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BacDive ID 4970
Type strain
Strain Designation D5050
Culture col. no. DSM 16358 ATCC 11296 NCTC 5050 CCUG 15938 CCM 5972 VTT E-97790 NBRC 105683 LMG 3118 LMG 3113 CIP 52.211 CECT 851 CCM 5792 BCRC 17592 JCM 1663 D5050 10 more
NCBI tax ID(s) 1218098 574
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 6400

BacDive-ID: 4970

DSM-Number: 16358

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Klebsiella pneumoniae subsp. ozaenae D5050 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from human nose.

NCBI tax id

NCBI tax idMatching level
1218098strain
574subspecies

strain history

@refhistory
6400<- NCTC <- E. P. Snijders
67770Y. Kosako 82058 <-- R. Sakazaki <-- ATCC 11296 <-- Walter Reed Army Med. Center, AMC 35-E-5.
121887CIP <- 1952, I. Orskov, Statens Serum Inst., Copenhagen, Denmark: strain D5050 <- E.P. Snijders, Amsterdam, The Netherlands

doi: 10.13145/bacdive4970.20250331.9.3

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. ozaenae
  • full scientific name: Klebsiella pneumoniae subsp. ozaenae (Abel 1893) Ørskov 1984

  • synonyms

    @refsynonym
    20215Bacillus ozaenae
    20215Klebsiella ozaenae

@ref: 6400

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Klebsiella

species: Klebsiella pneumoniae subsp. ozaenae

full scientific name: Klebsiella pneumoniae subsp. ozaenae (Abel 1893) Ørskov 1984

strain designation: D5050

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121887negativerod-shapedno
125438negative100
125439negative99.7

colony morphology

  • @ref: 121887
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36529MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121887CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121887CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121887CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
6400TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
6400COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf

culture temp

@refgrowthtypetemperature
6400positivegrowth30
36529positivegrowth30
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 121887
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12188717632nitrate+reduction
12188716301nitrite-reduction
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
12188735581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121887oxidase-
121887alcohol dehydrogenase-1.1.1.1
121887catalase+1.11.1.6
121887lysine decarboxylase+4.1.1.18
121887ornithine decarboxylase-4.1.1.17
121887urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121887-+++-++-+-++++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6400+-+-+------+++-+-+++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6400human noseSumatraIndonesiaIDNAsia
67770Nose
121887Human, NoseSumatraIndonesiaIDNAsia1931

isolation source categories

Cat1Cat2Cat3
#Host#Human
#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: Y17654
  • 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
64002Risk group (German classification)
1218872Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Klebsiella pneumoniae subsp. ozaenae 16S rRNA gene, strain ATCC11296T, partialY176541452nuccore574
6400Klebsiella pneumoniae subsp. ozaenae 16S ribosomal RNA gene, partial sequenceAF1309821436nuccore574
124043Klebsiella pneumoniae subsp. ozaenae gene for 16S rRNA, partial sequence, strain: NBRC 105683.AB6822591465nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone a11 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence.EU623191339nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone a12 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence.EU623192343nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b06 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence.EU623193343nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b10 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence.EU623194339nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b11 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence.EU623195339nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b08 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequence.EU623196429nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone f07 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequence.EU623197425nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone f08 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequence.EU623198425nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone f10 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequence.EU623199498nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b07 16S-23S ribosomal RNA intergenic spacer, partial sequence.EU623200198nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b09 16S-23S ribosomal RNA intergenic spacer, partial sequence.EU623201198nuccore574
124043Klebsiella pneumoniae subsp. ozaenae strain CCM5792 clone b12 16S-23S ribosomal RNA intergenic spacer, partial sequence.EU623202198nuccore574

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Klebsiella pneumoniae subsp. ozaenae NCTC5050GCA_900461485contigncbi574
66792Klebsiella pneumoniae subsp. ozaenae ATCC 11296GCA_000826585scaffoldncbi574
66792Klebsiella pneumoniae subsp. ozaenae ATCC 11296574.3wgspatric574
66792Klebsiella pneumoniae subsp. ozaenae NBRC 1056831218098.3wgspatric1218098
66792Klebsiella pneumoniae subsp. ozaenae strain NCTC5050574.22wgspatric574
66792Klebsiella pneumoniae ozaenae NBRC 1056832731957711draftimg1218098
66792Klebsiella pneumoniae ozaenae ATCC 112962645728049draftimg574
67770Klebsiella pneumoniae subsp. ozaenae NBRC 105683GCA_001598715contigncbi1218098

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe86
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.7
125439BacteriaNetmotilityAbility to perform movementyes82.5
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.7
125438gram-positivegram-positivePositive reaction to Gram-stainingno100no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.557yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.079no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no63.167yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.5no
125438motile2+flagellatedAbility to perform flagellated movementno76.505no

External links

@ref: 6400

culture collection no.: DSM 16358, ATCC 11296, NCTC 5050, CCUG 15938, CCM 5972, JCM 1663, BCRC 17592, CCM 5792, CECT 851, CIP 52.211, LMG 3113, LMG 3118, NBRC 105683, VTT E-97790

straininfo link

  • @ref: 74466
  • straininfo: 92695

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6400Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16358)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16358
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
36529Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14890
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)
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/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
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
74466Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92695.1StrainInfo: A central database for resolving microbial strain identifiers
121887Curators of the CIPCollection of Institut Pasteur (CIP 52.211)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2052.211
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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