Strain identifier

BacDive ID: 5102

Type strain: Yes

Species: Klebsiella ornithinolytica

Strain history: CIP <- 1989, JCM <- strain NIH 90-72

NCBI tax ID(s): 1349784 (strain), 54291 (species)

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General

@ref: 3169

BacDive-ID: 5102

DSM-Number: 7464

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

description: Klebsiella ornithinolytica DSM 7464 is a mesophilic bacterium that was isolated from urine.

NCBI tax id

NCBI tax idMatching level
54291species
1349784strain

strain history

@refhistory
3169<- JCM <- R. Sakazaki, NIH, 90-72
67770R. Sakazaki 90-72.
121449CIP <- 1989, JCM <- strain NIH 90-72

doi: 10.13145/bacdive5102.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Klebsiella
  • species: Klebsiella ornithinolytica
  • full scientific name: Klebsiella ornithinolytica Sakazaki et al. 1989

  • synonyms

    • @ref: 20215
    • synonym: Raoultella ornithinolytica

@ref: 3169

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Raoultella

species: Raoultella ornithinolytica

full scientific name: Raoultella ornithinolytica (Sakazaki et al. 1989) Drancourt et al. 2001

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3169COLUMBIA 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
3169CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
35540MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121449CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121449CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
35569CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3169positivegrowth30mesophilic
35540positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin+hydrolysis
6836827897tryptophan+energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
68368cytochrome oxidase+1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
3169+-+++-+-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3169urineJapanJPNAsia
67770Urine

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_873.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_78;99_873&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: U78182
  • Sequence Identity:
  • Total samples: 159
  • soil counts: 22
  • aquatic counts: 20
  • animal counts: 107
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31692Risk group (German classification)
1214492Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Klebsiella ornithinolytica strain ATCC 31898 16S ribosomal RNA gene, partial sequenceAF1294411436ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n17 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623102379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n18 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623103379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n19 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623104379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n20 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623105379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n21 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623106379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n22 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623107379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n23 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623108379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone p13 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623109379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone p14 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623110379ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone n16 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623111233ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone p15 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623112233ena54291
20218Raoultella ornithinolytica culture-collection ATCC:31898 clone p16 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623113233ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h02 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623091338ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h03 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623092379ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h06 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623093379ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h11 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623094379ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h12 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623095379ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h04 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623096539ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h08 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623097539ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h01 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623098232ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h05 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623099232ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h07 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623100232ena54291
20218Raoultella ornithinolytica strain CCM4873 clone h10 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU623101232ena54291
20218Raoultella ornithinolytica strain CIP 103364 16S ribosomal RNA gene, partial sequenceU781821502ena54291
3169Klebsiella ornithinolytica partial 16S rRNA gene, strain JCM6096TAJ2514671516ena54291

Genome sequences

  • @ref: 67770
  • description: Raoultella ornithinolytica NBRC 105727 = ATCC 31898
  • accession: GCA_001598295
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1349784

GC content

@refGC-contentmethod
316957.0thermal denaturation, midpoint method (Tm)
6777057thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.055no
gram-positiveno96.802no
anaerobicno97.347no
aerobicyes88.083no
halophileno87.014no
spore-formingno94.401no
glucose-utilyes94.148no
motileno78.144no
thermophileno99.58yes
glucose-fermentyes89.418yes

External links

@ref: 3169

culture collection no.: DSM 7464, CCM 4873, JCM 6096, NIH 90-72, ATCC 31898, CCUG 26769, CIP 103364, CIP 103576, NBRC 105727, CCUG 26625

straininfo link

  • @ref: 74596
  • straininfo: 40240

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology14693555Genetic and biochemical characterization of the chromosomal class A beta-lactamases of Raoultella (formerly Klebsiella) planticola and Raoultella ornithinolytica.Walckenaer E, Poirel L, Leflon-Guibout V, Nordmann P, Nicolas-Chanoine MHAntimicrob Agents Chemother10.1128/AAC.48.1.305-312.20042004Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, Cloning, Molecular, DNA, Bacterial/genetics, Enterobacteriaceae/*genetics, Isoelectric Focusing, Microbial Sensitivity Tests, Molecular Sequence Data, Plasmids/genetics, beta-Lactamases/*genetics/isolation & purification/*metabolism, beta-Lactams/pharmacologyGenetics
Phylogeny17304624Benzoic acid-degrading bacteria from the intestinal tract of Macrotermes michaelseni Sjostedt.Kamanda Ngugi D, Khamis Tsanuo M, Iddi Boga HJ Basic Microbiol10.1002/jobm.2006101422007Animals, Bacteria/*isolation & purification/*metabolism, Benzoic Acid/*metabolism, Gastrointestinal Tract/microbiology, Isoptera/*microbiology, PhylogenyMetabolism
Enzymology30233558Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source.Naganuma T, Iinuma Y, Nishiwaki H, Murase R, Masaki K, Nakai RFront Microbiol10.3389/fmicb.2018.020972018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3169Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7464)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7464
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
35540Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15153
35569Curators of the CIPCollection of Institut Pasteur (CIP 103576)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103576
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
74596Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40240.1StrainInfo: A central database for resolving microbial strain identifiers
121449Curators of the CIPCollection of Institut Pasteur (CIP 103364)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103364