Nucleic Acids Research

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Published online 25 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 4 1363-1371
© 2004 Oxford University Press

ARB: a software environment for sequence data

Wolfgang Ludwig^*, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier¹, Yadhukumar, Arno Buchner, Tina Lai, Susanne Steppi, Gangolf Jobb¹, Wolfram Förster¹, Igor Brettske, Stefan Gerber, Anton W. Ginhart¹, Oliver Gross, Silke Grumann¹, Stefan Hermann¹, Ralf Jost¹, Andreas König¹, Thomas Liss¹, Ralph Lüßmann¹, Michael May¹, Björn Nonhoff¹, Boris Reichel¹, Robert Strehlow¹, Alexandros Stamatakis¹, Norbert Stuckmann¹, Alexander Vilbig¹, Michael Lenke¹, Thomas Ludwig², Arndt Bode¹ and Karl-Heinz Schleifer

Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany ¹ Lehrstuhl für Rechnertechnik und Rechnerorganisation, Parallelrechnerarchitektur, Technische Universität München, D-85748 Garching, Germany ² Institut für Informatik, Ruprecht-Karls-Universität Heidelberg, D-69120 Heidelberg, Germany

*To whom correspondence should be addressed. Tel: +8161 71 5451; Fax: +8161 71 5475; Email: ludwig{at}mikro.biologie.tu-muenchen.de

The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

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				C. Boeckaert, B. Vlaeminck, V. Fievez, L. Maignien, J. Dijkstra, and N. Boon Accumulation of trans C18:1 Fatty Acids in the Rumen after Dietary Algal Supplementation Is Associated with Changes in the Butyrivibrio Community Appl. Envir. Microbiol., November 15, 2008; 74(22): 6923 - 6930. [Abstract] [Full Text] [PDF]

				A. B. de Menezes, R. J. Lockhart, M. J. Cox, H. E. Allison, and A. J. McCarthy Cellulose Degradation by Micromonosporas Recovered from Freshwater Lakes and Classification of These Actinomycetes by DNA Gyrase B Gene Sequencing Appl. Envir. Microbiol., November 15, 2008; 74(22): 7080 - 7084. [Abstract] [Full Text] [PDF]

				Y. Sekiguchi, M. Muramatsu, H. Imachi, T. Narihiro, A. Ohashi, H. Harada, S. Hanada, and Y. Kamagata Thermodesulfovibrio aggregans sp. nov. and Thermodesulfovibrio thiophilus sp. nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus Thermodesulfovibrio Int J Syst Evol Microbiol, November 1, 2008; 58(11): 2541 - 2548. [Abstract] [Full Text] [PDF]

				P. Kampfer, B. Huber, S. Buczolits, K. Thummes, I. Grun-Wollny, and H.-J. Busse Streptomyces specialis sp. nov. Int J Syst Evol Microbiol, November 1, 2008; 58(11): 2602 - 2606. [Abstract] [Full Text] [PDF]

				E G Zoetendal, M Rajilic-Stojanovic, and W M de Vos High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota Gut, November 1, 2008; 57(11): 1605 - 1615. [Abstract] [Full Text] [PDF]

				A. R. Rowe, B. J. Lazar, R. M. Morris, and R. E. Richardson Characterization of the Community Structure of a Dechlorinating Mixed Culture and Comparisons of Gene Expression in Planktonic and Biofloc-Associated "Dehalococcoides" and Methanospirillum Species Appl. Envir. Microbiol., November 1, 2008; 74(21): 6709 - 6719. [Abstract] [Full Text] [PDF]

				C. L. Zhang, Q. Ye, Z. Huang, W. Li, J. Chen, Z. Song, W. Zhao, C. Bagwell, W. P. Inskeep, C. Ross, et al. Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs Appl. Envir. Microbiol., October 15, 2008; 74(20): 6417 - 6426. [Abstract] [Full Text] [PDF]

				A. R. Oka, C. D. Phelps, L. M. McGuinness, A. Mumford, L. Y. Young, and L. J. Kerkhof Identification of Critical Members in a Sulfidogenic Benzene-Degrading Consortium by DNA Stable Isotope Probing Appl. Envir. Microbiol., October 15, 2008; 74(20): 6476 - 6480. [Abstract] [Full Text] [PDF]

				C. Baschien, W. Manz, T. R. Neu, L. Marvanova, and U. Szewzyk In Situ Detection of Freshwater Fungi in an Alpine Stream by New Taxon-Specific Fluorescence In Situ Hybridization Probes Appl. Envir. Microbiol., October 15, 2008; 74(20): 6427 - 6436. [Abstract] [Full Text] [PDF]

				K. Mori, M. Sunamura, K. Yanagawa, J.-i. Ishibashi, Y. Miyoshi, T. Iino, K.-i. Suzuki, and T. Urabe First Cultivation and Ecological Investigation of a Bacterium Affiliated with the Candidate Phylum OP5 from Hot Springs Appl. Envir. Microbiol., October 15, 2008; 74(20): 6223 - 6229. [Abstract] [Full Text] [PDF]

				H. Imachi, S. Sakai, H. Hirayama, S. Nakagawa, T. Nunoura, K. Takai, and K. Horikoshi Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney Int J Syst Evol Microbiol, October 1, 2008; 58(10): 2258 - 2265. [Abstract] [Full Text] [PDF]

				S. Takii, S. Hanada, Y. Hase, H. Tamaki, Y. Uyeno, Y. Sekiguchi, and K. Matsuura Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids Int J Syst Evol Microbiol, October 1, 2008; 58(10): 2433 - 2438. [Abstract] [Full Text] [PDF]

				F. Godoy-Vitorino, R. E. Ley, Z. Gao, Z. Pei, H. Ortiz-Zuazaga, L. R. Pericchi, M. A. Garcia-Amado, F. Michelangeli, M. J. Blaser, J. I. Gordon, et al. Bacterial Community in the Crop of the Hoatzin, a Neotropical Folivorous Flying Bird Appl. Envir. Microbiol., October 1, 2008; 74(19): 5905 - 5912. [Abstract] [Full Text] [PDF]

				Z. Liu, T. Z. DeSantis, G. L. Andersen, and R. Knight Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Nucleic Acids Res., October 1, 2008; 36(18): e120 - e120. [Abstract] [Full Text] [PDF]

				S. Schmitz-Esser, E. R. Toenshoff, S. Haider, E. Heinz, V. M. Hoenninger, M. Wagner, and M. Horn Diversity of Bacterial Endosymbionts of Environmental Acanthamoeba Isolates Appl. Envir. Microbiol., September 15, 2008; 74(18): 5822 - 5831. [Abstract] [Full Text] [PDF]

				S. Behrens, M. F. Azizian, P. J. McMurdie, A. Sabalowsky, M. E. Dolan, L. Semprini, and A. M. Spormann Monitoring Abundance and Expression of "Dehalococcoides" Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column Appl. Envir. Microbiol., September 15, 2008; 74(18): 5695 - 5703. [Abstract] [Full Text] [PDF]

				M. C. Gutierrez, A. M. Castillo, E. Pagaling, S. Heaphy, M. Kamekura, Y. Xue, Y. Ma, D. A. Cowan, B. E. Jones, W. D. Grant, et al. Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2031 - 2035. [Abstract] [Full Text] [PDF]

				N. Pinel, S. K. Davidson, and D. A. Stahl Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny) Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2147 - 2157. [Abstract] [Full Text] [PDF]

				M. Fahrbach, J. Kuever, M. Remesch, B. E. Huber, P. Kampfer, W. Dott, and J. Hollender Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2215 - 2223. [Abstract] [Full Text] [PDF]

				M. S. Elshahed, N. H. Youssef, A. M. Spain, C. Sheik, F. Z. Najar, L. O. Sukharnikov, B. A. Roe, J. P. Davis, P. D. Schloss, V. L. Bailey, et al. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere Appl. Envir. Microbiol., September 1, 2008; 74(17): 5422 - 5428. [Abstract] [Full Text] [PDF]

				S. Schmitz-Esser, I. Haferkamp, S. Knab, T. Penz, M. Ast, C. Kohl, M. Wagner, and M. Horn Lawsonia intracellularis Contains a Gene Encoding a Functional Rickettsia-Like ATP/ADP Translocase for Host Exploitation J. Bacteriol., September 1, 2008; 190(17): 5746 - 5752. [Abstract] [Full Text] [PDF]

				C. Gescher, K. Metfies, S. Frickenhaus, B. Knefelkamp, K. H. Wiltshire, and L. K. Medlin Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray Appl. Envir. Microbiol., September 1, 2008; 74(17): 5305 - 5316. [Abstract] [Full Text] [PDF]

				P. Junier, O.-S. Kim, O. Hadas, J. F. Imhoff, and K.-P. Witzel Evaluation of PCR Primer Selectivity and Phylogenetic Specificity by Using Amplification of 16S rRNA Genes from Betaproteobacterial Ammonia-Oxidizing Bacteria in Environmental Samples Appl. Envir. Microbiol., August 15, 2008; 74(16): 5231 - 5236. [Abstract] [Full Text] [PDF]

				C. R. Jackson and A. Q. Weeks Influence of Particle Size on Bacterial Community Structure in Aquatic Sediments as Revealed by 16S rRNA Gene Sequence Analysis Appl. Envir. Microbiol., August 15, 2008; 74(16): 5237 - 5240. [Abstract] [Full Text] [PDF]

				H. Rehrauer, S. Schonmann, L. Eberl, and R. Schlapbach PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays Bioinformatics, August 15, 2008; 24(16): i83 - i89. [Abstract] [Full Text] [PDF]

				J. A. Bryant, C. Lamanna, H. Morlon, A. J. Kerkhoff, B. J. Enquist, and J. L. Green Colloquium Paper: Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity PNAS, August 12, 2008; 105(Supplement_1): 11505 - 11511. [Abstract] [Full Text] [PDF]

				C.-C. Young, A. B. Arun, P. Kampfer, H.-J. Busse, W.-A. Lai, W.-M. Chen, F.-T. Shen, and P. D. Rekha Sphingobium rhizovicinum sp. nov., isolated from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle Int J Syst Evol Microbiol, August 1, 2008; 58(8): 1801 - 1806. [Abstract] [Full Text] [PDF]

				I. Kaesler, I. Graeber, M. S. Borchert, T. Pape, R. Dieckmann, H. von Dohren, P. Nielsen, R. Lurz, W. Michaelis, and U. Szewzyk Spongiispira norvegica gen. nov., sp. nov., a marine bacterium isolated from the boreal sponge Isops phlegraei Int J Syst Evol Microbiol, August 1, 2008; 58(8): 1815 - 1820. [Abstract] [Full Text] [PDF]

				K. Mori and K.-i. Suzuki Thiofaba tepidiphila gen. nov., sp. nov., a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the Gammaproteobacteria isolated from a hot spring Int J Syst Evol Microbiol, August 1, 2008; 58(8): 1885 - 1891. [Abstract] [Full Text] [PDF]

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