorphism
polymorphism
prediction
clone
relative abundance
electrokinesis
capillary electrophoresis
sampling
bacterium
mouth
genetic polymorphism
clones
bacteria
programme
method
comparison
microbiome
analysis

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Soil Science

Cite this

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abstract = "We have developed a new approach for the estimation of bacterial proportional compositions in microbiota based on terminal restriction length polymorphism (T-RFLP) data and a Monte Carlo algorithm. This program estimates proportional compositions by minimizing distances between peak values and the relative abundance of each group, containing several species, estimated from peak areas of capillary electrophoresis for T-RFLP analysis. Oral bacteria in 36 saliva samples obtained from three individuals were analyzed using the program. Upon comparison, the estimated proportional composition obtained from one of the samples matched that from a clone library. Additionally, comparisons among the bacterial proportional compositions of saliva samples obtained from three individuals four times per day for 3 days revealed that the types of microbiota present in each individual did not change within each 24-h time period and were distinguishable from those in other individuals.",
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AU - Nakano, Yoshio

AU - Takeshita, Toru

AU - Yasui, Masaki

AU - Yamashita, Yoshihisa

PY - 2010

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