Genes, Vol. 11, Pages 878: The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community
Genes, Vol. 11, Pages 878: The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community
Genes doi: 10.3390/genes11080878
Authors:
Maria A. Sierra
Qianhao Li
Smruti Pushalkar
Bidisha Paul
Tito A Sandoval
Angela R. Kamer
Patricia Corby
Yuqi Guo
Ryan Richard Ruff
Alexander V. Alekseyenko
Xin Li
Deepak Saxena
There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our...
Source: Genes - Category: Genetics & Stem Cells Authors: Maria A. Sierra Qianhao Li Smruti Pushalkar Bidisha Paul Tito A Sandoval Angela R. Kamer Patricia Corby Yuqi Guo Ryan Richard Ruff Alexander V. Alekseyenko Xin Li Deepak Saxena Tags: Article Source Type: research