Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method.

ABSTRACT: The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles. Modern approaches employ whole genome shotgun next-generation sequencing as the basis for these analyses. Sequencing depth as well as choice of next-generation sequencing data analysis method constitute two main interacting methodological factors for such an approach. In this study, we used 200 million sequence read pairs from one fecal sample for comparing different taxonomy classification methods, using default and custom-made reference databases, at different sequencing depths. A mock community data set with known composition was used for validating the classifica

SUBMITTER: Rajan SK 

PROVIDER: S-EPMC6748435 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature