Nucleic Acids Research, 2001, Vol. 29, No. 1 173-174
© 2001 Oxford University Press
The RDP-II (Ribosomal Database Project)
Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA, 1Department of Microbiology, University of Illinois, B-103 C&LSL Building, 601 South Goodwin Avenue, Urbana, IL 61801-3714, USA and 2Department of Microbiology and Molecular Genetics, Michigan State University, 294 Giltner Hall, East Lansing, MI 48824-1101, USA
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173–174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and ~75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.html). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator{at}cme.msu.edu to rdpstaff{at}msu.edu.
* To whom correspondence should be addressed. Tel: +1 517 432 4998; Fax: +1 517 353 8957; Email: rdpstaff{at}msu.edu
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A. Lopez-Cortes, M.-L. Fardeau, G. Fauque, C. Joulian, and B. Ollivier Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov. Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1495 - 1499. [Abstract] [Full Text] [PDF]
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M. M. Kendall, Y. Liu, M. Sieprawska-Lupa, K. O. Stetter, W. B. Whitman, and D. R. Boone Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1525 - 1529. [Abstract] [Full Text] [PDF]
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R. Osawa, T. Fujisawa, and R. Pukall Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces. Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1693 - 1696. [Abstract] [Full Text] [PDF]
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U. Friedrich and J. Lenke Improved enumeration of lactic Acid bacteria in mesophilic dairy starter cultures by using multiplex quantitative real-time PCR and flow cytometry-fluorescence in situ hybridization. Appl. Envir. Microbiol., June 1, 2006; 72(6): 4163 - 4171. [Abstract] [Full Text] [PDF]
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C. Bakermans, H. L. Ayala-del-Rio, M. A. Ponder, T. Vishnivetskaya, D. Gilichinsky, M. F. Thomashow, and J. M. Tiedje Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1285 - 1291. [Abstract] [Full Text] [PDF]
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T. D. Niederberger, D. K. Gotz, I. R. McDonald, R. S. Ronimus, and H. W. Morgan Ignisphaera aggregans gen. nov., sp. nov., a novel hyperthermophilic crenarchaeote isolated from hot springs in Rotorua and Tokaanu, New Zealand. Int J Syst Evol Microbiol, May 1, 2006; 56(Pt 5): 965 - 971. [Abstract] [Full Text] [PDF]
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A. Behnke, J. Bunge, K. Barger, H.-W. Breiner, V. Alla, and T. Stoeck Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway). Appl. Envir. Microbiol., May 1, 2006; 72(5): 3626 - 3636. [Abstract] [Full Text] [PDF]
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S. L'Haridon, M. L. Miroshnichenko, N. A. Kostrikina, B. J. Tindall, S. Spring, P. Schumann, E. Stackebrandt, E. A. Bonch-Osmolovskaya, and C. Jeanthon Vulcanibacillus modesticaldus gen. nov., sp. nov., a strictly anaerobic, nitrate-reducing bacterium from deep-sea hydrothermal vents. Int J Syst Evol Microbiol, May 1, 2006; 56(Pt 5): 1047 - 1053. [Abstract] [Full Text] [PDF]
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B. Nowlan, M. S. Dodia, S. P. Singh, and B. K. C. Patel Bacillus okhensis sp. nov., a halotolerant and alkalitolerant bacterium from an Indian saltpan. Int J Syst Evol Microbiol, May 1, 2006; 56(Pt 5): 1073 - 1077. [Abstract] [Full Text] [PDF]
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H. Biebl, B. J. Tindall, R. Pukall, H. Lunsdorf, M. Allgaier, and I. Wagner-Dobler Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 821 - 826. [Abstract] [Full Text] [PDF]
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R. Pukall, P. Schumann, C. Schutte, R. Gols, and M. Dicke Acaricomes phytoseiuli gen. nov., sp. nov., isolated from the predatory mite Phytoseiulus persimilis Int J Syst Evol Microbiol, February 1, 2006; 56(2): 465 - 469. [Abstract] [Full Text] [PDF]
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H. Kimura, M. Sugihara, K. Kato, and S. Hanada Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments Appl. Envir. Microbiol., January 1, 2006; 72(1): 21 - 27. [Abstract] [Full Text] [PDF]
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K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies Appl. Envir. Microbiol., December 1, 2005; 71(12): 7724 - 7736. [Abstract] [Full Text] [PDF]
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C. Lozupone and R. Knight UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Appl. Envir. Microbiol., December 1, 2005; 71(12): 8228 - 8235. [Abstract] [Full Text] [PDF]
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A. Pozhitkov, B. Chernov, G. Yershov, and P. A. Noble Evaluation of Gel-Pad Oligonucleotide Microarray Technology by Using Artificial Neural Networks Appl. Envir. Microbiol., December 1, 2005; 71(12): 8663 - 8676. [Abstract] [Full Text] [PDF]
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M. J. L. Coolen, E. Post, C. C. Davis, and L. J. Forney Characterization of Microbial Communities Found in the Human Vagina by Analysis of Terminal Restriction Fragment Length Polymorphisms of 16S rRNA Genes Appl. Envir. Microbiol., December 1, 2005; 71(12): 8729 - 8737. [Abstract] [Full Text] [PDF]
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 J.D. Rudney, R. Chen, and G. Zhang Streptococci Dominate the Diverse Flora within Buccal Cells Journal of Dental Research, December 1, 2005; 84(12): 1165 - 1171. [Abstract] [Full Text] [PDF]
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B. Gao and R. S. Gupta Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2401 - 2412. [Abstract] [Full Text] [PDF]
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Y. Hongoh, P. Deevong, T. Inoue, S. Moriya, S. Trakulnaleamsai, M. Ohkuma, C. Vongkaluang, N. Noparatnaraporn, and T. Kudo Intra- and Interspecific Comparisons of Bacterial Diversity and Community Structure Support Coevolution of Gut Microbiota and Termite Host Appl. Envir. Microbiol., November 1, 2005; 71(11): 6590 - 6599. [Abstract] [Full Text] [PDF]
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H. A. Vrionis, R. T. Anderson, I. Ortiz-Bernad, K. R. O'Neill, C. T. Resch, A. D. Peacock, R. Dayvault, D. C. White, P. E. Long, and D. R. Lovley Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site Appl. Envir. Microbiol., October 1, 2005; 71(10): 6308 - 6318. [Abstract] [Full Text] [PDF]
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H. E. O'Brien, J. L. Parrent, J. A. Jackson, J.-M. Moncalvo, and R. Vilgalys Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples Appl. Envir. Microbiol., September 1, 2005; 71(9): 5544 - 5550. [Abstract] [Full Text] [PDF]
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P. H. Summanen, B. Durmaz, M.-L. Vaisanen, C. Liu, D. Molitoris, E. Eerola, I. M. Helander, and S. M. Finegold Porphyromonas somerae sp. nov., a Pathogen Isolated from Humans and Distinct from Porphyromonas levii J. Clin. Microbiol., September 1, 2005; 43(9): 4455 - 4459. [Abstract] [Full Text] [PDF]
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 E de Madaria, J Martinez, B Lozano, L Sempere, S Benlloch, J Such, F Uceda, R Frances, and M Perez-Mateo Detection and identification of bacterial DNA in serum from patients with acute pancreatitis Gut, September 1, 2005; 54(9): 1293 - 1297. [Abstract] [Full Text] [PDF]
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A. Dhillon, M. Lever, K. G. Lloyd, D. B. Albert, M. L. Sogin, and A. Teske Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A (mcrA) Genes in Hydrothermal Sediments of the Guaymas Basin Appl. Envir. Microbiol., August 1, 2005; 71(8): 4592 - 4601. [Abstract] [Full Text] [PDF]
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E. Griffiths, A. K. Petrich, and R. S. Gupta Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification Microbiology, August 1, 2005; 151(8): 2647 - 2657. [Abstract] [Full Text] [PDF]
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M. G. Wise and G. R. Siragusa Quantitative Detection of Clostridium perfringens in the Broiler Fowl Gastrointestinal Tract by Real-Time PCR Appl. Envir. Microbiol., July 1, 2005; 71(7): 3911 - 3916. [Abstract] [Full Text] [PDF]
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Y. Kong, J. L. Nielsen, and P. H. Nielsen Identity and Ecophysiology of Uncultured Actinobacterial Polyphosphate-Accumulating Organisms in Full-Scale Enhanced Biological Phosphorus Removal Plants Appl. Envir. Microbiol., July 1, 2005; 71(7): 4076 - 4085. [Abstract] [Full Text] [PDF]
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K. P. Nevin, D. E. Holmes, T. L. Woodard, E. S. Hinlein, D. W. Ostendorf, and D. R. Lovley Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates Int J Syst Evol Microbiol, July 1, 2005; 55(4): 1667 - 1674. [Abstract] [Full Text] [PDF]
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L. D. Gray, K. L. Ketring, and Y.-W. Tang Clinical Use of 16S rRNA Gene Sequencing To Identify Mycoplasma felis and M. gateae Associated with Feline Ulcerative Keratitis J. Clin. Microbiol., July 1, 2005; 43(7): 3431 - 3434. [Abstract] [Full Text] [PDF]
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R. W. Hyman, M. Fukushima, L. Diamond, J. Kumm, L. C. Giudice, and R. W. Davis Microbes on the human vaginal epithelium PNAS, May 31, 2005; 102(22): 7952 - 7957. [Abstract] [Full Text] [PDF]
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 A. C. Frank, C. M. Alsmark, M. Thollesson, and S. G. E. Andersson Functional Divergence and Horizontal Transfer of Type IV Secretion Systems Mol. Biol. Evol., May 1, 2005; 22(5): 1325 - 1336. [Abstract] [Full Text] [PDF]
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Y. Song, C. Liu, M. Bolanos, J. Lee, M. McTeague, and S. M. Finegold Evaluation of 16S rRNA Sequencing and Reevaluation of a Short Biochemical Scheme for Identification of Clinically Significant Bacteroides Species J. Clin. Microbiol., April 1, 2005; 43(4): 1531 - 1537. [Abstract] [Full Text] [PDF]
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C. From, R. Pukall, P. Schumann, V. Hormazabal, and P. E. Granum Toxin-Producing Ability among Bacillus spp. Outside the Bacillus cereus Group Appl. Envir. Microbiol., March 1, 2005; 71(3): 1178 - 1183. [Abstract] [Full Text] [PDF]
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B. D. Eardly, S. M. Nour, P. van Berkum, and R. K. Selander Rhizobial 16S rRNA and dnaK Genes: Mosaicism and the Uncertain Phylogenetic Placement of Rhizobium galegae Appl. Envir. Microbiol., March 1, 2005; 71(3): 1328 - 1335. [Abstract] [Full Text] [PDF]
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