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Title: Comparative evaluation of common 16S ribosomal RNA (rRNA) gene sequence primers for phylogenetic identification of bacteria in soil communities      
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ID:
PRJEB18468
description:
Microbial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up microbial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. Often, soil microbial community analyses use primers that were developed some years ago against database versions that are now out of date. Here we evaluated the performance of four commonly used bacterial primers covering successive regions of the 16S rRNA gene against the most recent database versions available. Analyses were performed on empirically generated 454-sequences of diverse soil samples and in silico against the current SILVA123 database. Primer pair 341f-785r was found to be the most suitable for short-read sequencing studies of soil microbiomes because it produced the highest number of OTUs, phylogenetic richness, Shannon diversity, and most reproducible results, followed by 967f-1391r and 799f-1193r, while 68f-518r exhibited bias towards Alphaproteobacteria. Primer pair 341f-785r showed the highest in silico coverage of the domain Bacteria (96.1 %) and showed no obvious bias towards the majority of bacterial species. We suggest, based on overall performance, that primer pair 341f-785r whether or not in combination with 967f-1391r or 799f-1193r should be adopted for soil microbiome studies. The data presented here allows researchers to select primer sets that provide the most phylogenetic diverse, unbiased, and specific data sets for their samples while excluding Eukaryotic organelle gene amplification.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJEB18468
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abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject