A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

BMC Genomics
Rosalinda D'AmoreNeil Hall

Abstract

In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. We assembled 2 synthetic communities with an even (EM) and uneven (UM) distribution of archaeal and bacterial strains and species, as metagenomic control material, to assess performance of different experimental strategies. The 2 synthetic communities were used in this study, to highlight the limitations and the advantages of the leading sequencing platforms: MiSeq (Illumina), The Pacific Biosciences RSII, 454 GS-FLX/+ (Roche), and IonTorrent (Life Technologies). We describe an extensive survey based on synthetic communities using 3 experimental designs (fusion primers, ...Continue Reading

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Datasets Mentioned

BETA
ERP005737

Methods Mentioned

BETA
amplicon sequencing
454 sequencing
PCR
DNA
Chip
16S sequencing

Software Mentioned

Qubit
RTA
R
MCS
VarScan
PacBio
Nextera
AMPLImock
PANDAseq
fasta

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