ESPRIT: Estimating Species Richness Using Large Collections of 16S RRNA Pyrosequences

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2009 May 7

PMID 19417062

Citations 120

Authors

Yijun Sun

Yunpeng Cai

Li Liu

Fahong Yu

Michael L Farrell

William McKendree

William Farmerie

Affiliations

Soon will be listed here.

Abstract

Recent metagenomics studies of environmental samples suggested that microbial communities are much more diverse than previously reported, and deep sequencing will significantly increase the estimate of total species diversity. Massively parallel pyrosequencing technology enables ultra-deep sequencing of complex microbial populations rapidly and inexpensively. However, computational methods for analyzing large collections of 16S ribosomal sequences are limited. We proposed a new algorithm, referred to as ESPRIT, which addresses several computational issues with prior methods. We developed two versions of ESPRIT, one for personal computers (PCs) and one for computer clusters (CCs). The PC version is used for small- and medium-scale data sets and can process several tens of thousands of sequences within a few minutes, while the CC version is for large-scale problems and is able to analyze several hundreds of thousands of reads within one day. Large-scale experiments are presented that clearly demonstrate the effectiveness of the newly proposed algorithm. The source code and user guide are freely available at http://www.biotech.ufl.edu/people/sun/esprit.html.

Citing Articles

A toolbox of machine learning software to support microbiome analysis.

Marcos-Zambrano L, Lopez-Molina V, Bakir-Gungor B, Frohme M, Karaduzovic-Hadziabdic K, Klammsteiner T Front Microbiol. 2023; 14:1250806.

PMID: 38075858 PMC: 10704913. DOI: 10.3389/fmicb.2023.1250806.

Unique genotypic features of HIV-1 C gp41 membrane proximal external region variants during pregnancy relate to mother-to-child transmission via breastfeeding.

Yin L, Chang K, Nakamura K, Kuhn L, Aldrovandi G, Goodenow M J Clin Pediatr Neonatol. 2021; 1(1):9-20.

PMID: 34553192 PMC: 8454918. DOI: 10.46439/pediatrics.1.003.

Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization.

Torrell H, Cereto-Massague A, Kazakova P, Garcia L, Palacios H, Canela N Biomolecules. 2021; 11(7).

PMID: 34356622 PMC: 8301799. DOI: 10.3390/biom11070999.

An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies.

Gao B, Chi L, Zhu Y, Shi X, Tu P, Li B Biomolecules. 2021; 11(4).

PMID: 33918473 PMC: 8066849. DOI: 10.3390/biom11040530.

Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences.

Wei Z, Zhang X, Cao M, Liu F, Qian Y, Zhang S Front Microbiol. 2021; 12:644012.

PMID: 33841367 PMC: 8024490. DOI: 10.3389/fmicb.2021.644012.

References

Keijser B, Zaura E, Huse S, van der Vossen J, Schuren F, Montijn R . Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res. 2008; 87(11):1016-20. DOI: 10.1177/154405910808701104. View

Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy A . Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007; 4(6):495-500. DOI: 10.1038/nmeth1043. View

Eisen J . Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 2007; 5(3):e82. PMC: 1821061. DOI: 10.1371/journal.pbio.0050082. View

Margulies M, Egholm M, Altman W, Attiya S, Bader J, Bemben L . Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437(7057):376-80. PMC: 1464427. DOI: 10.1038/nature03959. View

Huber J, Mark Welch D, Morrison H, Huse S, Neal P, Butterfield D . Microbial population structures in the deep marine biosphere. Science. 2007; 318(5847):97-100. DOI: 10.1126/science.1146689. View

Edgar R . Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res. 2004; 32(1):380-5. PMC: 373290. DOI: 10.1093/nar/gkh180. View

Karlin S, Mrazek J, Campbell A . Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol. 1997; 179(12):3899-913. PMC: 179198. DOI: 10.1128/jb.179.12.3899-3913.1997. View

Rothberg J, Leamon J . The development and impact of 454 sequencing. Nat Biotechnol. 2008; 26(10):1117-24. DOI: 10.1038/nbt1485. View

Cole J, Wang Q, Cardenas E, Fish J, Chai B, Farris R . The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2008; 37(Database issue):D141-5. PMC: 2686447. DOI: 10.1093/nar/gkn879. View

10.

DeSantis Jr T, Hugenholtz P, Keller K, Brodie E, Larsen N, Piceno Y . NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006; 34(Web Server issue):W394-9. PMC: 1538769. DOI: 10.1093/nar/gkl244. View

11.

Roesch L, Fulthorpe R, Riva A, Casella G, Hadwin A, Kent A . Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007; 1(4):283-90. PMC: 2970868. DOI: 10.1038/ismej.2007.53. View

12.

Dalevi D, Dubhashi D, Hermansson M . Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures. Bioinformatics. 2006; 22(5):517-22. DOI: 10.1093/bioinformatics/btk029. View

13.

Gans J, Wolinsky M, Dunbar J . Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 2005; 309(5739):1387-90. DOI: 10.1126/science.1112665. View

14.

Schloss P, Handelsman J . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005; 71(3):1501-6. PMC: 1065144. DOI: 10.1128/AEM.71.3.1501-1506.2005. View

15.

Yu Y, Breitbart M, McNairnie P, Rohwer F . FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics. 2006; 7:57. PMC: 1386709. DOI: 10.1186/1471-2105-7-57. View

16.

Hurlbert S . The Nonconcept of Species Diversity: A Critique and Alternative Parameters. Ecology. 2017; 52(4):577-586. DOI: 10.2307/1934145. View

17.

Sogin M, Morrison H, Huber J, Welch D, Huse S, Neal P . Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A. 2006; 103(32):12115-20. PMC: 1524930. DOI: 10.1073/pnas.0605127103. View

18.

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View

19.

Borneman J, Triplett E . Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol. 1997; 63(7):2647-53. PMC: 168563. DOI: 10.1128/aem.63.7.2647-2653.1997. View

20.

Karlin S, Burge C . Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 1995; 11(7):283-90. DOI: 10.1016/s0168-9525(00)89076-9. View