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

被引：259

作者：

Bukin, Yu. S. ^{[1
,2
]}

Galachyants, Yu. P. ^{[1
,2
]}

Morozov, I. V. ^{[3
]}

Bukin, S. V. ^{[1
]}

Zakharenko, A. S. ^{[1
]}

Zemskaya, T. I. ^{[1
,2
]}

机构：

[1] RAS, SB, Limnol Inst, Irkutsk 664033, Russia

[2] RAS, SB, Irkutsk Sci Ctr, Irkutsk 664033, Russia

[3] RAS, SB, Inst Chem Biol & Fundamental Med, Novosibirsk 630090, Russia

来源：

SCIENTIFIC DATA | 2019年 / 6卷 / 1期

基金：

俄罗斯基础研究基金会;

关键词：

MICROBIAL COMMUNITY; SPECIES RICHNESS; LAKE BAIKAL; DIVERSITY; DISCHARGE; SEDIMENTS; DISSIMILARITY; BIODIVERSITY; SIMILARITY; SUBUNIT;

D O I：

10.1038/sdata.2019.7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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%.

引用

页数：14

共 59 条

[1]

[Anonymous], 2018, SRP102494

[2]

[Anonymous], 2018, SRP145556

[3] Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia [J].

Bashenkhaeva, Maria V. ;

Zakharova, Yulia R. ;

Petrova, Darya P. ;

Khanaev, Igor V. ;

Galachyants, Yuri P. ;

Likhoshway, Yelena V. .

MICROBIAL ECOLOGY, 2015, 70 (03) :751-765

[4] CONSTRUCTING CONFIDENCE SETS USING RANK STATISTICS [J].

BAUER, DF .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1972, 67 (339) :687-690

[5] Gut microbiome of juvenile coregonid fishes: comparison of sympatric species and their F1 hybrids [J].

Belkova, Natalia L. ;

Sidorova, Tuyana V. ;

Glyzina, Olga Y. ;

Yakchnenko, Veronika M. ;

Sapozhnikova, Yulia P. ;

Bukin, Yurij S. ;

Baturina, Olga A. ;

Sukhanova, Lyubov V. .

FUNDAMENTAL AND APPLIED LIMNOLOGY, 2017, 189 (03) :279-290

[6] The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions [J].

Bukin, Sergei V. ;

Pavlova, Olga N. ;

Manakov, Andrei Y. ;

Kostyreva, Elena A. ;

Chernitsyna, Svetlana M. ;

Mamaeva, Elena V. ;

Pogodaeva, Tatyana V. ;

Zemskaya, Tamara I. .

FRONTIERS IN MICROBIOLOGY, 2016, 7

[7] Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal [J].

Cabello-Yeves, Pedro J. ;

Zemskaya, Tamara I. ;

Rosselli, Riccardo ;

Coutinho, Felipe H. ;

Zakharenko, Alexandra S. ;

Blinov, Vadim V. ;

Rodriguez-Valera, Francisco .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2018, 84 (01)

[8]

Chernitsyna S M, 2016, Mikrobiologiia, V85, P522

[9] An Improved Nonparametric Lower Bound of Species Richness via a Modified Good-Turing Frequency Formula [J].

Chiu, Chun-Huo ;

Wang, Yi-Ting ;

Walther, Bruno A. ;

Chao, Anne .

BIOMETRICS, 2014, 70 (03) :671-682

[10] Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions [J].

Claesson, Marcus J. ;

Wang, Qiong ;

O'Sullivan, Orla ;

Greene-Diniz, Rachel ;

Cole, James R. ;

Ross, R. Paul ;

O'Toole, Paul W. .

NUCLEIC ACIDS RESEARCH, 2010, 38 (22) :e200

← 1 2 3 4 5 6 →