Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. 2013 January 08 Enivronmental Microbiology (2013), 15(6): 1882-1899
Taxonomic and functional characterization of microbial communities by rRNA gene and metagenomic sequencing have been used extensively. Determining accuracy and performing cross-comparisons between approaches are limited by data incongruences and the lack of knowledge of the true ecological diversityScience
We used complex mixes of bacterial and archaeal pure genomic DNAs to directly compare inferences from metagenomic and rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition. The accuracy of public analysis platforms (IMG, MG-RAST) and several widely used software was highly dependent on analysis parameters. Sources of errors were identified and we proposed alternatives to correct them.Significance
A synthetic community approach is important for calibrating and validating experimental design and data analysis in long term environmental studies.