DADA2: High-resolution Sample Inference from Illumina Amplicon Data

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2016 May 24

PMID 27214047

Citations 10741

Authors

Benjamin J Callahan

Paul J McMurdie

Michael J Rosen

Andrew W Han

Amy Jo A Johnson

Susan P Holmes

Affiliations

Soon will be listed here.

Abstract

We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

Citing Articles

Discovering the dynamics of peach fruit mycobiome throughout fruit development season by high-throughput sequencing.

Oncel S, Ozkilinc H Sci Rep. 2025; 15(1):8969.

PMID: 40089528 DOI: 10.1038/s41598-025-93090-6.

DNA metabarcoding and its potential in microbial risk assessment in waste sorting plants.

Eriksen E, Graff P, Eiler A, Straumfors A, Komlavi Afanou A Sci Rep. 2025; 15(1):8941.

PMID: 40089527 DOI: 10.1038/s41598-025-93697-9.

Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.

Duret M, Wallner A, Besaury L, Aziz A Environ Microbiome. 2025; 20(1):30.

PMID: 40087775 DOI: 10.1186/s40793-025-00690-w.

Interaction between the liver transcriptome and gut microbiota in mice during Toxoplasma gondii infection as identified by integrated transcriptomic and microbiome analysis.

Zou Y, Ma H, Yang X, Wei X, Chen C, Jiang J BMC Microbiol. 2025; 25(1):137.

PMID: 40087603 DOI: 10.1186/s12866-025-03852-5.

The comparison of gut microbiota between different types of epilepsy in children.

Fang S, Hu N, Zhou C, You J, Wu L, Pan X Microb Cell Fact. 2025; 24(1):64.

PMID: 40082906 PMC: 11908097. DOI: 10.1186/s12934-025-02684-2.

References

Kozich J, Westcott S, Baxter N, Highlander S, Schloss P . Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013; 79(17):5112-20. PMC: 3753973. DOI: 10.1128/AEM.01043-13. View

. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402):207-14. PMC: 3564958. DOI: 10.1038/nature11234. View

Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson G . Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods. 2012; 9(5):425-6. DOI: 10.1038/nmeth.1990. View

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer R . Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 2007; 17(8):1195-201. PMC: 1933516. DOI: 10.1101/gr.6468307. View

Eren A, Borisy G, Huse S, Welch J . Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci U S A. 2014; 111(28):E2875-84. PMC: 4104879. DOI: 10.1073/pnas.1409644111. View

Edgar R . UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013; 10(10):996-8. DOI: 10.1038/nmeth.2604. View

Guarner F . Decade in review-gut microbiota: the gut microbiota era marches on. Nat Rev Gastroenterol Hepatol. 2014; 11(11):647-9. DOI: 10.1038/nrgastro.2014.156. View

Rosen M, Callahan B, Fisher D, Holmes S . Denoising PCR-amplified metagenome data. BMC Bioinformatics. 2012; 13:283. PMC: 3563472. DOI: 10.1186/1471-2105-13-283. View

Quince C, Lanzen A, Davenport R, Turnbaugh P . Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011; 12:38. PMC: 3045300. DOI: 10.1186/1471-2105-12-38. View

10.

Sun Y, Cai Y, Liu L, Yu F, Farrell M, McKendree W . ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 2009; 37(10):e76. PMC: 2691849. DOI: 10.1093/nar/gkp285. View

11.

Rosen M, Davison M, Bhaya D, Fisher D . Microbial diversity. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science. 2015; 348(6238):1019-23. DOI: 10.1126/science.aaa4456. View

12.

Edgar R, Flyvbjerg H . Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics. 2015; 31(21):3476-82. DOI: 10.1093/bioinformatics/btv401. View

13.

MacIntyre D, Chandiramani M, Lee Y, Kindinger L, Smith A, Angelopoulos N . The vaginal microbiome during pregnancy and the postpartum period in a European population. Sci Rep. 2015; 5:8988. PMC: 4355684. DOI: 10.1038/srep08988. View

14.

Schirmer M, Ijaz U, DAmore R, Hall N, Sloan W, Quince C . Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015; 43(6):e37. PMC: 4381044. DOI: 10.1093/nar/gku1341. View

15.

Caporaso J, Kuczynski J, Stombaugh J, Bittinger K, Bushman F, Costello E . QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7(5):335-6. PMC: 3156573. DOI: 10.1038/nmeth.f.303. View

16.

Eren A, Morrison H, Lescault P, Reveillaud J, Vineis J, Sogin M . Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 2014; 9(4):968-79. PMC: 4817710. DOI: 10.1038/ismej.2014.195. View

17.

Schloss P, Westcott S, Ryabin T, Hall J, Hartmann M, Hollister E . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537-41. PMC: 2786419. DOI: 10.1128/AEM.01541-09. View

18.

Tikhonov M, Leach R, Wingreen N . Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 2014; 9(1):68-80. PMC: 4274427. DOI: 10.1038/ismej.2014.117. View

19.

Reeder J, Knight R . Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods. 2010; 7(9):668-9. PMC: 2945879. DOI: 10.1038/nmeth0910-668b. View

20.

Caporaso J, Lauber C, Walters W, Berg-Lyons D, Huntley J, Fierer N . Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6(8):1621-4. PMC: 3400413. DOI: 10.1038/ismej.2012.8. View