The effect of 16S rRNA region choice on bacterial community metabarcoding results

In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It...

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Bibliographic Details
Published inScientific data Vol. 6; no. 1; p. 190007
Main Authors Bukin, Yu S, Galachyants, Yu P, Morozov, I V, Bukin, S V, Zakharenko, A S, Zemskaya, T I
Format Journal Article
LanguageEnglish
Published England Nature Publishing Group 05.02.2019
Subjects
Bacteria - genetics
Biodiversity
Computational Biology - methods
Data Descriptor
DNA Barcoding, Taxonomic - methods
DNA sequencing
Estimates
Genetic testing
High-Throughput Nucleotide Sequencing
Laboratories
Lakes
Life sciences
Medical research
Metagenomics - methods
Microbiota - genetics
Nucleotide sequence
RNA, Ribosomal, 16S - genetics
rRNA 16S
Russia
Sediments
Sequence analysis
Sequence Analysis, DNA
Species
Taxonomy
Volcanoes
Water Microbiology
Russia
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Summary:In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.
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Bukin Yu.S. statistic comparisons of species diversity, statistic comparisons of the genetic diversity estimates, writing the text of the manuscript, formulating the main conclusions of the work. Galachyants Yu.P. read analysis, formulating the main conclusions of the work. Morozov I.V. amplification and sequencing, participation in setting research objectives, editing a manuscript. Bukin S.V. sampling, DNA extraction. Zakharenko A.S. sampling, DNA extraction. Zemskaya T.I. sampling, formulation of research goals and objectives, formulating the main conclusions of the work, editing a manuscript, general guidance and coordination of the team of authors.
ISSN:2052-4463
2052-4463
DOI:10.1038/sdata.2019.7