Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys

Is there a role for triclosan/copolymer toothpaste in the management of periodontal disease?

Dental caries and periodontal disease are the most common oral conditions experienced by adults today. The treatment of these diseases by the dental team can only be performed when patients attend dental practices. There is recognition that the preventive measures patients perform at home between dental visits is of vital importance in the control of these diseases. Water fluoridation and fluoridated toothpastes have made enormous progress into the prevention of dental caries worldwide. However, prevention of periodontal disease is yet to enjoy the same success. A number of toothpastes have been developed for the prevention and control of periodontal disease. One such toothpaste - containing triclosan/copolymer - has been thoroughly researched. The literature pertaining to the efficacy, mode of action and safety of triclosan/copolymer toothpaste has been reviewed. A MEDLINE search identified 198 articles dated from 1989 to 2008. The findings of this body of research are discussed and conclusions regarding the efficacy of triclosan/copolymer toothpaste in the home-care management of periodontal disease are presented.A. Blinkhorn, P. M. Bartold, M. P. Cullinan, T. E. Madden, R. I. Marshall, S. L. Raphael and G. J. Seymou