TY - JOUR
T1 - Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
AU - Logares, Ramiro
AU - Sunagawa, Shinichi
AU - Salazar, Guillem
AU - Cornejo-Castillo, Francisco M.
AU - Ferrera, Isabel
AU - Sarmento, Hugo
AU - Hingamp, Pascal
AU - Ogata, Hiroyuki
AU - de Vargas, Colomban
AU - Lima-Mendez, Gipsi
AU - Raes, Jeroen
AU - Poulain, Julie
AU - Jaillon, Olivier
AU - Wincker, Patrick
AU - Kandels-Lewis, Stefanie
AU - Karsenti, Eric
AU - Bork, Peer
AU - Acinas, Silvia G.
PY - 2014/9
Y1 - 2014/9
N2 - 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 (mitags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the TaraOceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454tags; 13 metagenomes, ca. 2.4Gb) and 16S rDNA amplicon (454tags; ca. 0.075Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mitags may provide more realistic estimates of community richness and evenness than amplicon 454tags. In addition, mitags can capture expected beta diversity patterns. Using mitags 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.
AB - 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 (mitags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the TaraOceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454tags; 13 metagenomes, ca. 2.4Gb) and 16S rDNA amplicon (454tags; ca. 0.075Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mitags may provide more realistic estimates of community richness and evenness than amplicon 454tags. In addition, mitags can capture expected beta diversity patterns. Using mitags 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.
UR - http://www.scopus.com/inward/record.url?scp=84906944378&partnerID=8YFLogxK
U2 - 10.1111/1462-2920.12250
DO - 10.1111/1462-2920.12250
M3 - Article
C2 - 24102695
AN - SCOPUS:84906944378
SN - 1462-2912
VL - 16
SP - 2659
EP - 2671
JO - Environmental Microbiology
JF - Environmental Microbiology
IS - 9
ER -