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Metagenomic 16S rDNA I llumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
Author(s) -
Logares Ramiro,
Sunagawa Shinichi,
Salazar Guillem,
CornejoCastillo Francisco M.,
Ferrera Isabel,
Sarmento Hugo,
Hingamp Pascal,
Ogata Hiroyuki,
Vargas Colomban,
LimaMendez Gipsi,
Raes Jeroen,
Poulain Julie,
Jaillon Olivier,
Wincker Patrick,
KandelsLewis Stefanie,
Karsenti Eric,
Bork Peer,
Acinas Silvia G.
Publication year - 2014
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.12250
Subject(s) - biology , amplicon , metagenomics , pyrosequencing , archaea , 16s ribosomal rna , shotgun sequencing , computational biology , species evenness , environmental dna , primer (cosmetics) , genetics , illumina dye sequencing , polymerase chain reaction , dna sequencing , evolutionary biology , gene , species richness , ecology , biodiversity , chemistry , organic chemistry
Summary Sequencing of 16S rDNA polymerase chain reaction ( PCR ) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR . Here we show that 16S rDNA fragments derived from Illumina‐sequenced environmental metagenomes ( mi tag s) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the T ara O ceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for R oche‐454 sequencing using both shotgun ( m454 tag s; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon ( 454 tag s; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tag s may provide more realistic estimates of community richness and evenness than amplicon 454 tag s. In addition, mi tag s can capture expected beta diversity patterns. Using mi tag s is now economically feasible given the dramatic reduction in high‐throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic ( B acteria, A rchaea and E ukarya) and functional information from the same microbial community.