Strain identifier

BacDive ID: 11313

Type strain: Yes

Species: Janthinobacterium lividum

Strain Designation: H-24, HB

Strain history: CIP <- 1989, LMG <- 1962, P.H.A. Sneath: strain HB <- 1955, R.J. Hans: strain H-24, Chromobacterium lividum

NCBI tax ID(s): 29581 (species)

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General

@ref: 808

BacDive-ID: 11313

DSM-Number: 1522

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

description: Janthinobacterium lividum H-24 is an aerobe, mesophilic, motile bacterium of the family Oxalobacteraceae.

NCBI tax id

  • NCBI tax id: 29581
  • Matching level: species

strain history

@refhistory
808<- NCIB <- P.H.A. Sneath, HB <- R.J. Hans, H-24
67770IAM 13948 <-- NCIB 9130 <-- P. H. A. Sneath HB <-- R. J. Hans H24.
120639CIP <- 1989, LMG <- 1962, P.H.A. Sneath: strain HB <- 1955, R.J. Hans: strain H-24, Chromobacterium lividum

doi: 10.13145/bacdive11313.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Janthinobacterium
  • species: Janthinobacterium lividum
  • full scientific name: Janthinobacterium lividum (Eisenberg 1891) De Ley et al. 1978 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Pseudomonas mephitica
    20215Bacillus lividus

@ref: 808

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Janthinobacterium

species: Janthinobacterium lividum

full scientific name: Janthinobacterium lividum (Eisenberg 1891) De Ley et al. 1978

strain designation: H-24, HB

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.15
6948099.989negative
120639nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
808REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
42290MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
808TRYPTICASE 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
808R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
808CASO 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
808TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
120639CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120639CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
120639CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
808positivegrowth25mesophilic
42290positivegrowth22psychrophilic
44518positivegrowth25-26mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 44518
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

compound production

@refcompound
8082,5 diketogluconate
808violacein

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
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
808+----+-+++++++-++++++

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typesampling dateisolation date
42290MichiganUSAUSANorth America
44518MichiganUSAUSANorth AmericaSoil1952
120639MichiganUnited States of AmericaUSANorth AmericaEnvironment, Soil1952

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1728.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_429;97_540;98_623;99_1728&stattab=map
  • Last taxonomy: Oxalobacteraceae
  • 16S sequence: Y08846
  • Sequence Identity:
  • Total samples: 6168
  • soil counts: 1725
  • aquatic counts: 1928
  • animal counts: 1687
  • plant counts: 828

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
8081Risk group (German classification)
1206391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: J.lividum 16S rRNA gene
  • accession: Y08846
  • length: 1469
  • database: ena
  • NCBI tax ID: 29581

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Janthinobacterium lividum NCTC9796GCA_900451145contigncbi29581
66792Janthinobacterium lividum H-24GCA_001758635contigncbi29581
66792Janthinobacterium lividum strain H-2429581.30wgspatric29581
66792Janthinobacterium lividum strain NCTC979629581.44wgspatric29581
66792Janthinobacterium lividum NCTC 97962816332556draftimg29581
66792Janthinobacterium lividum ATCC 124732893783347draftimg29581
66792Janthinobacterium lividum ATCC 12473GCA_020858175scaffoldncbi29581

GC content

@refGC-contentmethod
80865.5
6777065.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.663no
anaerobicno98.618yes
halophileno96.396no
spore-formingno93.03no
glucose-utilyes94.348yes
motileyes90.843no
flagellatedyes77.969no
thermophileno99.88yes
aerobicyes91.837no
glucose-fermentno90.55yes

External links

@ref: 808

culture collection no.: CCUG 2344, LMG 6034, LMG 2892, DSM 1522, ATCC 12473, CCM 160, NCIB 9130, NCTC 9796, JCM 9043, CECT 946, CGMCC 1.2308, CIP 103349, HAMBI 1919, IAM 13948, KCTC 2898, LMG 3917, NCCB 80003, NCIMB 9130, VKM B-1223, RIMD 0314001

straininfo link

  • @ref: 80546
  • straininfo: 3024

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8995797Systematic study of the genus Vogesella gen. nov. and its type species, Vogesella indigofera comb. nov.Grimes DJ, Woese CR, MacDonell MT, Colwell RRInt J Syst Bacteriol10.1099/00207713-47-1-191997Bacteriological Techniques, Culture Media/chemistry/metabolism, DNA, Bacterial/analysis, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/growth & development/ultrastructure, RNA, Ribosomal, 16S/analysis, RNA, Ribosomal, 5S/analysisGenetics
Enzymology11181369Metallo-beta-lactamase producers in environmental microbiota: new molecular class B enzyme in Janthinobacterium lividum.Rossolini GM, Condemi MA, Pantanella F, Docquier JD, Amicosante G, Thaller MCAntimicrob Agents Chemother10.1128/AAC.45.3.837-844.20012001Amino Acid Sequence, Base Sequence, Cloning, Molecular, Environmental Microbiology, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, Proteobacteria/drug effects/enzymology/*genetics/metabolism, Sequence Homology, Amino Acid, beta-Lactamases/classification/*genetics/metabolism, beta-Lactams/pharmacologyPhylogeny
Metabolism17381742Violacein and biofilm production in Janthinobacterium lividum.Pantanella F, Berlutti F, Passariello C, Sarli S, Morea C, Schippa SJ Appl Microbiol10.1111/j.1365-2672.2006.03155.x2007Biofilms/*growth & development, *Environmental Microbiology, Indoles/*metabolism, Proteobacteria/growth & development/*metabolism, Quorum Sensing/drug effectsBiotechnology
Phylogeny18175698Reclassification of Pseudomonas mephitica Claydon and Hammer 1939 as a later heterotypic synonym of Janthinobacterium lividum (Eisenberg 1891) De Ley et al. 1978.Kampfer P, Falsen E, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.65450-02008Bacterial Typing Techniques, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Oxalobacteraceae/chemistry/*classification/genetics/physiology, Phenotype, Phylogeny, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny32176602Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China.Lu H, Deng T, Cai Z, Liu F, Yang X, Wang Y, Xu MInt J Syst Evol Microbiol10.1099/ijsem.0.0040972020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
808Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1522)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1522
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
42290Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15137
44518Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2344)https://www.ccug.se/strain?id=2344
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/
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
80546Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3024.1StrainInfo: A central database for resolving microbial strain identifiers
120639Curators of the CIPCollection of Institut Pasteur (CIP 103349)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103349