A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

Briefings in Bioinformatics

Volumn 13, Issue 1, 2012, Pages 107-121

  Sun, Yijun ^a   Cai, Yunpeng ^b   Huse, Susan M ^c   Knight, Rob ^d   Farmerie, William G ^b   Wang, Xiaoyu ^e   Mai, Volker ^e  

^a University of Florida   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c MARINE BIOLOGICAL LABORATORY   (United States)

^d UNIVERSITY OF COLORADO   (United States)

^e Emerging Pathogens Institute   (United States)

Author keywords

16S rRNA; Clustering; Human microbiome; Massive data; Microbial diversity estimation; Pyrosequencing; Taxonomy independent analysis

Indexed keywords

RNA 16S;

ALGORITHM; ARTICLE; BACTERIAL GENOME; BIOLOGY; BIOTA; CLUSTER ANALYSIS; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT;

ALGORITHMS; BIOTA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT;

EID: 84862928738     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr009     Document Type: Article

References (33)

1. Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 2007;5:e82.
2. Rothberg J, Leamon J. The development and impact of 454 sequencing. Nat Biotechnol 2008;26:1117-24.
3. Peterson J, Garges S, Giovanni M, et al. The NIH Human Microbiome Project. Genome Res 2009;19:2317-23.
4. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. JMol Biol 1990;215:403-10.
5. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009;37:D141-5.
6. Sun Y, Cai Y, Liu L, et al. ESPRIT: Estimating species richness using large collections of 16 S rRNA pyrosequences. Nucleic Acids Res 2009;37(10):e76.
7. Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein database. Bioinformatics 2001;17:282-3.
8. Cai Y, Sun Y. ESPRIT-Tree: taxonomy independent analysis of millions of 16 S rRNA pyrosequences in quasilinear computational time. Technical Report.
9. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75(23):7537-41.
10. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010;26(19):2460-1.
11. Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 2005;71: 1501-6.
12. Huse SM, Welch DM, Morrison HG, et al. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. EnvironMicrobiol 2009;12(7):1889-98.
13. White JR, Navlakha S, Nagarajan N, et al. Alignment and clustering of pylogenetic markers - implications for microbial diversity studies. BMC Bioinfomatics 2010;11(1):152.
14. Sun Y, Cai Y, Mai V, et al. Advanced computational algorithms for microbial community analysis using massive 16 S rRNA sequence data. Nucleic Acids Res 2010;38(22): e205.
15. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME: allows analysis of high-throughput community sequencing data. NatMethods 2010;7:335-6.
16. Giongo A, Crabb DB, Davis-Richardson AG, et al. PANGEA: pipeline for analysis of next generation amplicons. ISMEJ 2010;4(7):852-61.
17. Studholme C, Hill DLG, Hawkes DJ. An overlap invariant entropy measure of 3D medical image alignment. Pattern Recognition 1999;32(1):71-86.
18. Van Rijsbergen CJ. Information Retrieval. 2nd edn. London: Butterworth-Heinemann, 1979.
19. Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". ProcNatl Acad SciUSA 2006;103:12115-20.
20. Keijser BJ, Zaura E, Huse SM, et al. Pyrosequencing analysis of the oral microflora of healthy adults. JDentRes 2008;87: 1016-20.
21. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. NucleicAcids Res 2004; 32:1792-7.
22. Katoh K, Kuma K, Toh H, et al. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005;33:511-8.
23. DeSantis TZ, Hugenholtz P, Keller K, et al. NAST: a multiple sequence alignment server for comparative analysis of 16 S rRNA genes. Nucleic Acids Res 2006;34:W394-9.
24. Schloss PD. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16 S rRNA gene-based studies. PLoS Comput Biol 2010;6(7):e1000844.
25. Ward JH. Hierarchical grouping to optimize an objective function. JAmStatAssoc 1963;58(301):236-44.
26. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457(7228):480-4.
27. Zhang H, DiBaise JK, Zuccolo A, et al. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 2009;106:2365-70.
28. Ward BB. How many species of prokaryotes are there? ProcNatl Acad SciUSA 2002;99:10234-6.
29. Quince C, Lanzén A, Curtis TP, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. NatMethods 2009;6(9):639-41.
30. Turnbaugh PJ, Ley RE, Hamady M, et al. The human microbiome project. Nature 2007;449:804-10.
31. Claesson MJ, Cusack S, O'Sullivan O, et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci USA; doi:10:1073/ pnas.1000097107.
32. Li Ellen. Effect of Crohn's Disease Risk Alleles on Enteric Microbiota. NIH project No. 1UH2DK083994-01. NCBI accession NO. SRX021353 and SRX021354.
33. Frank DNSt, Amand AL, Feldman RA, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. ProcNatl Acad SciUSA 104(34):13780-5.