Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

被引：6151

作者：

Klindworth, Anna ^{[1
,2
]}

Pruesse, Elmar ^{[1
,2
]}

Schweer, Timmy ^{[1
]}

Peplies, Joerg ^{[3
]}

Quast, Christian ^{[1
]}

Horn, Matthias ^{[4
]}

Gloeckner, Frank Oliver ^{[1
,2
]}

机构：

[1] Max Planck Inst Marine Microbiol, Microbial Genom & Bioinformat Res Grp, D-28359 Bremen, Germany

[2] Jacobs Univ Bremen, Sch Sci & Engn, D-28759 Bremen, Germany

[3] Ribocon GmbH, D-28359 Bremen, Germany

[4] Univ Vienna, Dept Microbial Ecol, A-1090 Vienna, Austria

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / 01期

基金：

欧洲研究理事会;

关键词：

BACTERIAL DIVERSITY; ONLINE RESOURCE; DEEP-SEA; DESIGN; POPULATIONS; GRADIENT; ATLANTIC; DATABASE; READS; SOILS;

D O I：

10.1093/nar/gks808

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of 'best available' primer pairs for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, epsilon 1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

引用

页数：11

共 52 条

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