Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing.

ABSTRACT: Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studi

SUBMITTER: Tessler M 

PROVIDER: S-EPMC5537354 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature