HmmUFOtu: An HMM and Phylogenetic Placement Based Ultra-fast Taxonomic Assignment and OTU Picking Tool for Microbiome Amplicon Sequencing Studies

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2018 Jun 29

PMID 29950165

Citations 18

Authors

Qi Zheng

Casey Bartow-McKenney

Jacquelyn S Meisel

Elizabeth A Grice

Affiliations

Soon will be listed here.

Abstract

Culture-independent analysis of microbial communities frequently relies on amplification and sequencing of the prokaryotic 16S ribosomal RNA gene. Typical analysis pipelines group sequences into operational taxonomic units (OTUs) to infer taxonomic and phylogenetic relationships. Here, we present HmmUFOtu, a novel tool for processing microbiome amplicon sequencing data, which performs rapid per-read phylogenetic placement, followed by phylogenetically informed clustering into OTUs and taxonomy assignment. Compared to standard pipelines, HmmUFOtu more accurately and reliably recapitulates microbial community diversity and composition in simulated and real datasets without relying on heuristics or sacrificing speed or accuracy.

Citing Articles

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.

Jiang Y, McDonald D, Perry D, Knight R, Mirarab S Bioinformatics. 2024; 40(6).

PMID: 38870525 PMC: 11193062. DOI: 10.1093/bioinformatics/btae361.

A Machine Learning-Based Diagnostic Model for Crohn's Disease and Ulcerative Colitis Utilizing Fecal Microbiome Analysis.

Kim H, Na J, Kim S, Kim T, Park S, Lee C Microorganisms. 2024; 12(1).

PMID: 38257863 PMC: 10820568. DOI: 10.3390/microorganisms12010036.

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.

Golob J, Oskotsky T, Tang A, Roldan A, Chung V, Ha C Cell Rep Med. 2023; 5(1):101350.

PMID: 38134931 PMC: 10829755. DOI: 10.1016/j.xcrm.2023.101350.

MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies.

Minot S, Garb B, Roldan A, Tang A, Oskotsky T, Rosenthal C Cell Rep Methods. 2023; 3(11):100639.

PMID: 37939711 PMC: 10694490. DOI: 10.1016/j.crmeth.2023.100639.

A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing.

Kim H, Kim J, Choi J, Ahn K, Park D, Kim S Genomics Inform. 2023; 21(3):e40.

PMID: 37813636 PMC: 10584646. DOI: 10.5808/gi.23044.

References

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

Zheng Q, Bartow-McKenney C, Meisel J, Grice E . HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies. Genome Biol. 2018; 19(1):82. PMC: 6020470. DOI: 10.1186/s13059-018-1450-0. View

Berger S, Krompass D, Stamatakis A . Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol. 2011; 60(3):291-302. PMC: 3078422. DOI: 10.1093/sysbio/syr010. View

Mistry J, Finn R, Eddy S, Bateman A, Punta M . Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013; 41(12):e121. PMC: 3695513. DOI: 10.1093/nar/gkt263. View

Haas B, Gevers D, Earl A, Feldgarden M, Ward D, Giannoukos G . Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011; 21(3):494-504. PMC: 3044863. DOI: 10.1101/gr.112730.110. View

DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K . Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069-72. PMC: 1489311. DOI: 10.1128/AEM.03006-05. View

Wang Q, Garrity G, Tiedje J, Cole J . Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73(16):5261-7. PMC: 1950982. DOI: 10.1128/AEM.00062-07. View

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P . The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012; 41(Database issue):D590-6. PMC: 3531112. DOI: 10.1093/nar/gks1219. View

Kim M, Morrison M, Yu Z . Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J Microbiol Methods. 2010; 84(1):81-7. DOI: 10.1016/j.mimet.2010.10.020. View

10.

Caporaso J, Bittinger K, Bushman F, DeSantis T, Andersen G, Knight R . PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2009; 26(2):266-7. PMC: 2804299. DOI: 10.1093/bioinformatics/btp636. View

11.

Yang Z . Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol. 2011; 11(9):367-72. DOI: 10.1016/0169-5347(96)10041-0. View

12.

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

13.

Koljalg U, Nilsson R, Abarenkov K, Tedersoo L, Taylor A, Bahram M . Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 2013; 22(21):5271-7. DOI: 10.1111/mec.12481. View

14.

Edgar R, Haas B, Clemente J, Quince C, Knight R . UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27(16):2194-200. PMC: 3150044. DOI: 10.1093/bioinformatics/btr381. View

15.

He Y, Caporaso J, Jiang X, Sheng H, Huse S, Rideout J . Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome. 2015; 3:20. PMC: 4438525. DOI: 10.1186/s40168-015-0081-x. View

16.

Hasegawa M, Kishino H, Yano T . Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22(2):160-74. DOI: 10.1007/BF02101694. View

17.

Gojobori T, Li W, Graur D . Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol. 1982; 18(5):360-9. DOI: 10.1007/BF01733904. View

18.

Felsenstein J . Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981; 17(6):368-76. DOI: 10.1007/BF01734359. View

19.

Kopylova E, Noe L, Touzet H . SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012; 28(24):3211-7. DOI: 10.1093/bioinformatics/bts611. View

20.

Yilmaz P, Parfrey L, Yarza P, Gerken J, Pruesse E, Quast C . The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2013; 42(Database issue):D643-8. PMC: 3965112. DOI: 10.1093/nar/gkt1209. View