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Strain identifier

BacDive ID: 12520

Type strain: Yes

Species: Odoribacter splanchnicus

Strain Designation: 1651/6

Strain history: CCUG 21054 A <-- CCM 6029 <-- H. Werner 1651/6.

NCBI tax ID(s): 709991 (strain), 28118 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9023

BacDive-ID: 12520

DSM-Number: 20712

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Odoribacter splanchnicus 1651/6 is an anaerobe, mesophilic bacterium that was isolated from abdominal abscess.

NCBI tax id

NCBI tax idMatching level
709991strain
28118species

strain history

doi: 10.13145/bacdive12520.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Odoribacteraceae
  • genus: Odoribacter
  • species: Odoribacter splanchnicus
  • full scientific name: Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008
  • synonyms

    • @ref: 20215
    • synonym: Bacteroides splanchnicus

@ref: 9023

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Odoribacteraceae

genus: Odoribacter

species: Odoribacter splanchnicus

full scientific name: Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 emend. Hahnke et al. 2016

strain designation: 1651/6

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.066

colony morphology

  • @ref: 47264
  • incubation period: 2-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20712_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9023COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
9023CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
9023positivegrowth37mesophilic
47264positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
9023anaerobe
47264anaerobe
69480anaerobe99.052

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.017

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 97.552

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan+energy source
6838017632nitrate-reduction
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase+4.1.99.1
68380alpha-fucosidase+3.2.1.51
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
9023--++-----+---+-+++-+-+--+----
9023--++-+/----+--++-+++-+-++/-+/-+-+/---
9023--++-----+--++-+++-+-++-+--+-
9023--++-----+--++-+++-+-+--+----

Isolation, sampling and environmental information

isolation

@refsample type
9023abdominal abscess
47264Human abdominal abscess
67770Abdominal abscess

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Other#Abdomen
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_2542.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_332;96_1367;97_1624;98_1975;99_2542&stattab=map
  • Last taxonomy: Odoribacter splanchnicus subclade
  • 16S sequence: NR_074535
  • Sequence Identity:
  • Total samples: 218669
  • soil counts: 1276
  • aquatic counts: 5874
  • animal counts: 211105
  • plant counts: 414

Safety information

risk assessment

  • @ref: 9023
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
9023Odoribacter splanchnicus strain DSM 220712 16S ribosomal RNA, partial sequenceNR_0745351512nuccore28118
67770Odoribacter splanchnicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 15291AB5476491485ena28118
67770Odoribacter splanchnicus strain NCTC 10825 16S ribosomal RNA gene, partial sequenceL164961467ena28118

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Odoribacter splanchnicus DSM 20712 DSM 220712GCA_000190535completencbi709991
66792Odoribacter splanchnicus NCTC10825GCA_900187175completencbi28118
66792Odoribacter splanchnicus DSM 20712 FDAARGOS_1579GCA_020736405chromosomencbi709991
66792Odoribacter splanchnicus DSM 220712709991.3completepatric709991
66792Odoribacter splanchnicus strain NCTC1082528118.6completepatric28118
66792Odoribacter splanchnicus 1651/6, DSM 20712649633078completeimg709991
66792Odoribacter splanchnicus NCTC 108252773857890completeimg28118
67770Odoribacter splanchnicus DSM 20712, complete genomeCP002544ena709991
66792Oscillospiraceae bacterium U_126914GCA_020860505scaffoldpatric2485925
66792Acinetobacter baumannii Ab-HCG1208-35GCA_021174485contigpatric470
66792uncultured Pelagibacteraceae bacterium AG-404-L08GCA_902563285contigpatric1667051
66792uncultured Pelagibacteraceae bacterium AG-435-K05GCA_902586685contigpatric1667051
66792uncultured Bacteroidales bacterium SRR12203239_bin.5_metaWRAP_v1.3_MAGGCA_946001035contigpatric194843

GC content

  • @ref: 9023
  • GC-content: 43.4
  • method: sequence analysis

External links

@ref: 9023

culture collection no.: DSM 20712, ATCC 29572, CCUG 21054, CIP 104287, LMG 8202, NCTC 10825, CCUG 21054 A, CCM 6029, JCM 15291

straininfo link

@refpassport
20218http://www.straininfo.net/strains/5244
20218http://www.straininfo.net/strains/5240
20218http://www.straininfo.net/strains/533890
20218http://www.straininfo.net/strains/217824
20218http://www.straininfo.net/strains/5239
20218http://www.straininfo.net/strains/5245

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny168701[A new butyric acid-producing bacteroides species: B. splanchnicus n. sp. (author's transl)].Werner H, Rintelen G, Kunstek-Santos HZentralbl Bakteriol Orig A1975Acetates/biosynthesis, Aminoglycosides, Anaerobiosis, Bacteria/classification, Bacteroides/*classification/enzymology/metabolism, Butyrates/biosynthesis, Carbohydrate Metabolism, Cephalosporins, Chloramphenicol, Erythromycin, Lincomycin, Penicillin Resistance, Penicillins, Polymyxins, Propionates/biosynthesis, Rifampin, Tetracycline, Valerates/biosynthesisMetabolism
Metabolism9236738Formation of a dipeptidyl arylamidase by Bacteroides splanchnicus NCTC 10825 with specificities towards glycylprolyl-x and valylalanine-x substrates.Macfarlane S, Macfarlane GTJ Med Microbiol1997Aminopeptidases/antagonists & inhibitors/*biosynthesis/isolation & purification/metabolism, Bacteroides/*enzymology/growth & development, Caseins/metabolism, Chromatography, Gel, Colon/microbiology, Culture Media, Dipeptides/*metabolism, Humans, Hydrogen-Ion Concentration, Isoelectric Focusing, Phenylmethylsulfonyl Fluoride/pharmacology, Protease Inhibitors/pharmacology, Substrate Specificity, Thimerosal/pharmacologyEnzymology10.1099/00222615-46-7-547
Phylogeny19542124Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces.Sakamoto M, Takagaki A, Matsumoto K, Kato Y, Goto K, Benno YInt J Syst Evol Microbiol2009Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, Butyric Acid/*metabolism, DNA, Bacterial/analysis, Fatty Acids/analysis, Feces/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rats, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/analysisGenetics10.1099/ijs.0.007674-0
Genetics21677857Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).Goker M, Gronow S, Zeytun A, Nolan M, Lucas S, Lapidus A, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HPStand Genomic Sci201110.4056/sigs.1714269

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9023Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20712)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20712
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
47264Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 21054 A)https://www.ccug.se/strain?id=21054
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)