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

Overview

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, ParanĂ¡, 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 studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.

publication date

  • July 31, 2017

Research

keywords

  • Bacteria
  • Biodiversity
  • High-Throughput Nucleotide Sequencing
  • Metagenomics
  • RNA, Ribosomal, 16S
  • Sequence Analysis, DNA
  • Water Microbiology

Identity

PubMed Central ID

  • PMC5537354

Scopus Document Identifier

  • 85026644382

Digital Object Identifier (DOI)

  • 10.1186/1471-2164-13-341

PubMed ID

  • 28761145

Additional Document Info

volume

  • 7

issue

  • 1