Article thumbnail

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

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

Abstract

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

Topics: Short Genome Reports
Publisher: Michigan State University
OAI identifier: oai:pubmedcentral.nih.gov:3111987
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (1975). A new butyric acid-producing Bacteroides species: B. splanchnicus n. sp. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1 Orig Reihe A
  2. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature
  3. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol
  4. (1980). An algorithm for suffix stripping. Program: electronic library and information systems
  5. Anaerobic Gram-negative straight, curved and helical rods. In: Krieg NR, Holt JG (eds),
  6. (2010). BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today
  7. Classification of bacteria and archaea in risk groups.
  8. (2009). Complete genome sequence of Kytococcus sedentarius type strain (541 T). Stand Genomic Sci
  9. (2011). Complete genome sequence of Paludibacter propionicigenes type strain (WB4T). Stand Genomic Sci
  10. (2007). De Moraes Russo CA. An empirical test of the midpoint rooting method.
  11. (1978). Distribution of sphingolipids in Bacteroides species.
  12. (2008). Draft taxonomic outline of the Bacteroidetes,
  13. (2010). En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol
  14. (2007). Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol
  15. (1997). Formation of a dipeptidyl arylamidase by Bacteroides splanchnicus NCTC 10825 with specificities towards glycylprolyl-x and valylalanine-x substrates.
  16. (2000). Gene Ontology: tool for the unification of biology.
  17. (2010). GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods
  18. (1983). Genus Bacteroides. A chemotaxonomical perspective.
  19. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol
  20. (2009). How many bootstrap replicates are necessary? Lect Notes Comput Sci
  21. (2009). IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics
  22. List of growth media used at DSMZ:
  23. (2002). Multiple sequence alignment using partial order graphs. Bioinformatics
  24. (1977). Pelviperitonitis and bacteremia due to Bacteroides splanchnicus. Report of a case. Zentralbl Bakteriol Orig A
  25. (1994). Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria.
  26. (2008). POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT,
  27. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification.
  28. (1986). Ribosomal ribonucleic acid homology among species of the genus Bacteroides.
  29. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
  30. (2001). Taxonomic outline of the Archaea and Bacteria,
  31. (2011). The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking
  32. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354.
  33. (1992). The genus Bacteroides and related species,
  34. (2008). The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol
  35. (2001). The Road Map to the Manual. In: Garrity GM,
  36. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
  37. (2008). 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.
  38. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res
  39. (1971). Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1 Orig Reihe A