Taxonomic classification of metagenomic shotgun sequences with CARMA3.

Gerlach W, Stoye J (2011)
Nucleic Acids Res 39(14): e91.

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Abstract / Bemerkung
The vast majority of microbes are unculturable and thus cannot be sequenced by means of traditional methods. High-throughput sequencing techniques like 454 or Solexa-Illumina make it possible to explore those microbes by studying whole natural microbial communities and analysing their biological diversity as well as the underlying metabolic pathways. Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences. However, the taxonomic classification of metagenomic sequences from novel species without close homologue in the biological sequence databases poses a challenge due to the high number of wrong taxonomic predictions on lower taxonomic ranks. Here we present CARMA3, a new method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches. We show that our method makes fewer wrong taxonomic predictions (at the same sensitivity) than other BLAST-based methods. CARMA3 is freely accessible via the web application WebCARMA from http://webcarma.cebitec.uni-bielefeld.de.
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Nucleic Acids Res
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e91
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Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res. 2011;39(14):e91.
Gerlach, W., & Stoye, J. (2011). Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res, 39(14), e91. doi:10.1093/nar/gkr225
Gerlach, W., and Stoye, J. (2011). Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 39, e91.
Gerlach, W., & Stoye, J., 2011. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res, 39(14), p e91.
W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”, Nucleic Acids Res, vol. 39, 2011, pp. e91.
Gerlach, W., Stoye, J.: Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res. 39, e91 (2011).
Gerlach, Wolfgang, and Stoye, Jens. “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”. Nucleic Acids Res 39.14 (2011): e91.
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52 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.
Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB., PeerJ 7(), 2019
PMID: 30631651
The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation.
Liu C, Zhang Y, Ren Y, Wang H, Li S, Jiang F, Yin L, Qiao X, Zhang G, Qian W, Liu B, Fan W., Gigascience 7(9), 2018
PMID: 30107526
Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes.
Li X, Liang S, Xia Z, Qu J, Liu H, Liu C, Yang H, Wang J, Madsen L, Hou Y, Li J, Jia H, Kristiansen K, Xiao L., Gigascience 7(9), 2018
PMID: 30137359
The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids.
Huang P, Zhang Y, Xiao K, Jiang F, Wang H, Tang D, Liu D, Liu B, Liu Y, He X, Liu H, Liu X, Qing Z, Liu C, Huang J, Ren Y, Yun L, Yin L, Lin Q, Zeng C, Su X, Yuan J, Lin L, Hu N, Cao H, Huang S, Guo Y, Fan W, Zeng J., Microbiome 6(1), 2018
PMID: 30482240
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads.
Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Møller Aarestrup F, Sicheritz-Pontén T., PLoS One 12(5), 2017
PMID: 28467460
A Metagenomic Approach to Cyanobacterial Genomics.
Alvarenga DO, Fiore MF, Varani AM., Front Microbiol 8(), 2017
PMID: 28536564
A clinician's guide to microbiome analysis.
Claesson MJ, Clooney AG, O'Toole PW., Nat Rev Gastroenterol Hepatol 14(10), 2017
PMID: 28790452
Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms.
Teeling H, Fuchs BM, Bennke CM, Krüger K, Chafee M, Kappelmann L, Reintjes G, Waldmann J, Quast C, Glöckner FO, Lucas J, Wichels A, Gerdts G, Wiltshire KH, Amann RI., Elife 5(), 2016
PMID: 27054497
A reference gene catalogue of the pig gut microbiome.
Xiao L, Estellé J, Kiilerich P, Ramayo-Caldas Y, Xia Z, Feng Q, Liang S, Pedersen AØ, Kjeldsen NJ, Liu C, Maguin E, Doré J, Pons N, Le Chatelier E, Prifti E, Li J, Jia H, Liu X, Xu X, Ehrlich SD, Madsen L, Kristiansen K, Rogel-Gaillard C, Wang J., Nat Microbiol 1(), 2016
PMID: 27643971
Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample.
Stöveken J, Singh R, Kolkenbrock S, Zakrzewski M, Wibberg D, Eikmeyer FG, Pühler A, Schlüter A, Moerschbacher BM., J Biotechnol 201(), 2015
PMID: 25240439
Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream.
Liljeqvist M, Ossandon FJ, González C, Rajan S, Stell A, Valdes J, Holmes DS, Dopson M., FEMS Microbiol Ecol 91(4), 2015
PMID: 25764459
Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions.
Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A., Biotechnol Biofuels 8(), 2015
PMID: 25688290
An overview of malaria transmission from the perspective of Amazon Anopheles vectors.
Pimenta PF, Orfano AS, Bahia AC, Duarte AP, Ríos-Velásquez CM, Melo FF, Pessoa FA, Oliveira GA, Campos KM, Villegas LM, Rodrigues NB, Nacif-Pimenta R, Simões RC, Monteiro WM, Amino R, Traub-Cseko YM, Lima JB, Barbosa MG, Lacerda MV., Mem Inst Oswaldo Cruz 110(1), 2015
PMID: 25742262
CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S., PLoS One 10(4), 2015
PMID: 25884504
MLgsc: A Maximum-Likelihood General Sequence Classifier.
Junier T, Hervé V, Wunderlin T, Junier P., PLoS One 10(7), 2015
PMID: 26148002
A catalog of the mouse gut metagenome.
Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJ, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Wang J, Madsen L, Kristiansen K., Nat Biotechnol 33(10), 2015
PMID: 26414350
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.
Peabody MA, Van Rossum T, Lo R, Brinkman FS., BMC Bioinformatics 16(), 2015
PMID: 26537885
Effects of selective digestive decontamination (SDD) on the gut resistome.
Buelow E, Gonzalez TB, Versluis D, Oostdijk EA, Ogilvie LA, van Mourik MS, Oosterink E, van Passel MW, Smidt H, D'Andrea MM, de Been M, Jones BV, Willems RJ, Bonten MJ, van Schaik W., J Antimicrob Chemother 69(8), 2014
PMID: 24710024
Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.
Orellana LH, Rodriguez-R LM, Higgins S, Chee-Sanford JC, Sanford RA, Ritalahti KM, Löffler FE, Konstantinidis KT., MBio 5(3), 2014
PMID: 24895307
An introduction to the analysis of shotgun metagenomic data.
Sharpton TJ., Front Plant Sci 5(), 2014
PMID: 24982662
Accurate genome relative abundance estimation for closely related species in a metagenomic sample.
Sohn MB, An L, Pookhao N, Li Q., BMC Bioinformatics 15(), 2014
PMID: 25027647
Lambda: the local aligner for massive biological data.
Hauswedell H, Singer J, Reinert K., Bioinformatics 30(17), 2014
PMID: 25161219
TIPP: taxonomic identification and phylogenetic profiling.
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T., Bioinformatics 30(24), 2014
PMID: 25359891
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.
Langenkämper D, Goesmann A, Nattkemper TW., BMC Bioinformatics 15(), 2014
PMID: 25495116
Advances in computational analysis of metagenome sequences.
Davenport CF, Tümmler B., Environ Microbiol 15(1), 2013
PMID: 22882611
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A., J Biotechnol 167(2), 2013
PMID: 23026555
Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms.
Eikmeyer FG, Rademacher A, Hanreich A, Hennig M, Jaenicke S, Maus I, Wibberg D, Zakrzewski M, Pühler A, Klocke M, Schlüter A., Biotechnol Biofuels 6(1), 2013
PMID: 23557021
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ., BMC Bioinformatics 14 Suppl 5(), 2013
PMID: 23734710
Computational meta'omics for microbial community studies.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C., Mol Syst Biol 9(), 2013
PMID: 23670539
Environmental bio-monitoring with high-throughput sequencing.
Wang J, McLenachan PA, Biggs PJ, Winder LH, Schoenfeld BI, Narayan VV, Phiri BJ, Lockhart PJ., Brief Bioinform 14(5), 2013
PMID: 23677899
Pathoscope: species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE., Genome Res 23(10), 2013
PMID: 23843222
Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling.
Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A., J Biotechnol 167(3), 2013
PMID: 23880441
Analytical tools and databases for metagenomics in the next-generation sequencing era.
Kim M, Lee KH, Yoon SW, Kim BS, Chun J, Yi H., Genomics Inform 11(3), 2013
PMID: 24124405
MetaID: a novel method for identification and quantification of metagenomic samples.
Srinivasan SM, Guda C., BMC Genomics 14 Suppl 8(), 2013
PMID: 24564518
Analysis of the salivary microbiome using culture-independent techniques.
Lazarevic V, Whiteson K, Gaïa N, Gizard Y, Hernandez D, Farinelli L, Osterås M, François P, Schrenzel J., J Clin Bioinforma 2(), 2012
PMID: 22300522
Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom.
Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, Kassabgy M, Huang S, Mann AJ, Waldmann J, Weber M, Klindworth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann FD, Callies U, Gerdts G, Wichels A, Wiltshire KH, Glöckner FO, Schweder T, Amann R., Science 336(6081), 2012
PMID: 22556258
A comparative evaluation of sequence classification programs.
Bazinet AL, Cummings MP., BMC Bioinformatics 13(), 2012
PMID: 22574964
Metagenomic microbial community profiling using unique clade-specific marker genes.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C., Nat Methods 9(8), 2012
PMID: 22688413
Genometa--a fast and accurate classifier for short metagenomic shotgun reads.
Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhöfer M, Wolf S, Tümmler B, Ahlers V, Sprengel F., PLoS One 7(8), 2012
PMID: 22927906
A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.
Jiang H, An L, Lin SM, Feng G, Qiu Y., PLoS One 7(10), 2012
PMID: 23049702

29 References

Daten bereitgestellt von Europe PubMed Central.

TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW., BMC Bioinformatics 10(), 2009
PMID: 19210774
Compositional biases of bacterial genomes and evolutionary implications.
Karlin S, Mrazek J, Campbell AM., J. Bacteriol. 179(12), 1997
PMID: 9190805
Accurate phylogenetic classification of variable-length DNA fragments.
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I., Nat. Methods 4(1), 2006
PMID: 17179938
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner FO., BMC Bioinformatics 5(), 2004
PMID: 15507136
Profile hidden Markov models.
Eddy SR., Bioinformatics 14(9), 1998
PMID: 9918945
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Identification of protein coding regions by database similarity search.
Gish W, States DJ., Nat. Genet. 3(3), 1993
PMID: 8485583
Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
Gerlach W, Junemann S, Tille F, Goesmann A, Stoye J., BMC Bioinformatics 10(), 2009
PMID: 20021646
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA., BMC Bioinformatics 9(), 2008
PMID: 18803844
MEGAN analysis of metagenomic data.
Huson DH, Auch AF, Qi J, Schuster SC., Genome Res. 17(3), 2007
PMID: 17255551
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences.
Monzoorul Haque M, Ghosh TS, Komanduri D, Mande SS., Bioinformatics 25(14), 2009
PMID: 19439565
The Pfam protein families database.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19920124
Amino acid substitution matrices from protein blocks.
Henikoff S, Henikoff JG., Proc. Natl. Acad. Sci. U.S.A. 89(22), 1992
PMID: 1438297
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
MetaSim: a sequencing simulator for genomics and metagenomics.
Richter DC, Ott F, Auch AF, Schmid R, Huson DH., PLoS ONE 3(10), 2008
PMID: 18841204
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Diversity of the human intestinal microbial flora.
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA., Science 308(5728), 2005
PMID: 15831718
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.
Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV., Nucleic Acids Res. 30(19), 2002
PMID: 12364605
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
Krober M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehover P, Puhler A, Schluter A., J. Biotechnol. 142(1), 2009
PMID: 19480946
Exploring prokaryotic diversity in the genomic era.
Hugenholtz P., Genome Biol. 3(2), 2002
PMID: 11864374
16 S rDNA primers and the unbiased assessment of thermophile diversity.
Baker GC, Cowan DA., Biochem. Soc. Trans. 32(Pt 2), 2004
PMID: 15046575
A human gut microbial gene catalogue established by metagenomic sequencing.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J, Antolin M, Artiguenave F, Blottiere H, Borruel N, Bruls T, Casellas F, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, van de Guchte M, Guedon E, Haimet F, Jamet A, Juste C, Kaci G, Kleerebezem M, Knol J, Kristensen M, Layec S, Le Roux K, Leclerc M, Maguin E, Minardi RM, Oozeer R, Rescigno M, Sanchez N, Tims S, Torrejon T, Varela E, de Vos W, Winogradsky Y, Zoetendal E., Nature 464(7285), 2010
PMID: 20203603
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM., Science 331(6016), 2011
PMID: 21273488
Clostridium bartlettii sp. nov., isolated from human faeces.
Song YL, Liu CX, McTeague M, Summanen P, Finegold SM., Anaerobe 10(3), 2004
PMID: 16701516
Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces.
Duncan SH, Hold GL, Barcenilla A, Stewart CS, Flint HJ., Int. J. Syst. Evol. Microbiol. 52(Pt 5), 2002
PMID: 12361264
Substrate-driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch.
Scott KP, Martin JC, Chassard C, Clerget M, Potrykus J, Campbell G, Mayer CD, Young P, Rucklidge G, Ramsay AG, Flint HJ., Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1(), 2010
PMID: 20679207
Database resources of the National Center for Biotechnology Information.
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19910364

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