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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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Streptomyces axinellae sp. nov., isolated from the Mediterranean sponge Axinella polypoides (Porifera)
Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1433 - 1437.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
F. D. Andreote, W. L. de Araujo, J. L. de Azevedo, J. D. van Elsas, U. N. da Rocha, and L. S. van Overbeek
Endophytic Colonization of Potato (Solanum tuberosum L.) by a Novel Competent Bacterial Endophyte, Pseudomonas putida Strain P9, and Its Effect on Associated Bacterial Communities
Appl. Envir. Microbiol., June 1, 2009; 75(11): 3396 - 3406.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
M. Stieglmeier, R. Wirth, G. Kminek, and C. Moissl-Eichinger
Cultivation of Anaerobic and Facultatively Anaerobic Bacteria from Spacecraft-Associated Clean Rooms
Appl. Envir. Microbiol., June 1, 2009; 75(11): 3484 - 3491.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
P. F. Andeer, D. A. Stahl, N. C. Bruce, and S. E. Strand
Lateral Transfer of Genes for Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX) Degradation
Appl. Envir. Microbiol., May 15, 2009; 75(10): 3258 - 3262.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
M. Herrmann, A. M. Saunders, and A. Schramm
Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments
Appl. Envir. Microbiol., May 15, 2009; 75(10): 3127 - 3136.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
H. Cadillo-Quiroz, J. B. Yavitt, and S. H. Zinder
Methanosphaerula palustris gen. nov., sp. nov., a hydrogenotrophic methanogen isolated from a minerotrophic fen peatland
Int J Syst Evol Microbiol, May 1, 2009; 59(5): 928 - 935.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
E. Jumas-Bilak, L. Roudiere, and H. Marchandin
Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'
Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1028 - 1035.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
D. B. Johnson, P. Bacelar-Nicolau, N. Okibe, A. Thomas, and K. B. Hallberg
Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria
Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1082 - 1089.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
A. F. Yassin
Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma
Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1148 - 1152.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
D. H. Choi, G. I. Zhang, J. H. Noh, W.-S. Kim, and B. C. Cho
Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture
Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1167 - 1172.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
C. Sanchez-Porro, V. Gallego, H.-J. Busse, P. Kampfer, and A. Ventosa
Transfer of Teichococcus ludipueritiae and Muricoccus roseus to the genus Roseomonas, as Roseomonas ludipueritiae comb. nov. and Roseomonas rosea comb. nov., respectively, and emended description of the genus Roseomonas
Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1193 - 1198.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
S. E. Morales and W. E. Holben
Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis
Appl. Envir. Microbiol., May 1, 2009; 75(9): 2677 - 2683.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
O. Geissinger, D. P. R. Herlemann, E. Morschel, U. G. Maier, and A. Brune
The Ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum
Appl. Envir. Microbiol., May 1, 2009; 75(9): 2831 - 2840.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
D. P. R. Herlemann, O. Geissinger, W. Ikeda-Ohtsubo, V. Kunin, H. Sun, A. Lapidus, P. Hugenholtz, and A. Brune
Genomic Analysis of "Elusimicrobium minutum," the First Cultivated Representative of the Phylum "Elusimicrobia" (Formerly Termite Group 1)
Appl. Envir. Microbiol., May 1, 2009; 75(9): 2841 - 2849.
[Abstract] [Full Text] [PDF]

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 Clin. Chem.Home page
J. F. Petrosino, S. Highlander, R. A. Luna, R. A. Gibbs, and J. Versalovic
Metagenomic Pyrosequencing and Microbial Identification
Clin. Chem., May 1, 2009; 55(5): 856 - 866.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
R. L. Hansman, S. Griffin, J. T. Watson, E. R. M. Druffel, A. E. Ingalls, A. Pearson, and L. I. Aluwihare
The radiocarbon signature of microorganisms in the mesopelagic ocean
PNAS, April 21, 2009; 106(16): 6513 - 6518.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
P. N. Evans, L. A. Hinds, L. I. Sly, C. S. McSweeney, M. Morrison, and A.-D. G. Wright
Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)
Appl. Envir. Microbiol., April 15, 2009; 75(8): 2598 - 2602.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
M. Goberna, H. Insam, and I. H. Franke-Whittle
Effect of Biowaste Sludge Maturation on the Diversity of Thermophilic Bacteria and Archaea in an Anaerobic Reactor
Appl. Envir. Microbiol., April 15, 2009; 75(8): 2566 - 2572.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
L. Speirs, T. Nittami, S. McIlroy, S. Schroeder, and R. J. Seviour
Filamentous Bacterium Eikelboom Type 0092 in Activated Sludge Plants in Australia Is a Member of the Phylum Chloroflexi
Appl. Envir. Microbiol., April 15, 2009; 75(8): 2446 - 2452.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
R. Sekar, L. T. Kaczmarsky, and L. L. Richardson
Effect of Freezing on PCR Amplification of 16S rRNA Genes from Microbes Associated with Black Band Disease of Corals
Appl. Envir. Microbiol., April 15, 2009; 75(8): 2581 - 2584.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
K. W. Finster, R. A. Herbert, K. U. Kjeldsen, P. Schumann, and B. A. Lomstein
Demequina lutea sp. nov., isolated from a high Arctic permafrost soil
Int J Syst Evol Microbiol, April 1, 2009; 59(4): 649 - 653.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
V. M. Gorlenko, I. A. Bryantseva, S. Rabold, T. P. Tourova, D. Rubtsova, E. Smirnova, V. Thiel, and J. F. Imhoff
Ectothiorhodospira variabilis sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes
Int J Syst Evol Microbiol, April 1, 2009; 59(4): 658 - 664.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
S.-Y. Lin, C. C. Young, H. Hupfer, C. Siering, A. B. Arun, W.-M. Chen, W.-A. Lai, F.-T. Shen, P. D. Rekha, and A. F. Yassin
Azospirillum picis sp. nov., isolated from discarded tar
Int J Syst Evol Microbiol, April 1, 2009; 59(4): 761 - 765.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
H. Imachi, S. Sakai, H. Nagai, T. Yamaguchi, and K. Takai
Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field
Int J Syst Evol Microbiol, April 1, 2009; 59(4): 800 - 805.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
K. W. Finster, R. A. Herbert, and B. A. Lomstein
Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma
Int J Syst Evol Microbiol, April 1, 2009; 59(4): 839 - 844.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
C. E. Robertson, J. R. Spear, J. K. Harris, and N. R. Pace
Diversity and Stratification of Archaea in a Hypersaline Microbial Mat
Appl. Envir. Microbiol., April 1, 2009; 75(7): 1801 - 1810.
[Abstract] [Full Text] [PDF]

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 J. Clin. Microbiol.Home page
T. K. Kim, S. M. Thomas, M. Ho, S. Sharma, C. I. Reich, J. A. Frank, K. M. Yeater, D. R. Biggs, N. Nakamura, R. Stumpf, et al.
Heterogeneity of Vaginal Microbial Communities within Individuals
J. Clin. Microbiol., April 1, 2009; 47(4): 1181 - 1189.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
B. J. Baker, G. W. Tyson, L. Goosherst, and J. F. Banfield
Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities
Appl. Envir. Microbiol., April 1, 2009; 75(7): 2192 - 2199.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
J. S. Blum, S. Han, B. Lanoil, C. Saltikov, B. Witte, F. R. Tabita, S. Langley, T. J. Beveridge, L. Jahnke, and R. S. Oremland
Ecophysiology of "Halarsenatibacter silvermanii" Strain SLAS-1T, gen. nov., sp. nov., a Facultative Chemoautotrophic Arsenate Respirer from Salt-Saturated Searles Lake, California
Appl. Envir. Microbiol., April 1, 2009; 75(7): 1950 - 1960.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
B. K. Harrison, H. Zhang, W. Berelson, and V. J. Orphan
Variations in Archaeal and Bacterial Diversity Associated with the Sulfate-Methane Transition Zone in Continental Margin Sediments (Santa Barbara Basin, California)
Appl. Envir. Microbiol., March 15, 2009; 75(6): 1487 - 1499.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
M. Ast, A. Gruber, S. Schmitz-Esser, H. E. Neuhaus, P. G. Kroth, M. Horn, and I. Haferkamp
Diatom plastids depend on nucleotide import from the cytosol
PNAS, March 3, 2009; 106(9): 3621 - 3626.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
A. F. Yassin, H. Hupfer, H.-P. Klenk, and C. Siering
Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006
Int J Syst Evol Microbiol, March 1, 2009; 59(3): 454 - 459.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
T. Katayama, T. Kato, M. Tanaka, T. A. Douglas, A. Brouchkov, M. Fukuda, F. Tomita, and K. Asano
Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge
Int J Syst Evol Microbiol, March 1, 2009; 59(3): 482 - 486.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
M. Arenas, P. I. Banon, J. L. Copa-Patino, C. Sanchez-Porro, A. Ventosa, and J. Soliveri
Halomonas ilicicola sp. nov., a moderately halophilic bacterium isolated from a saltern
Int J Syst Evol Microbiol, March 1, 2009; 59(3): 578 - 582.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
C. Kellermann and C. Griebler
Thiobacillus thiophilus sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments
Int J Syst Evol Microbiol, March 1, 2009; 59(3): 583 - 588.
[Abstract] [Full Text] [PDF]

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 MycologiaHome page
D. Persoh, M. Melcher, K. Graf, J. Fournier, M. Stadler, and G. Rambold
Molecular and morphological evidence for the delimitation of Xylaria hypoxylon
Mycologia, March 1, 2009; 101(2): 256 - 268.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
B. H. G. W. van Houten, R. J. W. Meulepas, W. van Doesburg, H. Smidt, G. Muyzer, and A. J. M. Stams
Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 229 - 233.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
S. P. Glaeser, P. Kampfer, H.-J. Busse, S. Langer, and J. Glaeser
Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 323 - 330.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
J. Wiese, V. Thiel, A. Gartner, R. Schmaljohann, and J. F. Imhoff
Kiloniella laminariae gen. nov., sp. nov., an alphaproteobacterium from the marine macroalga Laminaria saccharina
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 350 - 356.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
I. S. Kulichevskaya, O. I. Baulina, P. L. E. Bodelier, W. I. C. Rijpstra, J. S. S. Damste, and S. N. Dedysh
Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 357 - 364.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
J. Pinhassi, M. J. Pujalte, J. Pascual, J. M. Gonzalez, I. Lekunberri, C. Pedros-Alio, and D. R. Arahal
Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 373 - 377.
[Abstract] [Full Text] [PDF]

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 Int. J. Syst. Evol. Microbiol.Home page
C. Sanchez-Porro, R. R. de la Haba, N. Soto-Ramirez, M. C. Marquez, R. Montalvo-Rodriguez, and A. Ventosa
Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov.
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 397 - 405.
[Abstract] [Full Text] [PDF]


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