Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)
Abstract
Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Authors:
-
more »
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Helmholtz Centre for Infection Research, Braunschweig (Germany)
- German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG)
- OSTI Identifier:
- 1630562
- Alternate Identifier(s):
- OSTI ID: 1029229
- Grant/Contract Number:
- AC02-05CH11231; AC52-07NA27344; AC52-06NA25396; AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Volume: 4; Journal Issue: 1; Related Information: https://link.springer.com/article/10.4056/sigs.1513795; Journal ID: ISSN 1944-3277
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; strictly anaerobic; mesophilic; nonmotile; Gram-negative; chemoorganotrophic; pig abscess; animal pathogen; Bacteroidaceae; GEBA; 60 APPLIED LIFE SCIENCES
Citation Formats
Pati, Amrita, Gronow, Sabine, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Lucas, Susan. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T). United States: N. p., 2011.
Web. doi:10.4056/sigs.1513795.
Pati, Amrita, Gronow, Sabine, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, & Lucas, Susan. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T). United States. https://doi.org/10.4056/sigs.1513795
Pati, Amrita, Gronow, Sabine, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Lucas, Susan. Tue .
"Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)". United States. https://doi.org/10.4056/sigs.1513795. https://www.osti.gov/servlets/purl/1630562.
@article{osti_1630562,
title = {Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)},
author = {Pati, Amrita and Gronow, Sabine and Zeytun, Ahmet and Lapidus, Alla and Nolan, Matt and Hammon, Nancy and Deshpande, Shweta and Cheng, Jan-Fang and Tapia, Roxane and Han, Cliff and Goodwin, Lynne and Pitluck, Sam and Liolios, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Mavromatis, Konstantinos and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Chang, Yun-Juan and Jeffries, Cynthia D. and Detter, John C. and Brambilla, Evelyne and Rohde, Manfred and Göker, Markus and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter and Lucas, Susan},
abstractNote = {Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.1513795},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 4,
place = {United States},
year = {Tue Feb 22 00:00:00 EST 2011},
month = {Tue Feb 22 00:00:00 EST 2011}
}
Web of Science
Figures / Tables:
Works referenced in this record:
Preparation of transforming deoxyribonucleic acid by phenol treatment
journal, January 1963
- Saito, Hiuga; Miura, Kin-Ichiro
- Biochimica et Biophysica Acta (BBA) - Specialized Section on Nucleic Acids and Related Subjects, Vol. 72
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000
- Castresana, J.
- Molecular Biology and Evolution, Vol. 17, Issue 4
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 12
journal, January 1983
- ,
- International Journal of Systematic and Evolutionary Microbiology
Approved Lists of Bacterial Names
journal, January 1980
- Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
Bacteroides zoogleoformans (Weinberg, Nativelle, and Prevot 1937) corrig., comb. nov.: Emended Description
journal, July 1982
- Cato, E. P.; Kelley, R. W.; Moore, W. E. C.
- International Journal of Systematic Bacteriology, Vol. 32, Issue 3
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
journal, November 2009
- Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos
- Nucleic Acids Research, Vol. 38, Issue suppl_1
The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
journal, September 2008
- Yarza, Pablo; Richter, Michael; Peplies, Jörg
- Systematic and Applied Microbiology, Vol. 31, Issue 4
A Rapid Bootstrap Algorithm for the RAxML Web Servers
journal, October 2008
- Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques
- Systematic Biology, Vol. 57, Issue 5
Gene Ontology: tool for the unification of biology
journal, May 2000
- Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
- Nature Genetics, Vol. 25, Issue 1
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
Extensive DNA Inversions in the B. fragilis Genome Control Variable Gene Expression
journal, March 2005
- Cerdeno-Tarraga, A. M.
- Science, Vol. 307, Issue 5714
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Proposal To Restrict the Genus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and Closely Related Species
journal, January 1989
- Shah, H. N.; Collins, M. D.
- International Journal of Systematic Bacteriology, Vol. 39, Issue 1
Multiple sequence alignment using partial order graphs
journal, March 2002
- Lee, C.; Grasso, C.; Sharlow, M. F.
- Bioinformatics, Vol. 18, Issue 3
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010
- Klenk, H. -P.; Göker, M.
- Systematic and Applied Microbiology, Vol. 33, Issue 4
Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., New Species from Abscesses and Feces of Pigs
journal, August 1983
- Benno, Yoshimi; Watabe, Junko; Mitsuoka, Tomotari
- Systematic and Applied Microbiology, Vol. 4, Issue 3
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009
- Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
- Nature, Vol. 462, Issue 7276
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010
- Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
- Nature Methods, Vol. 7, Issue 6
Works referencing / citing this record:
A genomic approach to the cryptic secondary metabolome of the anaerobic world
journal, January 2013
- Letzel, Anne-Catrin; Pidot, Sacha J.; Hertweck, Christian
- Nat. Prod. Rep., Vol. 30, Issue 3
Genome-Based Taxonomic Classification of Bacteroidetes
journal, December 2016
- Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina
- Frontiers in Microbiology, Vol. 7
Figures / Tables found in this record: