Title: Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
Authors: Logares, Ramiro ×
Sunagawa, Shinichi
Salazar, Guillem
Cornejo-Castillo, Francisco M
Ferrera, Isabel
Sarmento, Hugo
Hingamp, Pascal
Ogata, Hiroyuki
de Vargas, Colomban
Lima Mendez, Gipsi
Raes, Jeroen
Poulain, Julie
Jaillon, Olivier
Wincker, Patrick
Kandels-Lewis, Stefanie
Karsenti, Eric
Bork, Peer
Acinas, Silvia G #
Issue Date: Sep-2014
Publisher: Blackwell Science
Series Title: Environmental Microbiology vol:16 issue:9 pages:2659-71
Article number: 10.1111/1462-2920.12250
Abstract: 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 tags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans 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 Roche-454 sequencing using both shotgun (m454 tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454 tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags. In addition, mi tags can capture expected beta diversity patterns. Using mi tags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.
ISSN: 1462-2912
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Non-KU Leuven Association publications
× corresponding author
# (joint) last author

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