Taxonomic classification and abundance estimation using 16S and WGS—A comparison using controlled reference samples

Publication date: May 2020Source: Forensic Science International: Genetics, Volume 46Author(s): Lusine Khachatryan, Rick H. de Leeuw, Margriet E.M. Kraakman, Nikos Pappas, Marije te Raa, Hailiang Mei, Peter de Knijff, Jeroen F.J. LarosAbstractThe assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed us...

Source: Forensic Science International: Genetics - February 12, 2020 Category: Forensic Medicine Source Type: research