Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)

Göker, Markus; Gronow, Sabine; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Lapidus, Alla; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Brambilla, Evelyne-Marie; Rohde, Manfred; Detter, John C.; Woyke, Tanja; Bristow, James; Markowitz, Victor; Hugenholtz, Philip; Eisen, Jonathan A.; Kyrpides, Nikos C.; Klenk, Hans-Peter

doi:10.4056/sigs.1714269

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6^T)

Journal Article · Fri Apr 29 00:00:00 EDT 2011 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1714269· OSTI ID:1630565

Göker, Markus ^[1]; Gronow, Sabine ^[1]; Zeytun, Ahmet ^[2]; Nolan, Matt ^[3]; Lucas, Susan ^[3]; Lapidus, Alla ^[3]; Hammon, Nancy ^[3]; Deshpande, Shweta ^[3]; Cheng, Jan-Fang ^[3]; Pitluck, Sam ^[3]; Liolios, Konstantinos ^[3]; Pagani, Ioanna ^[3]; Ivanova, Natalia ^[3]; Mavromatis, Konstantinos ^[3]; Ovchinikova, Galina ^[3]; Pati, Amrita ^[3]; Tapia, Roxane ^[2]; Han, Cliff ^[2]; Goodwin, Lynne ^[2]; Chen, Amy ^[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); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Helmholtz Centre for Infection Research, Braunschweig (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)

Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the genus Odoribacter, which belongs to the family Porphyromonadaceae in the order 'Bacteroidales'. The species is of interest because members of the Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the first completed genome sequence of a member of the genus Odoribacter and the fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome with its 3,672 protein-coding and 74 RNA genes 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:: German Research Foundation (DFG); USDOE Office of Science (SC), Biological and Environmental Research (BER)

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

OSTI ID:: 1630565

Alternate ID(s):: OSTI ID: 1018664

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 2 Vol. 4; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (30)

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
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
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
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
The DNA Bank Network: The Start from a German Initiative Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger Biopreservation and Biobanking, Vol. 9, Issue 1 https://doi.org/10.1089/bio.2010.0029	journal	March 2011
How Many Bootstrap Replicates Are Necessary? Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P. Journal of Computational Biology, Vol. 17, Issue 3 https://doi.org/10.1089/cmb.2009.0179	journal	March 2010
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
Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis Naito, M.; Hirakawa, H.; Yamashita, A. DNA Research, Vol. 15, Issue 4 https://doi.org/10.1093/dnares/dsn013	journal	May 2008
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
Ribosomal Ribonucleic Acid Homology among Species of the Genus Bacteroides Johnson, J. L.; Harich, B. International Journal of Systematic Bacteriology, Vol. 36, Issue 1 https://doi.org/10.1099/00207713-36-1-71	journal	January 1986
Formation of a dipeptidyl arylamidase by Bacteroides splanchnicus NCTC 10825 with specificities towards glycylprolyl-x and valylalanine-x substrates Macfarlane, S.; Macfarlane, G. T. Journal of Medical Microbiology, Vol. 46, Issue 7 https://doi.org/10.1099/00222615-46-7-547	journal	July 1997
Transfer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients Hardham, J. M.; King, K. W.; Dreier, K. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 1 https://doi.org/10.1099/ijs.0.63458-0	journal	January 2008
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
An algorithm for suffix stripping Porter, M. F. Program, Vol. 14, Issue 3 https://doi.org/10.1108/eb046814	journal	March 1980
An empirical test of the midpoint rooting method: A TEST FOR THE MIDPOINT ROOTING METHOD Hess, Pablo N.; De Moraes Russo, Claudia A. Biological Journal of the Linnean Society, Vol. 92, Issue 4 https://doi.org/10.1111/j.1095-8312.2007.00864.x	journal	December 2007
Genus Bacteroides A chemotaxonomical perspective Shah, H. N.; Collins, M. D. Journal of Applied Bacteriology, Vol. 55, Issue 3 https://doi.org/10.1111/j.1365-2672.1983.tb01680.x	journal	December 1983
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
Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria. Paster, B. J.; Dewhirst, F. E.; Olsen, I. Journal of Bacteriology, Vol. 176, Issue 3 https://doi.org/10.1128/jb.176.3.725-732.1994	journal	February 1994
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
Evolution of Symbiotic Bacteria in the Distal Human Intestine Xu, Jian; Mahowald, Michael A.; Ley, Ruth E. PLoS Biology, Vol. 5, Issue 7 https://doi.org/10.1371/journal.pbio.0050156	journal	June 2007
Distribution of Sphingolipids in Bacteroides Species Miyagawa, Eiichi; Azuma, Ryozo; Suto, Tsuneji The Journal of General and Applied Microbiology, Vol. 24, Issue 6 https://doi.org/10.2323/jgam.24.341	journal	January 1978
Complete genome sequence of Leadbetterella byssophila type strain (4M15T) Abt, Birte; Teshima, Hazuki; Lucas, Susan Standards in Genomic Sciences, Vol. 4, Issue 1 https://doi.org/10.4056/sigs.1413518	journal	April 2011
Complete genome sequence of Paludibacter propionicigenes type strain (WB4T) Gronow, Sabine; Munk, Christine; Lapidus, Alla Standards in Genomic Sciences, Vol. 4, Issue 1 https://doi.org/10.4056/sigs.1503846	journal	February 2011
Complete genome sequence of Kytococcus sedentarius type strain (541T) Sims, David; Brettin, Thomas; Detter, John C. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.761	journal	July 2009

Cited By (18)

Effect of daily intake of pomegranate juice on fecal microbiota and feces metabolites from healthy volunteers Mosele, Juana I.; Gosalbes, María-José; Macià, Alba Molecular Nutrition & Food Research, Vol. 59, Issue 10 https://doi.org/10.1002/mnfr.201500227	journal	August 2015
Pterostilbene-induced changes in gut microbiota composition in relation to obesity Etxeberria, Usune; Hijona, Elizabeth; Aguirre, Leixuri Molecular Nutrition & Food Research, Vol. 61, Issue 1 https://doi.org/10.1002/mnfr.201500906	journal	August 2016
Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach Turroni, Francesca; Milani, Christian; Duranti, Sabrina The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.236	journal	February 2016
Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice Fernández-Calleja, José M. S.; Konstanti, Prokopis; Swarts, Hans J. M. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-33619-0	journal	October 2018
Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice Lai, Zi-Lun; Tseng, Ching-Hung; Ho, Hsiu J. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-33893-y	journal	October 2018
Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome Patterson, E.; Ryan, P. M.; Wiley, N. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-51781-x	journal	November 2019
Early life nutrition influences susceptibility to chronic inflammatory colitis in later life Ley, Delphine; Desseyn, Jean-Luc; Gouyer, Valérie Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-54308-6	journal	December 2019
Changes of the human gut microbiome induced by a fermented milk product Veiga, Patrick; Pons, Nicolas; Agrawal, Anurag Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep06328	journal	September 2014
A genomic approach to the cryptic secondary metabolome of the anaerobic world Letzel, Anne-Catrin; Pidot, Sacha J.; Hertweck, Christian Nat. Prod. Rep., Vol. 30, Issue 3 https://doi.org/10.1039/c2np20103h	journal	January 2013
The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease–Like Ileitis Rodriguez-Palacios, Alexander; Harding, Andrew; Menghini, Paola Inflammatory Bowel Diseases, Vol. 24, Issue 5 https://doi.org/10.1093/ibd/izy060	journal	March 2018
Gut Microbiota Diversity across Ethnicities in the United States Brooks, Andrew W.; Priya, Sambhawa; Blekman, Ran PLoS Biology https://doi.org/10.1101/342915	posted_content	October 2018
Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan-rich hemicellulose extract in the diet Konkol, Yvonne; Keskitalo, Anniina; Vuorikoski, Heikki BJU International, Vol. 123, Issue 5 https://doi.org/10.1111/bju.14553	journal	November 2018
Race-dependent association of sulfidogenic bacteria with colorectal cancer Yazici, Cemal; Wolf, Patricia G.; Kim, Hajwa Gut, Vol. 66, Issue 11 https://doi.org/10.1136/gutjnl-2016-313321	journal	February 2017
Increased Systolic and Diastolic Blood Pressure Is Associated With Altered Gut Microbiota Composition and Butyrate Production in Early Pregnancy Gomez-Arango, Luisa F.; Barrett, Helen L.; McIntyre, H. David Hypertension, Vol. 68, Issue 4 https://doi.org/10.1161/hypertensionaha.116.07910	journal	October 2016
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Morgan, Xochitl C.; Tickle, Timothy L.; Sokol, Harry Genome Biology, Vol. 13, Issue 9 https://doi.org/10.1186/gb-2012-13-9-r79	journal	January 2012
Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer Miao, Ruizhong; Badger, Taylor C.; Groesch, Kathleen PLOS ONE, Vol. 15, Issue 1 https://doi.org/10.1371/journal.pone.0227707	journal	January 2020
Genome-Based Taxonomic Classification of Bacteroidetes Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.02003	journal	December 2016
Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon Gurwara, Shawn; Ajami, Nadim; Jang, Albert Nutrients, Vol. 11, Issue 3 https://doi.org/10.3390/nu11030613	journal	March 2019