Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility.

ABSTRACT: High-throughput sequencing technology provides an efficient method for evaluating microbial ecology. Different bioinformatics pipelines can be used to convert 16S ribosomal RNA gene amplicon sequencing data into an operational taxonomic unit (OTU) table that is used to analyze microbial communities. It is important to assess the robustness of these pipelines, each with specific algorithms and/or parameters, and their influence on the outcome of statistical tests. Articles with publicly available datasets on the oral microbiome were searched for, and five datasets were retrieved. These were from studies on changes in microbiota related to smoking, oral cancer, caries, diabetes, or periodontitis. Next, the data was processed with four pipelines based on VSEARCH, USEARCH, mothur, and UNOISE3.

SUBMITTER: Kang X 

PROVIDER: S-EPMC8566820 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature