Prediction of plausible bacterial composition based on terminal restriction fragment length polymorphisms using a Monte Carlo method.
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.
Nakano
Yoshio
Y
Section of Preventive Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan. nakano@dent.nihon-u.ac.jp
Takeshita
Toru
T
Yasui
Masaki
M
Yamashita
Yoshihisa
Y
D000465:Algorithms; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D003001:Cloning, Molecular; D004269:DNA, Bacterial / Q000235:genetics; D006801:Humans; D054892:Metagenome; D009010:Monte Carlo Method; D012150:Polymorphism, Restriction Fragment Length; D025341:Principal Component Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012463:Saliva / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000379:methods; D013997:Time Factors
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S