Strain identifier

BacDive ID: 10455

Type strain: No

Species: Chromobacterium violaceum

Strain Designation: strain Lewitus

Strain history: <- P. Kämpfer, Univ. Giessen, Germany <- LMG

NCBI tax ID(s): 536 (species)

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General

@ref: 16775

BacDive-ID: 10455

DSM-Number: 23279

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, human pathogen

description: Chromobacterium violaceum strain Lewitus is an aerobe, mesophilic, Gram-negative human pathogen of the family Chromobacteriaceae.

NCBI tax id

  • NCBI tax id: 536
  • Matching level: species

strain history

  • @ref: 16775
  • history: <- P. Kämpfer, Univ. Giessen, Germany <- LMG

doi: 10.13145/bacdive10455.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Chromobacterium
  • species: Chromobacterium violaceum
  • full scientific name: Chromobacterium violaceum Bergonzini 1880 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Chromobacterium pseudoviolaceum

@ref: 16775

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Chromobacterium

species: Chromobacterium violaceum

full scientific name: Chromobacterium violaceum Bergonzini 1880

strain designation: strain Lewitus

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29223negative1.75 µm0.4 µmrod-shapedyes
69480yes97.198
69480negative99.991

pigmentation

  • @ref: 29223
  • production: yes

multimedia

  • @ref: 16775
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23279.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16775NUTRIENT 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
16775TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16775positivegrowth28mesophilic
29223positiveoptimum32mesophilic

culture pH

@refabilitytypepHPH range
29223positivegrowth5-9.5alkaliphile
29223positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 29223
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.108

halophily

@refsaltgrowthtested relationconcentration
29223NaClpositivegrowth0-3.5 %
29223NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2922335391aspartate+carbon source
2922326271proline+carbon source
2922317272propionate+carbon source
2922317632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29223cytochrome oxidase+1.9.3.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16775+--+--+-+---+-+--+---

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_603.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_48;97_51;98_491;99_603&stattab=map
  • Last taxonomy: Chromobacterium violaceum subclade
  • 16S sequence: AJ871128
  • Sequence Identity:
  • Total samples: 1525
  • soil counts: 364
  • aquatic counts: 494
  • animal counts: 444
  • plant counts: 223

Safety information

risk assessment

  • @ref: 16775
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16775
  • description: Chromobacterium pseudoviolaceum partial 16S rRNA gene, type strain LMG 3953T
  • accession: AJ871128
  • length: 1416
  • database: ena
  • NCBI tax ID: 536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chromobacterium violaceum LMG 3953GCA_001953795contigncbi536
66792Chromobacterium pseudoviolaceum strain LMG 3953686830.3wgspatric536
66792Chromobacterium pseudoviolaceum LMG 39532846011027draftimg536

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno98.422yes
anaerobicno98.171yes
halophileno93.281yes
spore-formingno92.145no
glucose-utilyes92.691no
thermophileno99.674no
flagellatedyes86.513no
motileyes91.955no
aerobicyes87.451yes
glucose-fermentno60.55no

External links

@ref: 16775

culture collection no.: DSM 23279, CCM 2076, LMG 3953, NCIB 8182

straininfo link

  • @ref: 79732
  • straininfo: 1733

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19622653Chromobacterium piscinae sp. nov. and Chromobacterium pseudoviolaceum sp. nov., from environmental samples.Kampfer P, Busse HJ, Scholz HCInt J Syst Evol Microbiol10.1099/ijs.0.008888-02009Chromobacterium/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Environmental Microbiology, Lipids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Genetics28336604Draft Genome Sequence of Chromobacterium pseudoviolaceum LMG 3953(T), an Enigmatic Member of the Genus Chromobacterium.Soby SDGenome Announc10.1128/genomeA.01632-162017
Phylogeny30028284Chromobacterium pseudoviolaceum Kampfer et al. 2009 is a later heterotypic synonym of Chromobacterium violaceum Bergonzini 1880.Kampfer P, Glaeser SP, Soby SDInt J Syst Evol Microbiol10.1099/ijsem.0.0029302018Bacterial Typing Techniques, Chromobacterium/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16775Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23279)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23279
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
29223Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2564428776041
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)
68369Automatically annotated from API 20NE
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
79732Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1733.1StrainInfo: A central database for resolving microbial strain identifiers