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Tindall BJ, Sutton G, Garrity GM. Enterobacter aerogenes Hormaeche and Edwards 1960 (Approved Lists 1980) and Klebsiella mobilis Bascomb et al. 1971 (Approved Lists 1980) share the same nomenclatural type (ATCC 13048) on the Approved Lists and are homotypic synonyms, with consequences for the name Klebsiella mobilis Bascomb et al. 1971 (Approved Lists 1980). Int J Syst Evol Microbiol 2017; 67:502-504. [DOI: 10.1099/ijsem.0.001572] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- B. J. Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - G. Sutton
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, USA
| | - G. M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijs.0.000073] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Chain PSG, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Detter JC. Genomics. Genome project standards in a new era of sequencing. Science 2009; 326:236-7. [PMID: 19815760 DOI: 10.1126/science.1180614] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- P S G Chain
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
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Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009; 37:D141-5. [PMID: 19004872 PMCID: PMC2686447 DOI: 10.1093/nar/gkn879] [Citation(s) in RCA: 3406] [Impact Index Per Article: 227.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/16/2008] [Accepted: 10/17/2008] [Indexed: 02/07/2023] Open
Abstract
The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
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Affiliation(s)
- J R Cole
- Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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Tindall BJ, Garrity GM. Should we alter the way that authorship of a subspecies name that is automatically created under Rule 40d of the Bacteriological Code is cited? Int J Syst Evol Microbiol 2008; 58:1991-2. [DOI: 10.1099/ijs.0.2008/006148-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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6
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Tindall BJ, Garrity GM. Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic research. Int J Syst Evol Microbiol 2008; 58:1987-90. [DOI: 10.1099/ijs.0.2008/006155-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 2006; 35:D169-72. [PMID: 17090583 PMCID: PMC1669760 DOI: 10.1093/nar/gkl889] [Citation(s) in RCA: 769] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website ().
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Affiliation(s)
- J R Cole
- Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA.
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Abstract
The nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor and Popoff, has received wide acceptance, although it does not conform to the rules of the Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code, is being used by an ever-decreasing minority. As a result of a number of recent Requests for an Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies. However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret the taxonomic consequences. The Judicial Commission has therefore asked experts in the field of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic consequences of Opinion 80. The present article explains the nomenclatural consequences of Opinion 80, together with a clear presentation of the taxonomy that results when applying the currently widely accepted interpretation that the genus Salmonella currently includes only two species.
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Affiliation(s)
- B J Tindall
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - P A D Grimont
- Unité de Biodiversité des Bactéries Pathogènes Emergentes, INSERM U389, Institut Pasteur, F-75724 Paris Cedex 15, France
| | - G M Garrity
- Bergey's Manual Trust, Department of Microbiology and Molecular Genetics, 6162 Biomedical Physical Sciences Bldg, Michigan State University, East Lansing, MI 48824-4320, USA
| | - J P Euzéby
- Société de Bactériologie Systématique et Vétérinaire (SBSV) and Ecole Nationale Vétérinaire de Toulouse (ENVT), 23 Chemin des Capelles, BP 87614, F-31076 Toulouse Cedex 03, France
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9
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Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 2005; 33:D294-6. [PMID: 15608200 PMCID: PMC539992 DOI: 10.1093/nar/gki038] [Citation(s) in RCA: 1085] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 09/24/2004] [Accepted: 09/24/2004] [Indexed: 11/17/2022] Open
Abstract
The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101,632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff@msu.edu.
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Affiliation(s)
- J R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824-4320, USA.
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10
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Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 2003; 31:442-3. [PMID: 12520046 PMCID: PMC165486 DOI: 10.1093/nar/gkg039] [Citation(s) in RCA: 926] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Accepted: 09/24/2002] [Indexed: 11/13/2022] Open
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@msu.edu.
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Affiliation(s)
- J R Cole
- Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA.
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11
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Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM. The RDP-II (Ribosomal Database Project). Nucleic Acids Res 2001; 29:173-4. [PMID: 11125082 PMCID: PMC29785 DOI: 10.1093/nar/29.1.173] [Citation(s) in RCA: 959] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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 approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). 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@cme.msu.edu to rdpstaff@msu.edu.
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Affiliation(s)
- B L Maidak
- Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA
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12
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Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Stredwick JM, Garrity GM, Li B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 2000; 28:173-4. [PMID: 10592216 PMCID: PMC102428 DOI: 10.1093/nar/28.1.173] [Citation(s) in RCA: 362] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/1999] [Accepted: 10/06/1999] [Indexed: 11/14/2022] Open
Abstract
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, approx-i-mate 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.
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Affiliation(s)
- B L Maidak
- Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA.
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13
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Abstract
During the past ten years, species-rich nations in the developing world have sought to capitalize on their 'biological patrimony' through a variety of business relationships with multinational corporations as a means of underwriting their conservation efforts. Initially lauded, these relationships have generated more rhetoric than revenues to date. The ramifications of these results on bioprospecting are discussed along with the foreseeable changes in models of collaboration.
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Affiliation(s)
- G M Garrity
- Department of Microbiology, Bergey's Manual Trust, 152 Giltner Hall, Michigan State University, East Lansing, MI 48824-1101, USA.
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14
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Maidak BL, Cole JR, Parker CT, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 1999; 27:171-3. [PMID: 9847171 PMCID: PMC148126 DOI: 10.1093/nar/27.1.171] [Citation(s) in RCA: 676] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides 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. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
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Affiliation(s)
- B L Maidak
- Department of Microbiology, Michigan State University, 294 Giltner Hall, East Lansing, MI 48824-1101, USA
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Lingham RB, Hsu AH, O'Brien JA, Sigmund JM, Sanchez M, Gagliardi MM, Heimbuch BK, Genilloud O, Martin I, Diez MT, Hirsch CF, Zink DL, Liesch JM, Koch GE, Gartner SE, Garrity GM, Tsou NN, Salituro GM. Quinoxapeptins: novel chromodepsipeptide inhibitors of HIV-1 and HIV-2 reverse transcriptase. I. The producing organism and biological activity. J Antibiot (Tokyo) 1996; 49:253-9. [PMID: 8626240 DOI: 10.7164/antibiotics.49.253] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Quinoxapeptin A and B are novel chromodepsipeptides which were isolated from a nocardioform actinomycete with indeterminant morphology. Quinoxapeptins A and B are potent inhibitors of HIV-1 and HIV-2 reverse transcriptase and almost equally active against two single mutants forms as well as a double mutant form of HIV-1 reverse transcriptase. Quinoxapeptin A and B are specific inhibitors of HIV-1 and HIV-2 reverse transcriptase because they did not inhibit human DNA polymerase alpha, beta, gamma and delta. Quinoxapeptin A and B are structurally similar to luzopeptin A which was also active against HIV-1 and HIV-2 reverse transcriptase.
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Affiliation(s)
- R B Lingham
- Merck Research Laboratories, Rahway, NJ 07065, U.S.A
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Garrity GM, Heimbuch BK, Motamedi H, Shafiee A. Genetic relationships among actinomycetes that produce the immunosuppressant macrolides FK506, FK520/FK523 and rapamycin. J Ind Microbiol 1993; 12:42-7. [PMID: 7688970 DOI: 10.1007/bf01570127] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A polyphasic taxonomic study was undertaken to establish the genetic and phenotypic relationships among six actinomycetes that produce the immunosuppressant macrolides FK506, FK520/FK523 and rapamycin. Chemotaxonomic studies reveal that all have Type I cell walls. Gas chromatography (GC) of fatty acid methyl esters revealed patterns consistent for strains of Streptomyces with 16:0 and 15:0 anteiso predominating. Principal component analysis of GC data revealed distinct profiles for each culture. Reciprocal DNA homology studies at Tm-25 showed the rapamycin-producing strain and one FK506-producing strain to have 38-50% homology with the type strain of Streptomyces hygroscopicus (ATCC 27438). The remaining strains exhibited 6-17% homology. To further explore the relationships among these strains all were probed for the presence of an O-methyltransferase gene specific to this biosynthetic pathway. Among the strains of interest, only Streptomyces hygroscopicus subsp. yakushimaensis, the patent strain for FK520/FK523, failed to hybridize with the probes.
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Affiliation(s)
- G M Garrity
- Basic Microbiology Department, Merck Research Laboratories, Merck & Co., Rahway, NJ 07065
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18
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Lam YK, Williams DL, Sigmund JM, Sanchez M, Genilloud O, Kong YL, Stevens-Miles S, Huang L, Garrity GM. Cochinmicins, novel and potent cyclodepsipeptide endothelin antagonists from a Microbispora sp. I. Production, isolation, and characterization. J Antibiot (Tokyo) 1992; 45:1709-16. [PMID: 1468977 DOI: 10.7164/antibiotics.45.1709] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cochinmicins I, II, III are novel peptolides produced in submerged-fermentation cultures of Microbispora sp. ATCC 55140. These closely related compounds are separated by HPLC and are novel competitive endothelin antagonists. Cochinmicins II and III are stereoisomeric to each other. Cochinmicin I is the deschloro analog of cochinmicin III.
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Affiliation(s)
- Y K Lam
- Merck Research Laboratories, Rahway, New Jersey 07065
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19
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Lingham RB, Arison BH, Colwell LF, Hsu A, Dezeny G, Thompson WJ, Garrity GM, Gagliardi MM, Hartner FW, Darke PL. HIV-1 protease inhibitory activity of L-694,746, a novel metabolite of L-689,502. Biochem Biophys Res Commun 1991; 181:1456-61. [PMID: 1764098 DOI: 10.1016/0006-291x(91)92103-q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
L-689,502 is a potent inhibitor of HIV-1 protease activity in vitro. Microbial biotransformations of L-689,502 by cultures belonging to the genus Streptomyces sp. were performed. Extracts of culture broths were examined for the production of metabolites of L-689,502 that could inhibit HIV-1 protease activity. One culture, MA 6804 (Streptomyces lavendulae, ATCC 55095), produced L-694,746 that, while being structurally related to L-689,502, is a novel metabolite and a potent inhibitor of HIV-1 protease.
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Affiliation(s)
- R B Lingham
- Merck, Sharp and Dohme Research Laboratories, Rahway, New Jersey 07065
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20
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Lam YK, Bogen D, Chang RS, Faust KA, Hensens OD, Zink DL, Schwartz CD, Zitano L, Garrity GM, Gagliardi MM. Novel and potent gastrin and brain cholecystokinin antagonists from Streptomyces olivaceus. Taxonomy, fermentation, isolation, chemical conversions, and physico-chemical and biochemical properties. J Antibiot (Tokyo) 1991; 44:613-25. [PMID: 1906451 DOI: 10.7164/antibiotics.44.613] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The discovery and physico-chemical characterization of three novel and minor virginiamycin M1 analogs as potent gastrin antagonists from a culture of a strain of Streptomyces olivaceus are described. These analogs are L-156,586, L-156,587 and L-156,588. They are, respectively, 15-dihydro-13,14-anhydro-, 13,14-anhydro- and 13-desoxy-analogs of virginiamycin M1. We also chemically converted virginiamycin M1 (via L-156,587) to L-156,586 and its unnatural epimer, L-156,906. These analogs are competitive and selective antagonists of gastrin and brain cholecystokinin binding at nanomolar concentrations. These are the most potent gastrin/brain cholecystokinin antagonists from natural products. The same compounds showed poor Gram-positive antibiotic activity versus virginiamycin M1. Structurally related Gram-positive antibiotics, griseoviridin and madumycin I, were inactive in gastrin and brain cholecystokinin binding at up to 100 microM.
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Affiliation(s)
- Y K Lam
- Merck Sharp & Dohme Research Laboratories, Rahway, New Jersey 07065
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Chaiet L, Fromtling RA, Garrity GM, Monaghan RL, Hensens OD, Valiant ME, Zink DL. L-681,572--a new antifungal agent. Isolation, characterization, and biological activity. J Antibiot (Tokyo) 1989; 42:1718-21. [PMID: 2684948 DOI: 10.7164/antibiotics.42.1718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- L Chaiet
- Merck Sharp & Dohme Research Laboratories, Rahway, New Jersey 07065
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Firestone RA, Pisano JM, Garrity GM, Fromtling RA, Zimmerman SB. Lysosomotropic agents. 7. Broad-spectrum antifungal activity of lysosomotropic detergents. J Med Chem 1987; 30:1519-21. [PMID: 3302260 DOI: 10.1021/jm00391a043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lysosomotropic detergents, which kill mammalian cells by disrupting lysosomal membranes, have now been found to be antifungals also. All strains in our assay are susceptible. The mode of action is as yet undetermined, but intracellular vacuoles may be the primary targets.
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Brown A, Vickers RM, Elder EM, Lema M, Garrity GM. Plasmid and surface antigen markers of endemic and epidemic Legionella pneumophila strains. J Clin Microbiol 1982; 16:230-5. [PMID: 7119096 PMCID: PMC272335 DOI: 10.1128/jcm.16.2.230-235.1982] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Environmental and clinical isolates of Legionella pneumophila obtained from the Pittsburgh Veterans Administration Medical Center were studied for the presence of plasmids and for unique surface antigens. The majority of environmental isolates contained a single 80-megadalton plasmid. After an epidemic of nosocomial Legionnaires disease subsided in the Spring of 1981, plasmid-bearing environmental isolates persisted in the environment. Whereas L. pneumophila could not be reisolated from most sites with plasmidless isolates. During this epidemic the attack rate was highest on wards with plasmidless isolates. All clinical isolates were plasmidless. Strains were serotyped by the indirect immunofluorescence method with serum from a single immunized rat which was used both without absorption and after absorption with various plasmid-bearing and plasmidless isolates. These studies suggested that a plasmid-associated surface antigen was present and that the most common plasmidless environmental serotype was similar to the epidemic clinical serotype.
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Garrity GM, Elder EM, Davis B, Vickers RM, Brown A. Serological and genotypic diversity among serogroup 5- reacting environmental Legionella isolates. J Clin Microbiol 1982; 15:646-53. [PMID: 6175657 PMCID: PMC272161 DOI: 10.1128/jcm.15.4.646-653.1982] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Five strains of bacteria (strains 684, 687, U7W, U8W, and MICU-B) that were biochemically and morphologically indistinguishable from Legionella pneumophila were recovered from the environment. Strains U7W, U8W, and MICU-B were antigenically identical to L. pneumophila strain Dallas 1E (serogroup 5), as determined by direct fluorescent antibody staining and immunodiffusion. Although strains 694 and 687 shared antigenic determinants with L. pneumophila Dallas 1E, they could be distinguished by immunodiffusion and differential absorption studies. However, as determined by DNA hybridization, the antigenically distinct strains 684 belong to the same DNA homology cluster as previously described authentic strains of L. pneumophila, whereas strain U7W, U8W, and MICU-B belong to a separate homology group. Therefore, two groups could be identified among these environmental isolates; one represents an antigenic subclass of serogroup 5 L. pneumophila (strains 684, and 687), and the other, although antigenically indistinguishable from serogroup 5 L. pneumophila, probably represents a new Legionella species (strains U7W, U8W, and MICU-B).
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Abstract
Tatlockia (Legionella) micdadei, the Pittsburgh pneumonia agent, was isolated from a hospital shower. Although it was not possible, at the current time, to establish an epidemiological link to disease acquisition, this information may be significant because it provides further evidence that a water-associated reservoir of this organism exists within the hospital.
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Vickers RM, Brown A, Garrity GM. Dye-containing buffered charcoal-yeast extract medium for differentiation of members of the family Legionellaceae. J Clin Microbiol 1981; 13:380-2. [PMID: 7009642 PMCID: PMC273792 DOI: 10.1128/jcm.13.2.380-382.1981] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The addition of 0.001% bromocresol purple and 0.001% bromothymol blue to buffered charcoal-yeast extract agar allowed differentiation between members of the family Legionellaceae. On this medium, Legionella pneumophila grew as relatively flat, pale green colonies, whereas Tatlockia micdadei (gen. nov., comb. nov., Pittsburgh pneumonia agent) produced blue-gray colonies. Fluoribacter spp. (gen. nov., atypical Legionella-like organisms) developed glistening colonies which were brighter green than those of L. pneumophila.
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Brown A, Garrity GM. Detection and quantitation of amanitin using an RNA-polymerase competition binding assay. Toxicon 1980; 18:702-4. [PMID: 7222075 DOI: 10.1016/0041-0101(80)90104-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Garrity GM, Brown A. Competition binding assay using o-methyl-[3H]-demethyl-gamma-amanitin for study of RNA polymerase B. Proc Soc Exp Biol Med 1978; 159:98-104. [PMID: 714939 DOI: 10.3181/00379727-159-40292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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