Strain identifier

BacDive ID: 4967

Type strain: Yes

Species: Klebsiella pneumoniae subsp. rhinoscleromatis

Strain Designation: C 5046, R 70

Strain history: CIP <- 1952, I. Orskov, Statens Serum Inst., Copenhagen, Denmark: strain C 5046

NCBI tax ID(s): 667127 (strain), 39831 (subspecies)

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General

@ref: 6345

BacDive-ID: 4967

DSM-Number: 16231

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Klebsiella pneumoniae subsp. rhinoscleromatis C 5046 is a mesophilic, Gram-negative bacterium that was isolated from nose of patient with rhinoscleroma.

NCBI tax id

NCBI tax idMatching level
667127strain
39831subspecies

strain history

@refhistory
6345<- NCTC <- E. P. Snijders
417011952, I. Orskov, Ser. Inst., Copenhagen, Denmark: strain C 5046
67770R. Sakazaki 191 <-- ATCC 13884 <-- NCTC 5046 <-- E. Snijders R-70.
121881CIP <- 1952, I. Orskov, Statens Serum Inst., Copenhagen, Denmark: strain C 5046

doi: 10.13145/bacdive4967.20230509.8.1

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 pneumoniae subsp. rhinoscleromatis
  • full scientific name: Klebsiella pneumoniae subsp. rhinoscleromatis (Trevisan 1887) Ørskov 1984

  • synonyms

    • @ref: 20215
    • synonym: Klebsiella rhinoscleromatis

@ref: 6345

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Klebsiella

species: Klebsiella pneumoniae subsp. rhinoscleromatis

full scientific name: Klebsiella pneumoniae subsp. rhinoscleromatis (Trevisan 1887) Ørskov 1984

strain designation: C 5046, R 70

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.95
121881negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6345CASO 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
6345NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41701MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121881CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6345positivegrowth37mesophilic
41701positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.936

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose-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
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol-builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate+assimilation
6837427897tryptophan-energy source
6837417634D-glucose-builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose+builds acid from
6837418333D-arabitol+builds acid from
6837427082trehalose+builds acid from
6837462345L-rhamnose+builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole test
6837435581indole-
6836835581indole-

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
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
44197-----------++++--++--
6345---------+-+++++-+++-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
44197---------+-+---+-----++-+++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6345nose of patient with rhinoscleromaSumatraIndonesiaIDNAsia
44197NoseSumatraIndonesiaIDNAsia
67770Nose of a patientSumatraIndonesiaIDNAsia
121881NoseSumatraIndonesiaIDNAsia

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host Body-Site#Organ#Nose

taxonmaps

  • @ref: 69479
  • File name: preview.99_10.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_9;99_10&stattab=map
  • Last taxonomy: Klebsiella pneumoniae
  • 16S sequence: Y17657
  • Sequence Identity:
  • Total samples: 47492
  • soil counts: 1141
  • aquatic counts: 3887
  • animal counts: 41102
  • plant counts: 1362

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63452Risk group (German classification)
1218812Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Klebsiella pneumoniae subsp. rhinoscleromatis 16S ribosomal RNA gene, partial sequenceAF1309831436ena667127
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L21 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623215343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L26 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623216343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L33 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623217343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone S1 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623218343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone S4 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623219343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone S5 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623220343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone S7 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623221343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone S9 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequenceEU623222343ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L20 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623223498ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L27 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623224497ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L24 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623225498ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L30 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623226498ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L29 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623227498ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L36 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623228498ena39831
20218Klebsiella pneumoniae subsp. rhinoscleromatis culture-collection ATCC:13884 clone L37 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequenceEU623229498ena39831
20218Klebsiella pneumoniae 16S rRNA gene, strain ATCC13884T, partialY176571452ena573
20218Klebsiella rhinoscleromatis 16S ribosomal RNA gene, partial sequenceAF0091691088ena39831

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 UrmiteGCA_000827775scaffoldncbi667127
66792Klebsiella pneumoniae subsp. rhinoscleromatis NCTC5046GCA_900452125contigncbi39831
66792Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884667127.3wgspatric667127
66792Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 strain Urmite667127.8wgspatric667127
66792Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 strain Urmite667127.7wgspatric667127
66792Klebsiella pneumoniae subsp. rhinoscleromatis strain NCTC504639831.12wgspatric39831
66792Klebsiella pneumoniae rhinoscleromatis ATCC 13884647000262draftimg667127
66792Klebsiella pneumoniae rhinoscleromatis ATCC 13884 Urmite2663763389draftimg667127
67770Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884GCA_000163455scaffoldncbi667127

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno82.391no
motileno82.391no
flagellatedno92.718no
flagellatedno92.718no
gram-positiveno97.121no
gram-positiveno97.121no
anaerobicno96.328no
anaerobicno96.328no
aerobicyes90.305no
aerobicyes90.305no
halophileno87.792no
halophileno87.792no
spore-formingno93.285no
spore-formingno93.285no
glucose-utilyes95.009no
glucose-utilyes95.009no
thermophileno99.518yes
thermophileno99.518yes
glucose-fermentyes92.481no
glucose-fermentyes92.481no

External links

@ref: 6345

culture collection no.: CCUG 417, DSM 16231, ATCC 13884, NCTC 5046, JCM 1664, BCRC 17593, CCM 5791, CECT 852, CIP 52.210, LMG 3178, LMG 3184, NBRC 105682, NCDC 417-68, VTT E-083057, VTT E-981126

straininfo link

  • @ref: 74463
  • straininfo: 3149

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6345Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16231)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16231
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
41701Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14879
44197Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 417)https://www.ccug.se/strain?id=417
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68374Automatically annotated from API ID32E
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74463Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3149.1StrainInfo: A central database for resolving microbial strain identifiers
121881Curators of the CIPCollection of Institut Pasteur (CIP 52.210)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2052.210