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
Received October 4, 1999; Accepted October 6, 1999.
 |
ABSTRACT |
|---|
 TOP ABSTRACT DESCRIPTIONRDP-II CITATION AND ACCESSFUTURE CHANGES AND ADDITIONSREFERENCES |
|---|
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.
|
DESCRIPTION |
|---|
|
TOPABSTRACTDESCRIPTIONRDP-II CITATION AND ACCESSFUTURE CHANGES AND ADDITIONSREFERENCES |
|---|
The Ribosomal Database Project (RDP-II) provides data, programs and services related to the ribosome. This paper describes changes since the 1999 description (1). Details about specific analysis functions, data and available programs can be found at the WWW site http://rdp.cme.msu.edu/
Data
The ribosomal RNA sequences in the RDP-II alignments are mainly drawn from the major sequence repositories [GenBank (2), EMBL Data Library (3) and DDBJ (4)].
Release 7.1, September 17, 1999, contained more than 10 700 small subunit (SSU) rRNA sequences in aligned form and more than 21 000 sequences in unaligned form. It also included 3324 type strain sequences from 2460 different bacterial species. Phylogenetic trees continue to be available for the sequences in the rRNA alignments. They have been assembled by sequential addition of new sequences onto subtrees drawn from our previous trees, using a maximum-likelihood approach (5,6) for each addition. The RDP-II now offers a collection of SSU and LSU rRNA secondary structure diagrams in PDF format from the PostScript files generated and supplied by R. Gutell and his collaborators (7). To facilitate scientific research, RDP-II serves as a repository for published alignments and masks used in trees. Extracting these alignments and masks will support recalculation of published rRNA phylogenetic trees. These data are available for download from the RDP-II WWW (http://rdp.cme.msu.edu/ ) and anonymous ftp servers.
Analysis services
Two new analysis commands have been added: Sequence Selection and TAP T-RFLP. In addition, the interfaces to several other commands have been updated. The documentation pages for all analysis services have also been extensively revised. A brief description of each analysis command available on the WWW server is listed in Table 1.
|
|
RDP-II CITATION AND ACCESS |
|---|
|
TOPABSTRACTDESCRIPTIONRDP-II CITATION AND ACCESSFUTURE CHANGES AND ADDITIONSREFERENCES |
|---|
Research assisted by any RDP service should cite: the Ribosomal Database Project (RDP-II) at the Michigan State University in East Lansing, Michigan; the release number; and this article. Please state which data, programs and services were used and the method of access.
The RDP-II data and analysis services can be found at http://rdp.cme.msu.edu/ . A mirror site is being developed in cooperation with the Laboratory for Molecular Classification in the Center for Information Biology at the National Institute of Genetics (NIG), Japan. This new mirror site should provide better access to RDP-II for researchers in that part of the world. The mirror site address and other news will be announced at the RDP-II WWW site.
The Illinois site remains available with an automated electronic mail server; its address is server@rdp.life.uiuc.edu . To obtain an overview of what data and services are currently available, send an Email message with the phrase ‘help’ as the body of the message.
Electronic mail correspondence with RDP-II staff should be addressed to curator@cme.msu.edu . Those without access to Email may contact the RDP-II staff via telephone (+1 517 432 4998), fax (+1 517 353 8957) or regular mail.
|
FUTURE CHANGES AND ADDITIONS |
|---|
|
TOPABSTRACTDESCRIPTIONRDP-II CITATION AND ACCESSFUTURE CHANGES AND ADDITIONSREFERENCES |
|---|
Release 8.0 will occur in 2000 and it represents an anticipated doubling of the number of rRNA sequences available in the SSU prokaryotic alignment. Changes in the methods used to produce phylogenetic trees are being investigated. Using major phenotypic groupings, based on the outline in the second edition of Bergey’s Manual of Systematic Bacteriology (http://www.cme.msu.edu/Bergeys/ ), to move among tree nodes is being considered. Improved user query access to RDP data is also being developed.
|
ACKNOWLEDGEMENTS |
|---|
We thank several individuals for their past contributions: Robin Gutell (and his colleagues), Niels Larsen, Tom Macke, Michael J. McCaughey, Ross Overbeek, Mitch Sogin and Carl R. Woese. The National Science Foundation’s Science and Technology Center Program, the US Department of Energy Office of Science, and the State of Michigan currently support RDP-II.
|
FOOTNOTES |
|---|
* To whom correspondence should be addressed. Tel: +1 517 432 4998; Fax: +1 517 353 8957; Email: curator@cme.msu.edu
|
REFERENCES |
|---|
|
TOPABSTRACTDESCRIPTIONRDP-II CITATION AND ACCESSFUTURE CHANGES AND ADDITIONSREFERENCES |
|---|
-
1Maidak,B.L., Cole,J.R., Parker,C.T.,Jr, Garrity,G.M., Larsen,N., Li,B., Lilburn,T.G., McCaughey,M.J., Olsen,G.J., Overbeek,R., Pramanik,S., Schmidt,T.M., Tiedje,J.M. and Woese,C.R. (1999) Nucleic Acids Res., 27, 171–173.
2Benson,D.A., Boguski,M.S., Lipman,D.J., Ostell,J., Ouellette,B.F., Rapp,B.A. and Wheeler,D.L. (1999) Nucleic Acids Res., 27, 12–17. Updated article in this issue: Nucleic Acids Res. (2000) 28, 15–18.
3 Stoesser,G., Tuli,M.A., Lopez,R. and Sterk,P. (1999) Nucleic Acids Res., 27, 18–24. Updated article in this issue: Nucleic Acids Res. (2000) 28, 19–23.
4 Sugawara,H., Miyazaki,S., Gojobori,T. and Tateno,Y. (1999) Nucleic Acids Res., 27, 25–28. Updated article in this issue: Nucleic Acids Res. (2000) 28, 24–26.
5 Felsenstein,J. (1981) J. Mol. Evol., 17, 368–376.[Web of Science][Medline]
6 Olsen,G.J., Matsuda,H., Hagstrom,R. and Overbeek,R. (1994) Comput. Appl. Biosci., 10, 41–48.
7 Gutell,R.R. (1994) Nucleic Acids Res., 22, 3502–3507.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Alonso-Gutierrez, A. Figueras, J. Albaiges, N. Jimenez, M. Vinas, A. M. Solanas, and B. Novoa Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill Appl. Envir. Microbiol., June 1, 2009; 75(11): 3407 - 3418. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Wery, V. Bru-Adan, C. Minervini, J.-P. Delgenes, L. Garrelly, and J.-J. Godon Dynamics of Legionella spp. and Bacterial Populations during the Proliferation of L. pneumophila in a Cooling Tower Facility Appl. Envir. Microbiol., May 15, 2008; 74(10): 3030 - 3037. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. D. Long, M. E. Frischer, and C. Y. Robertson A Phaeocystis globosa bloom associated with upwelling in the subtropical South Atlantic Bight J. Plankton Res., September 1, 2007; 29(9): 769 - 774. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Villedieu, A. P. Roberts, E. Allan, H. Hussain, R. McNab, D. A. Spratt, M. Wilson, and P. Mullany Determination of the Genetic Support for tet(W) in Oral Bacteria Antimicrob. Agents Chemother., June 1, 2007; 51(6): 2195 - 2197. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Nibali, D.R. Ready, M. Parkar, P.M. Brett, M. Wilson, M.S. Tonetti, and G.S. Griffiths Gene Polymorphisms and the Prevalence of Key Periodontal Pathogens Journal of Dental Research, May 1, 2007; 86(5): 416 - 420. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. W. Weidler, M. Dornmayr-Pfaffenhuemer, F. W. Gerbl, W. Heinen, and H. Stan-Lotter Communities of Archaea and Bacteria in a Subsurface Radioactive Thermal Spring in the Austrian Central Alps, and Evidence of Ammonia-Oxidizing Crenarchaeota Appl. Envir. Microbiol., January 1, 2007; 73(1): 259 - 270. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Moss, A. Nocker, J. E. Lepo, and R. A. Snyder Stability and Change in Estuarine Biofilm Bacterial Community Diversity Appl. Envir. Microbiol., September 1, 2006; 72(9): 5679 - 5688. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Pang and W.-T. Liu Biological Filtration Limits Carbon Availability and Affects Downstream Biofilm Formation and Community Structure Appl. Envir. Microbiol., September 1, 2006; 72(9): 5702 - 5712. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Ready, J. Pratten, A. P. Roberts, R. Bedi, P. Mullany, and M. Wilson Potential Role of Veillonella spp. as a Reservoir of Transferable Tetracycline Resistance in the Oral Cavity. Antimicrob. Agents Chemother., August 1, 2006; 50(8): 2866 - 2868. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Delgado, J. Quillaguaman, S. Bakhtiar, B. Mattiasson, A. Gessesse, and R. Hatti-Kaul Nesterenkonia aethiopica sp. nov., an alkaliphilic, moderate halophile isolated from an Ethiopian soda lake Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1229 - 1232. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Tal, J. E. M. Watts, and H. J. Schreier Anaerobic Ammonium-Oxidizing (Anammox) Bacteria and Associated Activity in Fixed-Film Biofilters of a Marine Recirculating Aquaculture System Appl. Envir. Microbiol., April 1, 2006; 72(4): 2896 - 2904. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. G. Cirne, O. D. Delgado, S. Marichamy, and B. Mattiasson Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen. Int J Syst Evol Microbiol, March 1, 2006; 56(Pt 3): 625 - 628. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Meijer, P. J. M. Roholl, J. M. Ossewaarde, B. Jones, and B. F. Nowak Molecular Evidence for Association of Chlamydiales Bacteria with Epitheliocystis in Leafy Seadragon (Phycodurus eques), Silver Perch (Bidyanus bidyanus), and Barramundi (Lates calcarifer) Appl. Envir. Microbiol., January 1, 2006; 72(1): 284 - 290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. I. Miteva and J. E. Brenchley Detection and Isolation of Ultrasmall Microorganisms from a 120,000-Year-Old Greenland Glacier Ice Core Appl. Envir. Microbiol., December 1, 2005; 71(12): 7806 - 7818. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Vinas, J. Sabate, M. J. Espuny, and A. M. Solanas Bacterial Community Dynamics and Polycyclic Aromatic Hydrocarbon Degradation during Bioremediation of Heavily Creosote-Contaminated Soil Appl. Envir. Microbiol., November 1, 2005; 71(11): 7008 - 7018. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Lancaster, R. Bedi, M. Wilson, and P. Mullany The maintenance in the oral cavity of children of tetracycline-resistant bacteria and the genes encoding such resistance J. Antimicrob. Chemother., September 1, 2005; 56(3): 524 - 531. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Coates, K. A. Cole, U. Michaelidou, J. Patrick, M. J. McInerney, and L. A. Achenbach Biological Control of Hog Waste Odor through Stimulated Microbial Fe(III) Reduction Appl. Envir. Microbiol., August 1, 2005; 71(8): 4728 - 4735. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Jasti, M. E. Sieracki, N. J. Poulton, M. W. Giewat, and J. N. Rooney-Varga Phylogenetic Diversity and Specificity of Bacteria Closely Associated with Alexandrium spp. and Other Phytoplankton Appl. Envir. Microbiol., July 1, 2005; 71(7): 3483 - 3494. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 J. E. M. Watts, S. K. Fagervold, H. D. May, and K. R. Sowers A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls Microbiology, June 1, 2005; 151(6): 2039 - 2046. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. A. Vargas, O. D. Delgado, R. Hatti-Kaul, and B. Mattiasson Bacillus bogoriensis sp. nov., a novel alkaliphilic, halotolerant bacterium isolated from a Kenyan soda lake Int J Syst Evol Microbiol, March 1, 2005; 55(2): 899 - 902. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ramette, J. J. LiPuma, and J. M. Tiedje Species Abundance and Diversity of Burkholderia cepacia Complex in the Environment Appl. Envir. Microbiol., March 1, 2005; 71(3): 1193 - 1201. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Jernberg, A. Sullivan, C. Edlund, and J. K. Jansson Monitoring of Antibiotic-Induced Alterations in the Human Intestinal Microflora and Detection of Probiotic Strains by Use of Terminal Restriction Fragment Length Polymorphism Appl. Envir. Microbiol., January 1, 2005; 71(1): 501 - 506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Quillaguaman, O. Delgado, B. Mattiasson, and R. Hatti-Kaul Chromohalobacter sarecensis sp. nov., a psychrotolerant moderate halophile isolated from the saline Andean region of Bolivia Int J Syst Evol Microbiol, November 1, 2004; 54(6): 1921 - 1926. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. C. Minion, E. J. Lefkowitz, M. L. Madsen, B. J. Cleary, S. M. Swartzell, and G. G. Mahairas The Genome Sequence of Mycoplasma hyopneumoniae Strain 232, the Agent of Swine Mycoplasmosis J. Bacteriol., November 1, 2004; 186(21): 7123 - 7133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. L. Reardon, D. E. Cummings, L. M. Petzke, B. L. Kinsall, D. B. Watson, B. M. Peyton, and G. G. Geesey Composition and Diversity of Microbial Communities Recovered from Surrogate Minerals Incubated in an Acidic Uranium-Contaminated Aquifer Appl. Envir. Microbiol., October 1, 2004; 70(10): 6037 - 6046. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-L. Chen, H. Macarie, I. Ramirez, A. Olmos, S. L. Ong, O. Monroy, and W.-T. Liu Microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate Microbiology, October 1, 2004; 150(10): 3429 - 3440. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Feio, V. Zinkevich, I. B. Beech, E. Llobet-Brossa, P. Eaton, J. Schmitt, and J. Guezennec Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1747 - 1752. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Ready, H. Lancaster, F. Qureshi, R. Bedi, P. Mullany, and M. Wilson Effect of Amoxicillin Use on Oral Microbiota in Young Children Antimicrob. Agents Chemother., August 1, 2004; 48(8): 2883 - 2887. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, K. H. Nealson, and K. Horikoshi Methanotorris formicicus sp. nov., a novel extremely thermophilic, methane-producing archaeon isolated from a black smoker chimney in the Central Indian Ridge Int J Syst Evol Microbiol, July 1, 2004; 54(4): 1095 - 1100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Massana, J. Castresana, V. Balague, L. Guillou, K. Romari, A. Groisillier, K. Valentin, and C. Pedros-Alio Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles Appl. Envir. Microbiol., June 1, 2004; 70(6): 3528 - 3534. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. T. Novak, R. F. Gritzer, E. R. Leadbetter, and W. Godchaux Phototrophic utilization of taurine by the purple nonsulfur bacteria Rhodopseudomonas palustris and Rhodobacter sphaeroides Microbiology, June 1, 2004; 150(6): 1881 - 1891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Quillaguaman, R. Hatti-Kaul, B. Mattiasson, M. T. Alvarez, and O. Delgado Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile isolated from soil around a Bolivian hypersaline lake Int J Syst Evol Microbiol, May 1, 2004; 54(3): 721 - 725. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, H. Oida, Y. Suzuki, H. Hirayama, S. Nakagawa, T. Nunoura, F. Inagaki, K. H. Nealson, and K. Horikoshi Spatial Distribution of Marine Crenarchaeota Group I in the Vicinity of Deep-Sea Hydrothermal Systems Appl. Envir. Microbiol., April 1, 2004; 70(4): 2404 - 2413. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Frette, N. O. G. Jorgensen, H. Irming, and N. Kroer Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark Int J Syst Evol Microbiol, March 1, 2004; 54(2): 519 - 524. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, K. H. Nealson, and K. Horikoshi Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the {varepsilon}-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field Int J Syst Evol Microbiol, January 1, 2004; 54(1): 25 - 32. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. A. Broderick, K. F. Raffa, R. M. Goodman, and J. Handelsman Census of the Bacterial Community of the Gypsy Moth Larval Midgut by Using Culturing and Culture-Independent Methods Appl. Envir. Microbiol., January 1, 2004; 70(1): 293 - 300. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Haynes, A. C. Darby, T. J. Daniell, G. Webster, F. J. F. van Veen, H.C.J. Godfray, J. I. Prosser, and A. E. Douglas Diversity of Bacteria Associated with Natural Aphid Populations Appl. Envir. Microbiol., December 1, 2003; 69(12): 7216 - 7223. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Inagaki, M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, K. H. Nealson, and K. Horikoshi Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk Appl. Envir. Microbiol., December 1, 2003; 69(12): 7224 - 7235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, S. Nakagawa, Y. Sako, and K. Horikoshi Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system Int J Syst Evol Microbiol, November 1, 2003; 53(6): 1947 - 1954. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Coker, P. P. Sheridan, J. Loveland-Curtze, K. R. Gutshall, A. J. Auman, and J. E. Brenchley Biochemical Characterization of a {beta}-Galactosidase with a Low Temperature Optimum Obtained from an Antarctic Arthrobacter Isolate J. Bacteriol., September 15, 2003; 185(18): 5473 - 5482. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Y. Zhu, J. Lubeck, and J. J. Kilbane II Characterization of Microbial Communities in Gas Industry Pipelines Appl. Envir. Microbiol., September 1, 2003; 69(9): 5354 - 5363. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Gonzalez-Toril, E. Llobet-Brossa, E. O. Casamayor, R. Amann, and R. Amils Microbial Ecology of an Extreme Acidic Environment, the Tinto River Appl. Envir. Microbiol., August 1, 2003; 69(8): 4853 - 4865. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. P. Sheridan, J. Loveland-Curtze, V. I. Miteva, and J. E. Brenchley Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake Int J Syst Evol Microbiol, July 1, 2003; 53(4): 985 - 994. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. de la Torre, B. M. Goebel, E. I. Friedmann, and N. R. Pace Microbial Diversity of Cryptoendolithic Communities from the McMurdo Dry Valleys, Antarctica Appl. Envir. Microbiol., July 1, 2003; 69(7): 3858 - 3867. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Liu, S. M. Tiquia, G. Holguin, L. Wu, S. C. Nold, A. H. Devol, K. Luo, A. V. Palumbo, J. M. Tiedje, and J. Zhou Molecular Diversity of Denitrifying Genes in Continental Margin Sediments within the Oxygen-Deficient Zone off the Pacific Coast of Mexico Appl. Envir. Microbiol., June 1, 2003; 69(6): 3549 - 3560. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, H. Kobayashi, K. H. Nealson, and K. Horikoshi Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer Int J Syst Evol Microbiol, May 1, 2003; 53(3): 823 - 827. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, H. Kobayashi, K. H. Nealson, and K. Horikoshi Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent Int J Syst Evol Microbiol, May 1, 2003; 53(3): 839 - 846. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Kashefi, D. E. Holmes, J. A. Baross, and D. R. Lovley Thermophily in the Geobacteraceae: Geothermobacter ehrlichii gen. nov., sp. nov., a Novel Thermophilic Member of the Geobacteraceae from the "Bag City" Hydrothermal Vent Appl. Envir. Microbiol., May 1, 2003; 69(5): 2985 - 2993. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Teyssier, H. Marchandin, M. Simeon De Buochberg, M. Ramuz, and E. Jumas-Bilak Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies J. Bacteriol., May 1, 2003; 185(9): 2901 - 2909. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. P. Sheridan, V. I. Miteva, and J. E. Brenchley Phylogenetic Analysis of Anaerobic Psychrophilic Enrichment Cultures Obtained from a Greenland Glacier Ice Core Appl. Envir. Microbiol., April 1, 2003; 69(4): 2153 - 2160. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. S. Martinez, J. N. Carter-Franklin, E. L. Mann, J. D. Martin, M. G. Haygood, and A. Butler Bioinorganic Chemistry Special Feature: Structure and membrane affinity of a suite of amphiphilic siderophores produced by a marine bacterium PNAS, April 1, 2003; 100(7): 3754 - 3759. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Villedieu, M. L. Diaz-Torres, N. Hunt, R. McNab, D. A. Spratt, M. Wilson, and P. Mullany Prevalence of Tetracycline Resistance Genes in Oral Bacteria Antimicrob. Agents Chemother., March 1, 2003; 47(3): 878 - 882. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Massana, L. Guillou, B. Diez, and C. Pedros-Alio Unveiling the Organisms behind Novel Eukaryotic Ribosomal DNA Sequences from the Ocean Appl. Envir. Microbiol., September 1, 2002; 68(9): 4554 - 4558. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. W. Reed, Y. Fujita, M. E. Delwiche, D. B. Blackwelder, P. P. Sheridan, T. Uchida, and F. S. Colwell Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin Appl. Envir. Microbiol., August 1, 2002; 68(8): 3759 - 3770. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Dunbar, S. M. Barns, L. O. Ticknor, and C. R. Kuske Empirical and Theoretical Bacterial Diversity in Four Arizona Soils Appl. Envir. Microbiol., June 1, 2002; 68(6): 3035 - 3045. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Takai, H. Hirayama, Y. Sakihama, F. Inagaki, Y. Yamato, and K. Horikoshi Isolation and Metabolic Characteristics of Previously Uncultured Members of the Order Aquificales in a Subsurface Gold Mine Appl. Envir. Microbiol., June 1, 2002; 68(6): 3046 - 3054. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. J. Paster, W. A. Falkler Jr., C. O. Enwonwu, E. O. Idigbe, K. O. Savage, V. A. Levanos, M. A. Tamer, R. L. Ericson, C. N. Lau, and F. E. Dewhirst Prevalent Bacterial Species and Novel Phylotypes in Advanced Noma Lesions J. Clin. Microbiol., June 1, 2002; 40(6): 2187 - 2191. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Ready, A. P. Roberts, J. Pratten, D. A. Spratt, M. Wilson, and P. Mullany Composition and antibiotic resistance profile of microcosm dental plaques before and after exposure to tetracycline J. Antimicrob. Chemother., May 1, 2002; 49(5): 769 - 775. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Orcutt, U. Rasmussen, E. A. Webb, J. B. Waterbury, K. Gundersen, and B. Bergman Characterization of Trichodesmium spp. by Genetic Techniques Appl. Envir. Microbiol., May 1, 2002; 68(5): 2236 - 2245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Coates, K. A. Cole, R. Chakraborty, S. M. O'Connor, and L. A. Achenbach Diversity and Ubiquity of Bacteria Capable of Utilizing Humic Substances as Electron Donors for Anaerobic Respiration Appl. Envir. Microbiol., May 1, 2002; 68(5): 2445 - 2452. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Oberreuter, J. Charzinski, and S. Scherer Intraspecific diversity of Brevibacterium linens, Corynebacterium glutamicum and Rhodococcus erythropolis based on partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy Microbiology, May 1, 2002; 148(5): 1523 - 1532. [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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
E. R. Hendrickson, J. A. Payne, R. M. Young, M. G. Starr, M. P. Perry, S. Fahnestock, D. E. Ellis, and R. C. Ebersole Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe Appl. Envir. Microbiol., February 1, 2002; 68(2): 485 - 495. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Dang and C. R. Lovell Numerical Dominance and Phylotype Diversity of Marine Rhodobacter Species during Early Colonization of Submerged Surfaces in Coastal Marine Waters as Determined by 16S Ribosomal DNA Sequence Analysis and Fluorescence In Situ Hybridization Appl. Envir. Microbiol., February 1, 2002; 68(2): 496 - 504. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. D. Leser, J. Z. Amenuvor, T. K. Jensen, R. H. Lindecrona, M. Boye, and K. Moller Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited Appl. Envir. Microbiol., February 1, 2002; 68(2): 673 - 690. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Wu, J. E. M. Watts, K. R. Sowers, and H. D. May Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines Appl. Envir. Microbiol., February 1, 2002; 68(2): 807 - 812. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 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]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||