Nucleic Acids Research, Vol 25, Issue 1 109-111, Copyright © 1997 by Oxford University Press
BL Maidak, GJ Olsen, N Larsen, R Overbeek, MJ McCaughey and CR Woese
The Ribosomal Database Project (RDP) is a curated database that offers
ribosome-related data, analysis services and associated computer programs.
The offerings include phylogenetically ordered alignments of ribosomal RNA
(rRNA) sequences, derived phylogenetic trees, rRNA secondary structure
diagrams, and various software for handling, analyzing and displaying
alignments and trees. The data are available via anonymous FTP
(rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher
(rdpgopher.life.uiuc.edu) and WWW (http://rdpwww.life.uiuc.edu/ ). The
electronic mail and WWW servers provide ribosomal probe checking,
approximate phylogenetic placement of user-submitted sequences, screening
for possible chimeric rRNA sequences, automated alignment, and a suggested
placement of an unknown sequence on an existing phylogenetic tree.
ARTICLES
The RDP (Ribosomal Database Project)
Department of Microbiology, University of Illinois, B103 C&LSL, 601 South Goodwin Avenue, Urbana, IL 61801, USA. b-maidak@uiuc.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. R. Carlsohn, I. Groth, H.-P. Saluz, P. Schumann, and E. Stackebrandt Fodinicola feengrottensis gen. nov., sp. nov., an actinomycete isolated from a medieval mine Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1529 - 1536. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Bouchet, H. Huot, and R. Goldstein Molecular Genetic Basis of Ribotyping Clin. Microbiol. Rev., April 1, 2008; 21(2): 262 - 273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. M. Toth, P. Schumann, A. K. Borsodi, Z. Keki, A. L. Kovacs, and K. Marialigeti Wohlfahrtiimonas chitiniclastica gen. nov., sp. nov., a new gammaproteobacterium isolated from Wohlfahrtia magnifica (Diptera: Sarcophagidae) Int J Syst Evol Microbiol, April 1, 2008; 58(4): 976 - 981. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. S. Gomez-Conde, J. Garcia, S. Chamorro, P. Eiras, P. G. Rebollar, A. Perez de Rozas, I. Badiola, C. de Blas, and R. Carabano Neutral detergent-soluble fiber improves gut barrier function in twenty-five-day-old weaned rabbits J Anim Sci, December 1, 2007; 85(12): 3313 - 3321. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Satoh, Y. Miura, I. Tsushima, and S. Okabe Layered Structure of Bacterial and Archaeal Communities and Their In Situ Activities in Anaerobic Granules Appl. Envir. Microbiol., November 15, 2007; 73(22): 7300 - 7307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. R. Brown, R. F. Whitcomb, and J. M. Bradbury Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes) Int J Syst Evol Microbiol, November 1, 2007; 57(11): 2703 - 2719. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Carlsohn, I. Groth, C. Sproer, B. Schutze, H.-P. Saluz, T. Munder, and E. Stackebrandt Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine Int J Syst Evol Microbiol, September 1, 2007; 57(9): 1943 - 1947. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kindaichi, I. Tsushima, Y. Ogasawara, M. Shimokawa, N. Ozaki, H. Satoh, and S. Okabe In Situ Activity and Spatial Organization of Anaerobic Ammonium-Oxidizing (Anammox) Bacteria in Biofilms Appl. Envir. Microbiol., August 1, 2007; 73(15): 4931 - 4939. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. S. Somvanshi, E. Lang, P. Schumann, R. Pukall, R. M. Kroppenstedt, S. Ganguly, and E. Stackebrandt Leucobacter iarius sp. nov., in the family Microbacteriaceae Int J Syst Evol Microbiol, April 1, 2007; 57(4): 682 - 686. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Maszenan, H. L. Jiang, J.-H. Tay, P. Schumann, R. M. Kroppenstedt, and S. T.-L. Tay Granulicoccus phenolivorans gen. nov., sp. nov., a Gram-positive, phenol-degrading coccus isolated from phenol-degrading aerobic granules Int J Syst Evol Microbiol, April 1, 2007; 57(4): 730 - 737. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Lang, B. Griese, C. Sproer, P. Schumann, M. Steffen, and S. Verbarg Characterization of 'Pseudomonas azelaica' DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym Int J Syst Evol Microbiol, April 1, 2007; 57(4): 878 - 882. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Stackebrandt, E. Lang, S. Cousin, O. Pauker, E. Brambilla, R. Kroppenstedt, and H. Lunsdorf Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria Int J Syst Evol Microbiol, March 1, 2007; 57(3): 639 - 645. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Satoh, Y. Nakamura, and S. Okabe Influences of Infaunal Burrows on the Community Structure and Activity of Ammonia-Oxidizing Bacteria in Intertidal Sediments Appl. Envir. Microbiol., February 15, 2007; 73(4): 1341 - 1348. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Okabe, M. Odagiri, T. Ito, and H. Satoh Succession of Sulfur-Oxidizing Bacteria in the Microbial Community on Corroding Concrete in Sewer Systems Appl. Envir. Microbiol., February 1, 2007; 73(3): 971 - 980. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Ben-Dov, O. H. Shapiro, N. Siboni, and A. Kushmaro Advantage of Using Inosine at the 3' Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity Appl. Envir. Microbiol., November 1, 2006; 72(11): 6902 - 6906. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Rudi, M. Zimonja, and T. Naes Alignment-independent bilinear multivariate modelling (AIBIMM) for global analyses of 16S rRNA gene phylogeny. Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1565 - 1575. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. H. Wubbeler, T. Lutke-Eversloh, S. Van Trappen, P. Vandamme, and A. Steinbuchel Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3'-dithiodipropionic acid Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1305 - 1310. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. S. Somvanshi, E. Lang, B. Straubler, C. Sproer, P. Schumann, S. Ganguly, A. K. Saxena, and E. Stackebrandt Providencia vermicola sp. nov., isolated from infective juveniles of the entomopathogenic nematode Steinernema thermophilum. Int J Syst Evol Microbiol, March 1, 2006; 56(Pt 3): 629 - 633. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Lefranc, A. Thenot, C. Lepere, and D. Debroas Genetic Diversity of Small Eukaryotes in Lakes Differing by Their Trophic Status Appl. Envir. Microbiol., October 1, 2005; 71(10): 5935 - 5942. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Waar, J. E Degener, M. J van Luyn, and H. J. Harmsen Fluorescent in situ hybridization with specific DNA probes offers adequate detection of Enterococcus faecalis and Enterococcus faecium in clinical samples J. Med. Microbiol., October 1, 2005; 54(10): 937 - 944. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Maszenan, J.-H. Tay, P. Schumann, H.-L. Jiang, and S. T.-L. Tay Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules Int J Syst Evol Microbiol, September 1, 2005; 55(5): 1771 - 1777. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Tonolla, R. Peduzzi, and D. Hahn Long-Term Population Dynamics of Phototrophic Sulfur Bacteria in the Chemocline of Lake Cadagno, Switzerland Appl. Envir. Microbiol., July 1, 2005; 71(7): 3544 - 3550. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-S. An, W.-T. Im, H.-C. Yang, M. S. Kang, K. K. Kim, L. Jin, M. K. Kim, and S.-T. Lee Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1705 - 1709. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Graber and J. A. Breznak Folate Cross-Feeding Supports Symbiotic Homoacetogenic Spirochetes Appl. Envir. Microbiol., April 1, 2005; 71(4): 1883 - 1889. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Tamaki, Y. Sekiguchi, S. Hanada, K. Nakamura, N. Nomura, M. Matsumura, and Y. Kamagata Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques Appl. Envir. Microbiol., April 1, 2005; 71(4): 2162 - 2169. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. B. Sheehan, J. M. Henson, and M. J. Ferris Legionella Species Diversity in an Acidic Biofilm Community in Yellowstone National Park Appl. Envir. Microbiol., January 1, 2005; 71(1): 507 - 511. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. Pavan, R. J. Franco, J. M. Rodriguez, P. Gadaleta, S. L. Abbott, J. M. Janda, and J. Zorzopulos Phylogenetic relationships of the genus Kluyvera: transfer of Enterobacter intermedius Izard et al. 1980 to the genus Kluyvera as Kluyvera intermedia comb. nov. and reclassification of Kluyvera cochleae as a later synonym of K. intermedia Int J Syst Evol Microbiol, January 1, 2005; 55(1): 437 - 442. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Ferris, A. Masztal, and D. H. Martin Use of Species-Directed 16S rRNA Gene PCR Primers for Detection of Atopobium vaginae in Patients with Bacterial Vaginosis J. Clin. Microbiol., December 1, 2004; 42(12): 5892 - 5894. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Jaspers and J. Overmann Ecological Significance of Microdiversity: Identical 16S rRNA Gene Sequences Can Be Found in Bacteria with Highly Divergent Genomes and Ecophysiologies Appl. Envir. Microbiol., August 1, 2004; 70(8): 4831 - 4839. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. T. A. S. Semedo, R. C. Gomes, A. A. Linhares, G. F. Duarte, R. P. Nascimento, A. S. Rosado, M. Margis-Pinheiro, R. Margis, K. R. A. Silva, C. S. Alviano, et al. Streptomyces drozdowiczii sp. nov., a novel cellulolytic streptomycete from soil in Brazil Int J Syst Evol Microbiol, July 1, 2004; 54(4): 1323 - 1328. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kindaichi, T. Ito, and S. Okabe Ecophysiological Interaction between Nitrifying Bacteria and Heterotrophic Bacteria in Autotrophic Nitrifying Biofilms as Determined by Microautoradiography-Fluorescence In Situ Hybridization Appl. Envir. Microbiol., March 1, 2004; 70(3): 1641 - 1650. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Yakimov, L. Giuliano, R. Denaro, E. Crisafi, T. N. Chernikova, W.-R. Abraham, H. Luensdorf, K. N. Timmis, and P. N. Golyshin Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons Int J Syst Evol Microbiol, January 1, 2004; 54(1): 141 - 148. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Bonch-Osmolovskaya, M. L. Miroshnichenko, A. V. Lebedinsky, N. A. Chernyh, T. N. Nazina, V. S. Ivoilov, S. S. Belyaev, E. S. Boulygina, Y. P. Lysov, A. N. Perov, et al. Radioisotopic, Culture-Based, and Oligonucleotide Microchip Analyses of Thermophilic Microbial Communities in a Continental High-Temperature Petroleum Reservoir Appl. Envir. Microbiol., October 1, 2003; 69(10): 6143 - 6151. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Rapp and L. H. E. Gabriel-Jurgens Degradation of alkanes and highly chlorinated benzenes, and production of biosurfactants, by a psychrophilic Rhodococcus sp. and genetic characterization of its chlorobenzene dioxygenase Microbiology, October 1, 2003; 149(10): 2879 - 2890. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Williams and E. B. Braun-Howland Growth of Escherichia coli in Model Distribution System Biofilms Exposed to Hypochlorous Acid or Monochloramine Appl. Envir. Microbiol., September 1, 2003; 69(9): 5463 - 5471. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Yakimov, L. Giuliano, G. Gentile, E. Crisafi, T. N. Chernikova, W.-R. Abraham, H. Lunsdorf, K. N. Timmis, and P. N. Golyshin Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water Int J Syst Evol Microbiol, May 1, 2003; 53(3): 779 - 785. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Yang and J. Zeyer Specific Detection of Dehalococcoides Species by Fluorescence In Situ Hybridization with 16S rRNA-Targeted Oligonucleotide Probes Appl. Envir. Microbiol., May 1, 2003; 69(5): 2879 - 2883. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Jumpponen, K. K. Newsham, and D. J. Neises Filamentous ascomycetes inhabiting the rhizoid environment of the liverwort Cephaloziella varians in Antarctica are assessed by direct PCR and cloning Mycologia, May 1, 2003; 95(3): 457 - 466. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. V. S. Albuquerque de Barros, G. P. Manfio, V. Ribeiro Maitan, L. A. Mendes Bataus, S. B. Kim, L. A. Maldonado, and M. Goodfellow Nocardiacerradoensis sp. nov., a novel isolate from Cerrado soil in Brazil Int J Syst Evol Microbiol, January 1, 2003; 53(1): 29 - 33. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Rosch, A. Mergel, and H. Bothe Biodiversity of Denitrifying and Dinitrogen-Fixing Bacteria in an Acid Forest Soil Appl. Envir. Microbiol., August 1, 2002; 68(8): 3818 - 3829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Frias-Lopez, A. L. Zerkle, G. T. Bonheyo, and B. W. Fouke Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces Appl. Envir. Microbiol., May 1, 2002; 68(5): 2214 - 2228. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Kashefi, D. E. Holmes, A.-L. Reysenbach, and D. R. Lovley Use of Fe(III) as an Electron Acceptor To Recover Previously Uncultured Hyperthermophiles: Isolation and Characterization of Geothermobacterium ferrireducens gen. nov., sp. nov. Appl. Envir. Microbiol., April 1, 2002; 68(4): 1735 - 1742. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Rychlik and J. B. Russell Bacteriocin-Like Activity of Butyrivibrio fibrisolvens JL5 and Its Effect on Other Ruminal Bacteria and Ammonia Production Appl. Envir. Microbiol., March 1, 2002; 68(3): 1040 - 1046. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Heuer, R. M. Kroppenstedt, J. Lottmann, G. Berg, and K. Smalla Effects of T4 Lysozyme Release from Transgenic Potato Roots on Bacterial Rhizosphere Communities Are Negligible Relative to Natural Factors Appl. Envir. Microbiol., March 1, 2002; 68(3): 1325 - 1335. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ito, S. Okabe, H. Satoh, and Y. Watanabe Successional Development of Sulfate-Reducing Bacterial Populations and Their Activities in a Wastewater Biofilm Growing under Microaerophilic Conditions Appl. Envir. Microbiol., March 1, 2002; 68(3): 1392 - 1402. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Becker, B. J. Paster, E. J. Leys, M. L. Moeschberger, S. G. Kenyon, J. L. Galvin, S. K. Boches, F. E. Dewhirst, and A. L. Griffen Molecular Analysis of Bacterial Species Associated with Childhood Caries J. Clin. Microbiol., March 1, 2002; 40(3): 1001 - 1009. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Wade Unculturable bacteria--the uncharacterized organisms that cause oral infections J R Soc Med, January 2, 2002; 95(2): 81 - 83. [Full Text] [PDF]
|
|
|
|
|
|
H. G.H.J. Heilig, E. G. Zoetendal, E. E. Vaughan, P. Marteau, A. D.L. Akkermans, and W. M. de Vos Molecular Diversity of Lactobacillus spp. and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA Appl. Envir. Microbiol., January 1, 2002; 68(1): 114 - 123. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. O. Wirsen, S. M. Sievert, C. M. Cavanaugh, S. J. Molyneaux, A. Ahmad, L. T. Taylor, E. F. DeLong, and C. D. Taylor Characterization of an Autotrophic Sulfide-Oxidizing Marine Arcobacter sp. That Produces Filamentous Sulfur Appl. Envir. Microbiol., January 1, 2002; 68(1): 316 - 325. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ito, J. L. Nielsen, S. Okabe, Y. Watanabe, and P. H. Nielsen Phylogenetic Identification and Substrate Uptake Patterns of Sulfate-Reducing Bacteria Inhabiting an Oxic-Anoxic Sewer Biofilm Determined by Combining Microautoradiography and Fluorescent In Situ Hybridization Appl. Envir. Microbiol., January 1, 2002; 68(1): 356 - 364. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R. Hristova, C. M. Lutenegger, and K. M. Scow Detection and Quantification of Methyl tert-Butyl Ether-Degrading Strain PM1 by Real-Time TaqMan PCR Appl. Envir. Microbiol., November 1, 2001; 67(11): 5154 - 5160. [Abstract] [Full Text]
|
|
|
|
|
|
A. Sessitsch, A. Weilharter, M. H. Gerzabek, H. Kirchmann, and E. Kandeler Microbial Population Structures in Soil Particle Size Fractions of a Long-Term Fertilizer Field Experiment Appl. Envir. Microbiol., September 1, 2001; 67(9): 4215 - 4224. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Harmsen, C. Singer, J. Rothgänger, T. Tønjum, G. Sybren de Hoog, H. Shah, J. Albert, and M. Frosch Diagnostics of Neisseriaceae and Moraxellaceae by Ribosomal DNA Sequencing: Ribosomal Differentiation of Medical Microorganisms J. Clin. Microbiol., March 1, 2001; 39(3): 936 - 942. [Abstract] [Full Text]
|
|
|
|
|
|
G. F. Duarte, A. S. Rosado, L. Seldin, W. de Araujo, and J. D. van Elsas Analysis of Bacterial Community Structure in Sulfurous-Oil-Containing Soils and Detection of Species Carrying Dibenzothiophene Desulfurization (dsz) Genes Appl. Envir. Microbiol., March 1, 2001; 67(3): 1052 - 1062. [Abstract] [Full Text]
|
|
|
|
 |
|
 M. Summit and J. A. Baross Special Feature: A novel microbial habitat in the mid-ocean ridge subseafloor PNAS, February 27, 2001; 98(5): 2158 - 2163. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Wu, W.-T. Liu, I-C. Tseng, and S.-S. Cheng Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system Microbiology, February 1, 2001; 147(2): 373 - 382. [Abstract] [Full Text]
|
|
|
|
|
|
N. S. Webster, K. J. Wilson, L. L. Blackall, and R. T. Hill Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Rhopaloeides odorabile Appl. Envir. Microbiol., January 1, 2001; 67(1): 434 - 444. [Abstract] [Full Text]
|
|
|
|
|
|
Z. Yu, G. R. Stewart, and W. W. Mohn Apparent Contradiction: Psychrotolerant Bacteria from Hydrocarbon-Contaminated Arctic Tundra Soils That Degrade Diterpenoids Synthesized by Trees Appl. Envir. Microbiol., December 1, 2000; 66(12): 5148 - 5154. [Abstract] [Full Text]
|
|
|
|
|
|
E. Barbieri, L. Potenza, I. Rossi, D. Sisti, G. Giomaro, S. Rossetti, C. Beimfohr, and V. Stocchi Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium Appl. Envir. Microbiol., November 1, 2000; 66(11): 5035 - 5042. [Abstract] [ |