ArticlePloS one2013
The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 1 of them a synthesis that pooled it.
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Who cites it
75 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Three marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading alginate, chitin, laminarin, starch, and xylan.Scientific reports · 2023Article
- Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems.Environmental microbiome · 2023Article
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- Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems.Oecologia · 2023Article
- Novel primers for 16S rRNA gene-based archaeal and bacterial community analysis in oceanic trench sediments.Applied microbiology and biotechnology · 2022Article
- Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain).Frontiers in microbiology · 2022Article
- Soil microbial communities shift along an urban gradient in Berlin, Germany.Frontiers in microbiology · 2022Article
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- The growth of plants and indigenous bacterial community were significantly affected by cadmium contamination in soil-plant system.AMB Express · 2021Article
15 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts. All the unknowns associated with sequencing data, i.e. primer coverage rate, phylogeny, OTU-richness and taxonomic assignment, were therefore implemented in one study for ten well established universal primers (338f/r, 518f/r, 799f/r, 926f/r and 1062f/r) targeting dispersed regions of the bacterial 16S rRNA gene. All analyses were performed on nearly full length and in silico generated short read sequence libraries containing 1175 sequences that were carefully chosen as to present a representative substitute of the SILVA SSU database. The 518f and 799r primers, targeting the V4 region of the 16S rRNA gene, were found to be particularly suited for short read sequencing studies, while the primer 1062r, targeting V6, seemed to be least reliable. Our results will assist scientists in considering whether the best option for their study is to select the most informative primer, or the primer that excludes interferences by host-organelle DNA. The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment.
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