Nucleic Acids Research, 2003, Vol. 31, No. 1 442-443
© 2003 Oxford University Press
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA 1 Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
*To whom correspondence should be addressed. Tel: +1 5174324998; Fax: +1 5173538957; Email: rdpstaff{at}msu.edu
Received September 13, 2002; Accepted September 24, 2002
ABSTRACT
The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff{at}msu.edu.
DESCRIPTION
This paper describes changes since the 2001 description (1). Details about specific data and analysis functions can be found at the Ribosomal Database Project-II (RDP-II) site (http://rdp.cme.msu.edu).
Data
The RDP-II obtains rRNA sequence data from the major International Nucleotide Sequence Databases (GenBank/EMBL/DDBJ). These sequences are provided to our users in aligned and annotated format. Release 8.1 contains 16 277 archaeal and bacterial, 1503 mitochondrial, and 5201 eukaryotic small subunit rRNA sequences. The number of eukaryotic sequences has more than doubled since our previous release. In order to provide a phylogenetic context for the data, RDP-II makes available over 100 trees that span the phylogenetic breadth of life. Most of these trees are new since our last update and were created using the WEIGHBOR algorithm (2). As a service to our users, we also provide a repository for published user-submitted alignments.
In addition to the release 8.1 alignments, we are offering a release 9 preview (beta) alignment containing over 50 000 (eu)bacterial small subunit rRNA sequences. This new alignment marks a major departure from prior RDP releases. Previous alignments incorporated secondary-structure constraints through manual inspection of each sequence. The new alignment was created using a modified version of the RNACAD (3), a Stochastic Context-Free Grammar (SCFG) based rRNA alignment program that incorporates rRNA secondary structure information directly in the internal model. The SCFGs are a class of probabilistic models related to the Hidden Markov Models (HMM) widely accepted in protein alignment and classification. We feel that this more automated alignment strategy will provide our users with a broader selection of up-to-date rRNA sequences in alignments that, for many purposes, are as good as hand-tuned alignments but without any unintended bias or other artifacts that may occur as a consequence of manual modification.
In addition to aligned sequences and trees, the RDP places the sequences into a phylogenetically consistent hierarchy. This hierarchy provides order to the collection. It provides a phylogenetic framework into which to place results of the RDP analysis functions, and it provides an entry point for users looking for sequences from specific groups of organisms.
Until very recently, the naming of higher-order prokaryotic taxa was based on phenotypic features rather than phylogeny. For this reason, the RDP has made a point to use trivial or colloquial names for its phylogenetically based hierarchy. In the second edition of the Bergey's Manual of Systematic Bacteriology, Garrity and Holt (4) presented a new hierarchical classification of the prokaryotes. Their principal objective was to devise a scheme that reflected the phylogeny of prokaryotes (based on 16S rRNA sequence analysis). We have leveraged this new taxonomy for preview release 9, placing the sequences into a hierarchy that, as much as possible, is consistent with this updated taxonomy. We are assigning rRNA sequences to this phylogenetically consistent taxonomic hierarchy using a naïve Bayes classifier trained on a set of known type sequences supplemented with sequences from lineages that are only represented by unnamed or yet-uncultivated organisms.
Analysis services
A detailed description of each analysis command can be found on the www server.
The new Hierarchy Browser is a sequence search and selection tool that displays the sequences in an expandable hierarchical framework. It has visual indicators of sequence length and quality. Sequences and related annotation can be viewed online, selected for download, or selected for inclusion in other RDP-II analysis functions. For release 9, sequences may be viewed in either the new taxonomy or in a separate hierarchy matching their assignment in the NCBI taxonomy database (5). Subsets of the sequence data can be selected in release 9, including sequences from type strains only (identified in collaboration with Bergey's Trust), and near full-length sequences of 1200 or more bases.
Phylip Interface is a new interactive analysis function that permits phylogenetic reconstruction with a combination of user and RDP sequences. This tool offers a choice of either the PHYLIP (6) neighbor-joining, or WEIGHBOR (2) weighted neighbor-joining programs for phylogenetic calculation. The results can be viewed in a new interactive tree applet that allows phenogram rooting (and re-rooting) and branch rotation. The resulting phenogram can be downloaded in newick, postscript, eps and pdf formats.
Also new is an online interactive tutorial to guide users through the basics of rRNA sequence analysis. This tutorial is suitable both for the researcher new to rRNA based phylogenetic analysis and as a teaching module for upper-level undergraduate and graduate classes. The tutorial offers an introductory module plus individual modules for five of the RDP-II analysis functions: Chimera Check, Sequence Match, Sequence Aligner, Similarity Matrix and Phylip Interface.
Other tools are provided for comparing a user submitted sequence to the RDP-II database (Sequence Match), aligning a user sequence against the nearest RDP sequence (Sequence Aligner), examining probe and primer specificity (Probe Match), testing for chimeric sequences (Chimera Check), generating a similarity matrix (Similarity Matrix), analyzing T-RFLP data (T-RFLP and TAP-TRFLP), and browsing RDP phylogenetic trees (SubTree).
FUTURE CHANGES AND ADDITIONS
We expect feedback from our user community to determine the extent to which we adopt SCFG-based alignments but anticipate the release of additional SCFG alignments for Archaea and eukaryotes in the coming months, with the goal of monthly or better updates for these new alignments.
RDP-II ACCESS AND CONTACT
The RDP-II data and analysis services can be found at http://rdp.cme.msu.edu/. A mirror site is available at the Laboratory for Molecular Classification in the Center for Information Biology at the National Institute of Genetics (NIG), Japan (http://rdp.genes.nig.ac.jp/).
The address for email correspondence with RDP-II staff is rdpstaff{at}msu.edu. Telephone support is available at (+1 5174324998). The RDP-II staff may also be contacted via fax (+1 5173538957) or regular mail.
ACKNOWLEDGEMENTS
We thank several individuals for their past contributions: Robin Gutell (and his colleagues), Bonnie Maidak, Tim Lilburn, Niels Larsen, Tom Macke, Michael J. McCaughey, Ross Overbeek, Sakti Pramanik, Scott Dawson, Mitch L. Sogin, Gary Olsen and Carl Woese. The US Department of Energy Office of Science and the State of Michigan currently support RDP-II.
REFERENCES
- Maidak,B.L., Cole,J.R., Lilburn,T.G., Parker,C.T., Saxman,P.R., Farris,R.J., Garrity,G.M., Olsen,G.J., Schmidt,T.M. and Tiedje,J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res., 29, 173–174.
[Abstract/Free Full Text] - Bruno,W.J., Socci,N.D. and Halpern,A.L. (2000) Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol., 17, 189–197.
[Abstract/Free Full Text] - Brown,M.P.S. (2000) Small subunit ribosomal RNA modeling using stochastic context-free grammar. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). San Diego, California, USA, pp. 57–66.
- Garrity,G.M., Winters,M., Kuo,A.W. and Searles,D.B. (2002) Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology, 2nd Edn, Springer-Verlag, NY.
- Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Database Resources of the National Center for Biotechnology Information. Nucleic Acids Res., 28, 10–14.
[Abstract/Free Full Text] - Felsenstein,J. (1989) PHYLIP—Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164–166.
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M. Sapp, A. Wichels, and G. Gerdts Impacts of Cultivation of Marine Diatoms on the Associated Bacterial Community Appl. Envir. Microbiol., May 1, 2007; 73(9): 3117 - 3120. [Abstract] [Full Text] [PDF]
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L. Dethlefsen and T. M. Schmidt Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria J. Bacteriol., April 15, 2007; 189(8): 3237 - 3245. [Abstract] [Full Text] [PDF]
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 C. R. Cox and M. S. Gilmore Native Microbial Colonization of Drosophila melanogaster and Its Use as a Model of Enterococcus faecalis Pathogenesis Infect. Immun., April 1, 2007; 75(4): 1565 - 1576. [Abstract] [Full Text] [PDF]
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H. Kimura, J.-I. Ishibashi, H. Masuda, K. Kato, and S. Hanada Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere Appl. Envir. Microbiol., April 1, 2007; 73(7): 2110 - 2117. [Abstract] [Full Text] [PDF]
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 J. E. Thies Soil Microbial Community Analysis using Terminal Restriction Fragment Length Polymorphisms Soil Sci. Soc. Am. J., March 12, 2007; 71(2): 579 - 591. [Abstract] [Full Text] [PDF]
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K. J. Martin Introduction to Molecular Analysis of Ectomycorrhizal Communities Soil Sci. Soc. Am. J., March 12, 2007; 71(2): 601 - 610. [Abstract] [Full Text] [PDF]
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M. Sizova and N. Panikov Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soil Int J Syst Evol Microbiol, March 1, 2007; 57(3): 616 - 619. [Abstract] [Full Text] [PDF]
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D. Z. Sousa, M. A. Pereira, A. J. M. Stams, M. M. Alves, and H. Smidt Microbial Communities Involved in Anaerobic Degradation of Unsaturated or Saturated Long-Chain Fatty Acids Appl. Envir. Microbiol., February 15, 2007; 73(4): 1054 - 1064. [Abstract] [Full Text] [PDF]
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M. Park, S. H. Ryu, T.-H. T. Vu, H.-S. Ro, P.-Y. Yun, and C. O. Jeon Flavobacterium defluvii sp. nov., isolated from activated sludge Int J Syst Evol Microbiol, February 1, 2007; 57(2): 233 - 237. [Abstract] [Full Text] [PDF]
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Y.-G. Kim, D. H. Choi, S. Hyun, and B. C. Cho Oceanobacillus profundus sp. nov., isolated from a deep-sea sediment core Int J Syst Evol Microbiol, February 1, 2007; 57(2): 409 - 413. [Abstract] [Full Text] [PDF]
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M. E. Gentile, C. M. Jessup, J. L. Nyman, and C. S. Criddle Correlation of Functional Instability and Community Dynamics in Denitrifying Dispersed-Growth Reactors Appl. Envir. Microbiol., February 1, 2007; 73(3): 680 - 690. [Abstract] [Full Text] [PDF]
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C. J. Brown, M. Wong, C. C. Davis, A. Kanti, X. Zhou, and L. J. Forney Preliminary characterization of the normal microbiota of the human vulva using cultivation-independent methods J. Med. Microbiol., February 1, 2007; 56(2): 271 - 276. [Abstract] [Full Text] [PDF]
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S. Lu, S. H. Ryu, B. S. Chung, Y. R. Chung, W. Park, and C. O. Jeon Simplicispira limi sp. nov., isolated from activated sludge Int J Syst Evol Microbiol, January 1, 2007; 57(1): 31 - 34. [Abstract] [Full Text] [PDF]
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F. Cappitelli, J. D. Nosanchuk, A. Casadevall, L. Toniolo, L. Brusetti, S. Florio, P. Principi, S. Borin, and C. Sorlini Synthetic Consolidants Attacked by Melanin-Producing Fungi: Case Study of the Biodeterioration of Milan (Italy) Cathedral Marble Treated with Acrylics Appl. Envir. Microbiol., January 1, 2007; 73(1): 271 - 277. [Abstract] [Full Text] [PDF]
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K. H. Sharp, B. Eam, D. J. Faulkner, and M. G. Haygood Vertical Transmission of Diverse Microbes in the Tropical Sponge Corticium sp. Appl. Envir. Microbiol., January 1, 2007; 73(2): 622 - 629. [Abstract] [Full Text] [PDF]
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S. H. Ryu, T. T. H. Nguyen, W. Park, C.-J. Kim, and C. O. Jeon Runella limosa sp. nov., isolated from activated sludge Int J Syst Evol Microbiol, December 1, 2006; 56(12): 2757 - 2760. [Abstract] [Full Text] [PDF]
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D. H. Choi and B. C. Cho Citreimonas salinaria gen. nov., sp. nov., a member of the Roseobacter clade isolated from a solar saltern Int J Syst Evol Microbiol, December 1, 2006; 56(12): 2799 - 2803. [Abstract] [Full Text] [PDF]
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 W. P Hanage, C. Fraser, and B. G Spratt Sequences, sequence clusters and bacterial species Phil Trans R Soc B, November 29, 2006; 361(1475): 1917 - 1927. [Abstract] [Full Text] [PDF]
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D. Sassera, T. Beninati, C. Bandi, E. A. P. Bouman, L. Sacchi, M. Fabbi, and N. Lo 'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle. Int J Syst Evol Microbiol, November 1, 2006; 56(Pt 11): 2535 - 2540. [Abstract] [Full Text] [PDF]
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J.-M. Lim, C. O. Jeon, D.-J. Park, L.-H. Xu, C.-L. Jiang, and C.-J. Kim Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China. Int J Syst Evol Microbiol, November 1, 2006; 56(Pt 11): 2579 - 2582. [Abstract] [Full Text] [PDF]
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 N. Popp, M. Schlomann, and M. Mau Bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils. Microbiology, November 1, 2006; 152(Pt 11): 3291 - 3304. [Abstract] [Full Text] [PDF]
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M. D. J. Lynch and R. G. Thorn Diversity of Basidiomycetes in Michigan Agricultural Soils Appl. Envir. Microbiol., November 1, 2006; 72(11): 7050 - 7056. [Abstract] [Full Text] [PDF]
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S. Blanquart and N. Lartillot A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution Mol. Biol. Evol., November 1, 2006; 23(11): 2058 - 2071. [Abstract] [Full Text] [PDF]
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A. Chauhan and A. Ogram Phylogeny of Acetate-Utilizing Microorganisms in Soils along a Nutrient Gradient in the Florida Everglades. Appl. Envir. Microbiol., October 1, 2006; 72(10): 6837 - 6840. [Abstract] [Full Text] [PDF]
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M. Park, S. Lu, S. H. Ryu, B. S. Chung, W. Park, C.-J. Kim, and C. O. Jeon Flavobacterium croceum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol, October 1, 2006; 56(Pt 10): 2443 - 2447. [Abstract] [Full Text] [PDF]
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A. Edlund and J. K. Jansson Changes in Active Bacterial Communities before and after Dredging of Highly Polluted Baltic Sea Sediments Appl. Envir. Microbiol., October 1, 2006; 72(10): 6800 - 6807. [Abstract] [Full Text] [PDF]
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K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras Appl. Envir. Microbiol., September 1, 2006; 72(9): 5734 - 5741. [Abstract] [Full Text] [PDF]
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R. Sekar, D. K. Mills, E. R. Remily, J. D. Voss, and L. L. Richardson Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased Siderastrea siderea Appl. Envir. Microbiol., September 1, 2006; 72(9): 5963 - 5973. [Abstract] [Full Text] [PDF]
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Ch. V. Ramana, Ch. Sasikala, K. Arunasri, P. Anil Kumar, T. N. R. Srinivas, S. Shivaji, P. Gupta, J. Suling, and J. F. Imhoff Rubrivivax benzoatilyticus sp. nov., an aromatic, hydrocarbon-degrading purple betaproteobacterium. Int J Syst Evol Microbiol, September 1, 2006; 56(Pt 9): 2157 - 2164. [Abstract] [Full Text] [PDF]
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A. Blazejak, J. Kuever, C. Erseus, R. Amann, and N. Dubilier Phylogeny of 16S rRNA, Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, and Adenosine 5'-Phosphosulfate Reductase Genes from Gamma- and Alphaproteobacterial Symbionts in Gutless Marine Worms (Oligochaeta) from Bermuda and the Bahamas Appl. Envir. Microbiol., August 1, 2006; 72(8): 5527 - 5536. [Abstract] [Full Text] [PDF]
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J. L. Macalady, E. H. Lyon, B. Koffman, L. K. Albertson, K. Meyer, S. Galdenzi, and S. Mariani Dominant Microbial Populations in Limestone-Corroding Stream Biofilms, Frasassi Cave System, Italy Appl. Envir. Microbiol., August 1, 2006; 72(8): 5596 - 5609. [Abstract] [Full Text] [PDF]
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C. Y. Hwang, D. H. Choi, and B. C. Cho Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1831 - 1836. [Abstract] [Full Text] [PDF]
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D. H. Choi and B. C. Cho Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1869 - 1873. [Abstract] [Full Text] [PDF]
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J.-C. Lee, J.-M. Lim, D.-J. Park, C. O. Jeon, W.-J. Li, and C.-J. Kim Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains L-lysine in its cell wall. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1893 - 1898. [Abstract] [Full Text] [PDF]
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 A. Busch and R. Backofen INFO-RNA--a fast approach to inverse RNA folding Bioinformatics, August 1, 2006; 22(15): 1823 - 1831. [Abstract] [Full Text] [PDF]
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T. A. Auchtung, C. D. Takacs-Vesbach, and C. M. Cavanaugh 16S rRNA Phylogenetic Investigation of the Candidate Division "Korarchaeota". Appl. Envir. Microbiol., July 1, 2006; 72(7): 5077 - 5082. [Abstract] [Full Text] [PDF]
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G. R. Noel and N. Atibalentja 'Candidatus Paenicardinium endonii', an endosymbiont of the plant-parasitic nematode Heterodera glycines (Nemata: Tylenchida), affiliated to the phylum Bacteroidetes. Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1697 - 1702. [Abstract] [Full Text] [PDF]
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S. J. Green, E. Inbar, F. C. Michel Jr., Y. Hadar, and D. Minz Succession of Bacterial Communities during Early Plant Development: Transition from Seed to Root and Effect of Compost Amendment. Appl. Envir. Microbiol., June 1, 2006; 72(6): 3975 - 3983. [Abstract] [Full Text] [PDF]
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C. Y. Hwang and B. C. Cho Flectobacillus lacus sp. nov., isolated from a highly eutrophic pond in Korea Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1197 - 1201. [Abstract] [Full Text] [PDF]
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E. B. M. Denner, M. Kolari, D. Hoornstra, I. Tsitko, P. Kampfer, H.-J. Busse, and M. Salkinoja-Salonen Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1355 - 1362. [Abstract] [Full Text] [PDF]
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M. A. Patel, M. S. Ou, R. Harbrucker, H. C. Aldrich, M. L. Buszko, L. O. Ingram, and K. T. Shanmugam Isolation and characterization of Acid-tolerant, thermophilic bacteria for effective fermentation of biomass-derived sugars to lactic Acid. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3228 - 3235. [Abstract] [Full Text] [PDF]
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S. Kleinsteuber, V. Riis, I. Fetzer, H. Harms, and S. Muller Population Dynamics within a Microbial Consortium during Growth on Diesel Fuel in Saline Environments. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3531 - 3542. [Abstract] [Full Text] [PDF]
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V. Souza, L. Espinosa-Asuar, A. E. Escalante, L. E. Eguiarte, J. Farmer, L. Forney, L. Lloret, J. M. Rodriguez-Martinez, X. Soberon, R. Dirzo, et al. From the Cover: An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert PNAS, April 25, 2006; 103(17): 6565 - 6570. [Abstract] [Full Text] [PDF]
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D. R. Brown, D. L. Demcovitz, D. R. Plourde, S. M. Potter, M. E. Hunt, R. D. Jones, and D. S. Rotstein Mycoplasma iguanae sp. nov., from a green iguana (Iguana iguana) with vertebral disease. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 761 - 764. [Abstract] [Full Text] [PDF]
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D. H. Choi and B. C. Cho Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 771 - 776. [Abstract] [Full Text] [PDF]
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M. B. Leigh, P. Prouzova, M. Mackova, T. Macek, D. P. Nagle, and J. S. Fletcher Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site Appl. Envir. Microbiol., April 1, 2006; 72(4): 2331 - 2342. [Abstract] [Full Text] [PDF]
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A. Chauhan and A. Ogram Fatty Acid-Oxidizing Consortia along a Nutrient Gradient in the Florida Everglades Appl. Envir. Microbiol., April 1, 2006; 72(4): 2400 - 2406. [Abstract] [Full Text] [PDF]
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