Complete genome sequence of Weeksella virosa type strain (9751T)

Lang, Elke; Teshima, Hazuki; Lucas, Susan; Lapidus, Alla; Hammon, Nancy; Deshpande, Shweta; Nolan, Matt; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mikhailova, Natalia; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brambilla, Evelyne-Marie; Kopitz, Markus; Rohde, Manfred; Göker, Markus; Tindall, Brian J.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

doi:10.4056/sigs.1603927

Complete genome sequence of Weeksella virosa type strain (9751^T)

Journal Article · Tue Feb 22 04:00:00 EST 2011 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1603927· OSTI ID:1630561

Lang, Elke ^[1]; Teshima, Hazuki ^[2]; Lucas, Susan ^[3]; Lapidus, Alla ^[3]; Hammon, Nancy ^[3]; Deshpande, Shweta ^[3]; Nolan, Matt ^[3]; Cheng, Jan-Fang ^[3]; Pitluck, Sam ^[3]; Liolios, Konstantinos ^[3]; Pagani, Ioanna ^[3]; Mikhailova, Natalia ^[3]; Ivanova, Natalia ^[3]; Mavromatis, Konstantinos ^[3]; Pati, Amrita ^[3]; Tapia, Roxane ^[2]; Han, Cliff ^[2]; Goodwin, Lynne ^[2]; Chen, Amy ^[4]; Palaniappan, Krishna ^[4] more »

German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig (Germany)v
Helmholtz Centre for Infection Research, Braunschweig (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
4Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)

Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella which belongs to the family Flavobacteriaceae of the phylum Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided the basis for the taxon description. While the species seems to be a saprophyte of the mucous membranes of healthy man and warm-blooded animals a causal relationship with disease has been reported in a few instances. Except for the ability to produce indole and to hydrolyze Tween and proteins such as casein and gelatin, this aerobic, non-motile, non-pigmented bacterial species is metabolically inert in most traditional biochemical tests. The 2,272,954 bp long genome with its 2,105 protein-coding and 76 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG)

Grant/Contract Number:: AC02-05CH11231; AC52-07NA27344; AC05-00OR22725

OSTI ID:: 1630561

Alternate ID(s):: OSTI ID: 1029237

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 4; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (34)

En route to a genome-based classification of Archaea and Bacteria? Klenk, H. -P.; Göker, M. Systematic and Applied Microbiology, Vol. 33, Issue 4 https://doi.org/10.1016/j.syapm.2010.03.003	journal	June 2010
How Many Bootstrap Replicates Are Necessary? Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P. Lecture Notes in Computer Science https://doi.org/10.1007/978-3-642-02008-7_13	book	January 2009
Weeksella virosa gen. no v., sp. nov. (Formerly group IIf), found in human clinical specimens Holmes, B.; Steigerwalt, A. G.; Weaver, R. E. Systematic and Applied Microbiology, Vol. 8, Issue 3 https://doi.org/10.1016/S0723-2020(86)80075-3	journal	October 1986
Lymphoepithelioma-like Carcinoma of the Urinary Bladder in a Cow Associated with Bovine Papillomavirus Type-2 Brun, R.; Urraro, C.; Medaglia, C. Journal of Comparative Pathology, Vol. 139, Issue 2-3 https://doi.org/10.1016/j.jcpa.2008.06.002	journal	August 2008
Oral colonization of aerobic and facultatively anaerobic gram-negative rods and cocci in irradiated, dentate, xerostomic individuals Leung, W. K.; Jin, L. J.; Yam, W. C. Oral Microbiology and Immunology, Vol. 16, Issue 1 https://doi.org/10.1034/j.1399-302x.2001.160101.x	journal	February 2001
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
The incidence of Weeksella- and Bergeyella-like bacteria in the food environment Botha, W. C.; Jooste, P. J.; Hugo, C. J. Journal of Applied Microbiology, Vol. 84, Issue 3 https://doi.org/10.1046/j.1365-2672.1998.00346.x	journal	March 1998
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
Multiple sequence alignment using partial order graphs Lee, C.; Grasso, C.; Sharlow, M. F. Bioinformatics, Vol. 18, Issue 3 https://doi.org/10.1093/bioinformatics/18.3.452	journal	March 2002
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
A case of spontaneous peritonitis caused by Weeksella virosa Boixeda, D.; de Luis, D. A.; Meseguer, M. A. European Journal of Gastroenterology & Hepatology, Vol. 10, Issue 10 https://doi.org/10.1097/00042737-199810000-00016	journal	January 1998
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 23 No authors listed International Journal of Systematic Bacteriology, Vol. 37, Issue 2, p. 179-179 https://doi.org/10.1099/00207713-37-2-179	journal	April 1987
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 41 No authors listed International Journal of Systematic Bacteriology, Vol. 42, Issue 2, p. 327-328 https://doi.org/10.1099/00207713-42-2-327	journal	April 1992
NOTES: New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Vandamme, P.; Bernardet, J. -F.; Segers, P. International Journal of Systematic Bacteriology, Vol. 44, Issue 4 https://doi.org/10.1099/00207713-44-4-827	journal	October 1994
Cutting a Gordian Knot: Emended Classification and Description of the Genus Flavobacterium, Emended Description of the Family Flavobacteriaceae, and Proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978) Bernardet, J. -F.; Segers, P.; Vancanneyt, M. International Journal of Systematic Bacteriology, Vol. 46, Issue 1 https://doi.org/10.1099/00207713-46-1-128	journal	January 1996
Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family Bernardet, J. F. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 3 https://doi.org/10.1099/ijs.0.02136-0	journal	May 2002
Chryseobacterium joostei sp. nov., isolated from the dairy environment Hugo, C. J. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 3 https://doi.org/10.1099/ijs.0.02232-0	journal	May 2003
Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. O'Sullivan, L. A. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 1 https://doi.org/10.1099/ijs.0.63941-0	journal	January 2006
Description of Wautersiella falsenii gen. nov., sp. nov., to accommodate clinical isolates phenotypically resembling members of the genera Chryseobacterium and Empedobacter Kämpfer, Peter; Avesani, Véronique; Janssens, Michèle International Journal of Systematic and Evolutionary Microbiology, Vol. 56, Issue 10 https://doi.org/10.1099/ijs.0.64393-0	journal	October 2006
Aerococcus suis sp. nov., isolated from clinical specimens from swine Vela, A. I.; García, N.; Latre, M. V. International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 6 https://doi.org/10.1099/ijs.0.64537-0	journal	June 2007
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
The taxonomic relationship of certain environmental flavobacteria to the genus Weeksella Botha, W. C.; Jooste, P. J.; Britz, T. J. Journal of Applied Bacteriology, Vol. 67, Issue 5 https://doi.org/10.1111/j.1365-2672.1989.tb02527.x	journal	November 1989
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
Microbiological characteristics of Weeksella virosa (formerly CDC group IIf) isolated from the human genitourinary tract. Reina, J.; Gil, J.; Salva, F. Journal of Clinical Microbiology, Vol. 28, Issue 10 https://doi.org/10.1128/JCM.28.10.2357-2359.1990	journal	January 1990
Phenotypic characteristics, fatty acid composition, and isoprenoid quinone content of CDC group IIg bacteria. Hollis, D. G.; Daneshvar, M. I.; Moss, C. W. Journal of clinical microbiology, Vol. 33, Issue 3 https://doi.org/10.1128/JCM.33.3.762-764.1995	journal	January 1995
Incidence of vaginal Weeksella virosa (formerly group IIf). Mardy, C.; Holmes, B. Journal of Clinical Pathology, Vol. 41, Issue 2 https://doi.org/10.1136/jcp.41.2.211	journal	February 1988
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Study on the bacterial midgut microbiota associated to different Brazilian populations of Lutzomyia longipalpis (Lutz & Neiva) (Diptera: Psychodidae) Gouveia, Cheryl; Asensi, Marise D.; Zahner, Viviane Neotropical Entomology, Vol. 37, Issue 5 https://doi.org/10.1590/S1519-566X2008000500016	journal	January 2008

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