Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys-Reference-Cited by-同舟云学术

Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys

Published:2021-06-29 Issue:3 Volume:6 Page:
ISSN:2379-5077
Container-title:mSystems
language:en
Short-container-title:mSystems

Author:

McNichol Jesse¹^ORCID,Berube Paul M.²^ORCID,Biller Steven J.²³^ORCID,Fuhrman Jed A.¹^ORCID

Affiliation:

1. Department of Biological Sciences, University of Southern California, Los Angeles, California, USA

2. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

3. Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA

Abstract

PCR amplification and sequencing of marker genes are a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time but will work optimally only if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally distributed short-read oceanic metagenomes.

Funder

Gordon and Betty Moore Foundation

National Science Foundation

Simons Foundation

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

Link

https://journals.asm.org/doi/pdf/10.1128/mSystems.00565-21

Reference48 articles.

1. A communal catalogue reveals Earth’s multiscale microbial diversity

2. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

3. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

4. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

5. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

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