Abstract

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%.

Design Type(s)

sequence analysis objective • biodiversity assessment objective

Measurement Type(s)

rRNA_16S

Technology Type(s)

DNA sequencing assay

Factor Type(s)

aquatic natural environment • sequence_variant

Sample Characteristic(s)

soil metagenome • freshwater metagenome • Lake Baikal • lake sediment • oil seep • mud volcano

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Details

Title
The effect of 16S rRNA region choice on bacterial community metabarcoding results
Author
Bukin, Yu S 1 ; Galachyants, Yu P 1 ; Morozov, I V 2   VIAFID ORCID Logo  ; Bukin, S V 3 ; Zakharenko, A S 3 ; Zemskaya, T I 1 

1  Limnological institute SB RAS, 3, 664033, Irkutsk, Russia (GRID:grid.425246.3) (ISNI:0000 0004 0440 2197); Irkutsk Scientific Center SB RAS, 664033, Irkutsk, Russia (GRID:grid.415877.8) (ISNI:0000 0001 2254 1834) 
2  Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090, Novosibirsk, Russia (GRID:grid.418910.5) (ISNI:0000 0004 0638 0593) 
3  Limnological institute SB RAS, 3, 664033, Irkutsk, Russia (GRID:grid.425246.3) (ISNI:0000 0004 0440 2197) 
Publication year
2019
Publication date
2019
Publisher
Nature Publishing Group
e-ISSN
20524463
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/sdata.2019.7
ProQuest document ID
2640580921
Copyright
© The Author(s) 2019. corrected publication 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.