Nucleic Acids Research, 2000, Vol. 28, No. 1 173-174
© 2000 Oxford University Press
The RDP (Ribosomal Database Project) continues
Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA, 1Department of Microbiology, Michigan State University, 294 Giltner Hall, East Lansing, MI 48824-1101, USA, 2Department of Microbiology, University of Illinois, B-103 C&LSL Building, 601 South Goodwin Avenue, Urbana, IL 61801-3714, USA and 3Department of Computer Science and Engineering, 2148 Engineering Building, Michigan State University, East Lansing, MI 48824-1226, USA
The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. 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 length polymorphism (T-RFLP) experiments.
* To whom correspondence should be addressed. Tel: +1 517 432 4998; Fax: +1 517 353 8957; Email: curator@cme.msu.edu
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R. A. Sanford, J. R. Cole, and J. M. Tiedje Characterization and Description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an Aryl-Halorespiring Facultative Anaerobic Myxobacterium Appl. Envir. Microbiol., February 1, 2002; 68(2): 893 - 900. [Abstract] [Full Text] [PDF]
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M. Ferrero, E. Llobet-Brossa, J. Lalucat, E. Garcia-Valdes, R. Rossello-Mora, and R. Bosch Coexistence of Two Distinct Copies of Naphthalene Degradation Genes in Pseudomonas Strains Isolated from the Western Mediterranean Region Appl. Envir. Microbiol., February 1, 2002; 68(2): 957 - 962. [Abstract] [Full Text] [PDF]
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J. M. Regan, G. W. Harrington, and D. R. Noguera Ammonia- and Nitrite-Oxidizing Bacterial Communities in a Pilot-Scale Chloraminated Drinking Water Distribution System Appl. Envir. Microbiol., January 1, 2002; 68(1): 73 - 81. [Abstract] [Full Text] [PDF]
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X. Y. Zhu, T. Zhong, Y. Pandya, and R. D. Joerger 16S rRNA-Based Analysis of Microbiota from the Cecum of Broiler Chickens Appl. Envir. Microbiol., January 1, 2002; 68(1): 124 - 137. [Abstract] [Full Text] [PDF]
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L. A. O'Sullivan, A. J. Weightman, and J. C. Fry New Degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S Ribosomal DNA-Targeted Oligonucleotide Probes Reveal High Bacterial Diversity in River Taff Epilithon Appl. Envir. Microbiol., January 1, 2002; 68(1): 201 - 210. [Abstract] [Full Text] [PDF]
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A. M. Sass, H. Sass, M. J. L. Coolen, H. Cypionka, and J. Overmann Microbial Communities in the Chemocline of a Hypersaline Deep-Sea Basin (Urania Basin, Mediterranean Sea) Appl. Envir. Microbiol., December 1, 2001; 67(12): 5392 - 5402. [Abstract] [Full Text] [PDF]
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K. Takai, D. P. Moser, M. DeFlaun, T. C. Onstott, and J. K. Fredrickson Archaeal Diversity in Waters from Deep South African Gold Mines Appl. Envir. Microbiol., December 1, 2001; 67(12): 5750 - 5760. [Abstract] [Full Text] [PDF]
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Z. Zhong, A. Toukdarian, D. Helinski, V. Knauf, S. Sykes, J. E. Wilkinson, C. O'Bryne, T. Shea, C. DeLoughery, and R. Caspi Sequence Analysis of a 101-Kilobase Plasmid Required for Agar Degradation by a Microscilla Isolate Appl. Envir. Microbiol., December 1, 2001; 67(12): 5771 - 5779. [Abstract] [Full Text] [PDF]
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 I. DEMIRKAN, S.D. CARTER, C. WINSTANLEY, K.D. BRUCE, N.M. McNAIR, M. WOODSIDE, and C.A. HART Isolation and characterisation of a novel spirochaete from severe virulent ovine foot rot J. Med. Microbiol., December 1, 2001; 50(12): 1061 - 1068. [Abstract] [Full Text] [PDF]
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 J. A. McCloskey, D. E. Graham, S. Zhou, P. F. Crain, M. Ibba, J. Konisky, D. Soll, and G. J. Olsen Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales Nucleic Acids Res., November 15, 2001; 29(22): 4699 - 4706. [Abstract] [Full Text] [PDF]
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C. S. Ting, G. Rocap, J. King, and S. W. Chisholm Phycobiliprotein genes of the marine photosynthetic prokaryote Prochlorococcus: evidence for rapid evolution of genetic heterogeneity Microbiology, November 1, 2001; 147(11): 3171 - 3182. [Abstract] [Full Text] [PDF]
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J. DOWNES, M. A. MUNSON, D. A. SPRATT, E. KONONEN, E. TARKKA, H. JOUSIMIES-SOMER, and W. G. WADE Characterisation of Eubacterium-like strains isolated from oral infections J. Med. Microbiol., November 1, 2001; 50(11): 947 - 951. [Abstract] [Full Text] [PDF]
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E. Zchori-Fein, Y. Gottlieb, S. E. Kelly, J. K. Brown, J. M. Wilson, T. L. Karr, and M. S. Hunter A newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps PNAS, October 5, 2001; (2001) 221467498. [Abstract] [Full Text] [PDF]
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A. P. Roberts, G. Cheah, D. Ready, J. Pratten, M. Wilson, and P. Mullany Transfer of Tn916-Like Elements in Microcosm Dental Plaques Antimicrob. Agents Chemother., October 1, 2001; 45(10): 2943 - 2946. [Abstract] [Full Text]
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B. B. McSpadden Gardener and D. M. Weller Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat Appl. Envir. Microbiol., October 1, 2001; 67(10): 4414 - 4425. [Abstract] [Full Text]
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J. Gulledge, A. Ahmad, P. A. Steudler, W. J. Pomerantz, and C. M. Cavanaugh Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes for Ecological Studies of Methanotrophic Bacteria Appl. Envir. Microbiol., October 1, 2001; 67(10): 4726 - 4733. [Abstract] [Full Text]
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C. Y. Turenne, L. Tschetter, J. Wolfe, and A. Kabani Necessity of Quality-Controlled 16S rRNA Gene Sequence Databases: Identifying Nontuberculous Mycobacterium Species J. Clin. Microbiol., October 1, 2001; 39(10): 3637 - 3648. [Abstract] [Full Text] [PDF]
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V. T. Marteinsson, S. Hauksdottir, C. F. V. Hobel, H. Kristmannsdottir, G. O. Hreggvidsson, and J. K. Kristjansson Phylogenetic Diversity Analysis of Subterranean Hot Springs in Iceland Appl. Envir. Microbiol., September 1, 2001; 67(9): 4242 - 4248. [Abstract] [Full Text] [PDF]
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H. J. Rolph, A. Lennon, M. P. Riggio, W. P. Saunders, D. MacKenzie, L. Coldero, and J. Bagg Molecular Identification of Microorganisms from Endodontic Infections J. Clin. Microbiol., September 1, 2001; 39(9): 3282 - 3289. [Abstract] [Full Text] [PDF]
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K. Takai, T. Komatsu, F. Inagaki, and K. Horikoshi Distribution of Archaea in a Black Smoker Chimney Structure Appl. Envir. Microbiol., August 1, 2001; 67(8): 3618 - 3629. [Abstract] [Full Text] [PDF]
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B. Diez, C. Pedros-Alio, and R. Massana Study of Genetic Diversity of Eukaryotic Picoplankton in Different Oceanic Regions by Small-Subunit rRNA Gene Cloning and Sequencing Appl. Envir. Microbiol., July 1, 2001; 67(7): 2932 - 2941. [Abstract] [Full Text] [PDF]
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B. Diez, C. Pedros-Alio, T. L. Marsh, and R. Massana Application of Denaturing Gradient Gel Electrophoresis (DGGE) To Study the Diversity of Marine Picoeukaryotic Assemblages and Comparison of DGGE with Other Molecular Techniques Appl. Envir. Microbiol., July 1, 2001; 67(7): 2942 - 2951. [Abstract] [Full Text] [PDF]
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W. Eder, L. L. Jahnke, M. Schmidt, and R. Huber Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods Appl. Envir. Microbiol., July 1, 2001; 67(7): 3077 - 3085. [Abstract] [Full Text] [PDF]
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B. J. Paster, S. K. Boches, J. L. Galvin, R. E. Ericson, C. N. Lau, V. A. Levanos, A. Sahasrabudhe, and F. E. Dewhirst Bacterial Diversity in Human Subgingival Plaque J. Bacteriol., June 15, 2001; 183(12): 3770 - 3783. [Abstract] [Full Text]
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B. E. Logan, H. Zhang, P. Mulvaney, M. G. Milner, I. M. Head, and R. F. Unz Kinetics of Perchlorate- and Chlorate-Respiring Bacteria Appl. Envir. Microbiol., June 1, 2001; 67(6): 2499 - 2506. [Abstract] [Full Text]
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L. L. Daane, I. Harjono, G. J. Zylstra, and M. M. Häggblom Isolation and Characterization of Polycyclic Aromatic Hydrocarbon-Degrading Bacteria Associated with the Rhizosphere of Salt Marsh Plants Appl. Envir. Microbiol., June 1, 2001; 67(6): 2683 - 2691. [Abstract] [Full Text]
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J. Gorodkin, S. L. Stricklin, and G. D. Stormo Discovering common stem-loop motifs in unaligned RNA sequences Nucleic Acids Res., May 15, 2001; 29(10): 2135 - 2144. [Abstract] [Full Text] [PDF]
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C. Rudolph, G. Wanner, and R. Huber Natural Communities of Novel Archaea and Bacteria Growing in Cold Sulfurous Springs with a String-of-Pearls-Like Morphology Appl. Envir. Microbiol., May 1, 2001; 67(5): 2336 - 2344. [Abstract] [Full Text]
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A. Iten, S. Graf, M. Egger, M. Täuber, and J. Graf Helicobacter sp. Flexispira Bacteremia in an Immunocompetent Young Adult J. Clin. Microbiol., May 1, 2001; 39(5): 1716 - 1720. [Abstract] [Full Text]
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B. Nogales, E. R. B. Moore, E. Llobet-Brossa, R. Rossello-Mora, R. Amann, and K. N. Timmis Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil Appl. Envir. Microbiol., April 1, 2001; 67(4): 1874 - 1884. [Abstract] [Full Text]
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C. W. Kaplan, J. C. Astaire, M. E. Sanders, B. S. Reddy, and C. L. Kitts 16S Ribosomal DNA Terminal Restriction Fragment Pattern Analysis of Bacterial Communities in Feces of Rats Fed Lactobacillus acidophilus NCFM Appl. Envir. Microbiol., April 1, 2001; 67(4): 1935 - 1939. [Abstract] [Full Text]
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 Z.-C. Tu, F. E. Dewhirst, and M. J. Blaser Evidence that the Campylobacter fetus sap Locus Is an Ancient Genomic Constituent with Origins before Mammals and Reptiles Diverged Infect. Immun., April 1, 2001; 69(4): 2237 - 2244. [Abstract] [Full Text] [PDF]
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