Strain identifier

BacDive ID: 157757

Type strain: Yes

Species: Klebsiella grimontii

Strain Designation: 06D021

Strain history: CIP <- 2017, S. Brisse, Inst. Pasteur, Paris, France: strain 06D021, Klebsiella grimontae <- 1997, Lille Hosp., Lille, France

NCBI tax ID(s): 2058152 (species)

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General

@ref: 64328

BacDive-ID: 157757

DSM-Number: 105630

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Klebsiella grimontii 06D021 is a mesophilic, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Wound or Soft tissue infection.

NCBI tax id

  • NCBI tax id: 2058152
  • Matching level: species

strain history

@refhistory
64328<- S. Brisse, Institut Pasteur, Paris; 06D021
119742CIP <- 2017, S. Brisse, Inst. Pasteur, Paris, France: strain 06D021, Klebsiella grimontae <- 1997, Lille Hosp., Lille, France

doi: 10.13145/bacdive157757.20230509.8.1

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 grimontii
  • full scientific name: Klebsiella grimontii Passet and Brisse 2018

@ref: 64328

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Clostridiales

family: Enterobacteriaceae

genus: Klebsiella

species: Klebsiella grimontii

full scientific name: Klebsiella grimontii Passet and Brisse 2018

strain designation: 06D021

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
65311negativerod-shapedno
119742negativerod-shapedno

colony morphology

  • @ref: 65311
  • colony color: white
  • colony shape: circular

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64328COLUMBIA 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
64328TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
119742CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 64328
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 65311
  • spore formation: no

observation

@refobservation
65311cells are capsulated
65311The strain was previously named SB73 and assigned to phylogenetic group Ko6/ bla OXY -6 [9]. It is melezitose-negative.

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
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6531115688acetoinyes
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6531115688acetoin+
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
65311urease-3.5.1.5
65311beta-galactosidase+3.2.1.23
65311lysine decarboxylase+4.1.1.18
65311ornithine 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
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
64328+-+-+---++-+++++++++-
64328+---+---++-+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
64328Wound or Soft tissue infectionLilleFranceFRAEurope
65311soft-tissue infection cultureLilleFranceFRAEurope1997
119742Human, Soft tissue infectionsLilleFranceFRAEurope1997-07-22

isolation source categories

Cat1Cat2
#Engineered#Laboratory
#Infection

taxonmaps

  • @ref: 69479
  • File name: preview.99_117.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_17;99_117&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: AJ871861
  • Sequence Identity:
  • Total samples: 4010
  • soil counts: 121
  • aquatic counts: 233
  • animal counts: 3440
  • plant counts: 216

Safety information

risk assessment

  • @ref: 119742
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 64328
  • description: Klebsiella oxytoca partial 16S rRNA gene, strain SB73
  • accession: AJ871861
  • length: 1454
  • database: ena
  • NCBI tax ID: 2058152

Genome sequences

  • @ref: 66792
  • description: Klebsiella grimontii 06D021
  • accession: GCA_900200035
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2058152

GC content

  • @ref: 65311
  • GC-content: 55.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno83.68yes
flagellatedno92.716yes
gram-positiveno97.609no
anaerobicno96.671no
aerobicyes86.398no
halophileno89.27no
spore-formingno93.685yes
thermophileno99.603no
glucose-utilyes94.091no
glucose-fermentyes88.106no

External links

@ref: 64328

culture collection no.: DSM 105630, CIP 111401

straininfo link

  • @ref: 110617
  • straininfo: 402485

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29205126Description of Klebsiella grimontii sp. nov.Passet V, Brisse SInt J Syst Evol Microbiol10.1099/ijsem.0.0025172017Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Humans, Klebsiella/*classification/genetics, Klebsiella Infections/microbiology, *Phylogeny, Sequence Analysis, DNAPathogenicity
Phylogeny32375936Klebsiella indica sp. nov., isolated from the surface of a tomato.Gujarati S, Chaudhari D, Hagir A, Khairnar M, Shouche Y, Rahi PInt J Syst Evol Microbiol10.1099/ijsem.0.0041682020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fruit/*microbiology, India, Klebsiella/*classification/isolation & purification, Lycopersicon esculentum/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64328Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105630Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105630)
65311Virginie Passet, Sylvain BrisseDescription of Klebsiella grimontii sp. nov.10.1099/ijsem.0.002517IJSEM 68: 377-381 201829205126
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
110617Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402485.1
119742Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111401Collection of Institut Pasteur (CIP 111401)