Strain identifier

BacDive ID: 13045

Type strain: Yes

Species: Chryseomonas luteola

Strain Designation: 4239, KS 0921

Strain history: CIP <- 1987, IAM <- G.L. Gilardi: strain 4239

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2931

BacDive-ID: 13045

DSM-Number: 6975

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

description: Chryseomonas luteola 4239 is an obligate aerobe, mesophilic, motile bacterium that was isolated from human wound.

NCBI tax id

NCBI tax idMatching level
47886species
1215106strain

strain history

@refhistory
2931<- ATCC; ATCC 43273 (Chryseomonas luteola) <- JCM; JCM 3352 <- K. Kodama, University of Tokyo, Tokyo, Japan; KS 0921 <- G. Gilardi; 4239
67770K. Kodama KS 0921 <-- G. L. Gilardi #4239.
120689CIP <- 1987, IAM <- G.L. Gilardi: strain 4239

doi: 10.13145/bacdive13045.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Chryseomonas
  • species: Chryseomonas luteola
  • full scientific name: Chryseomonas luteola (Kodama et al. 1985) Holmes et al. 1987
  • synonyms

    @refsynonym
    20215Pseudomonas luteola
    20215Chryseomonas polytricha
    20215Pseudomonas zeshuii

@ref: 2931

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas luteola

full scientific name: Pseudomonas luteola Kodama et al. 1985

strain designation: 4239, KS 0921

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.902
6948099.993negative
120689nonegativerod-shaped

pigmentation

  • @ref: 120689
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33753MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2931TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: 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 waterhttps://mediadive.dsmz.de/medium/92
2931COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
120689CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2931positivegrowth30mesophilic
33753positivegrowth30mesophilic
67770positivegrowth30mesophilic
120689positivegrowth10-41
120689nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120689
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.992

halophily

@refsaltgrowthtested relationconcentration
120689NaClpositivegrowth0-8 %
120689NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

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
12068916947citrate+carbon source
1206894853esculin+hydrolysis
12068917632nitrate+reduction
12068916301nitrite-reduction
12068917632nitrate-respiration

antibiotic resistance

  • @ref: 120689
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12068935581indoleno

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
120689oxidase+
120689beta-galactosidase+3.2.1.23
120689alcohol dehydrogenase-1.1.1.1
120689gelatinase-
120689amylase-
120689DNase-
120689caseinase-3.4.21.50
120689catalase+1.11.1.6
120689tween esterase-
120689lecithinase-
120689lipase-
120689lysine decarboxylase-4.1.1.18
120689ornithine decarboxylase-4.1.1.17
120689phenylalanine ammonia-lyase-4.3.1.24
120689tryptophan deaminase-
120689urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    53991C12:06.912
    53991C14:0114
    53991C16:01816
    53991C18:00.218
    53991C10:0 3OH3.811.423
    53991C12:0 2OH3.213.178
    53991C12:0 3OH3.513.455
    53991C16:1 ω7c23.315.819
    53991C18:1 ω7c /12t/9t39.717.824
    53991C19:0 CYCLO ω8c0.318.9
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120689-+++-++-+-++--+-+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2931+--+-+-+++++-+++-++-+
2931+--+-+-+++++-+++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120689+++++----++-------++++-++-+----+++-----+---++--+++++-++++---+-+++------+-+-+++-++-+---+-++++++++++-

Isolation, sampling and environmental information

isolation

@refsample type
2931human wound
53991Human wound
120689Human, Wound

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_1236.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_224;97_842;98_978;99_1236&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: D84002
  • Sequence Identity:
  • Total samples: 23564
  • soil counts: 2524
  • aquatic counts: 6287
  • animal counts: 12446
  • plant counts: 2307

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29312Risk group (German classification)
1206891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas luteola gene for 16S rRNA, complete sequence, strain: IAM 13000D840021527ena47886
20218Pseudomonas luteola gene for 16S rRNA, partial sequence, strain: NBRC 103146AB6819551462ena47886

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas luteola NBRC 103146GCA_002091675contigncbi1215106
66792Pseudomonas luteola NBRC 103146 strain NBRC 1031461215106.3wgspatric1215106
66792Pseudomonas luteola NBRC 1031462806311027draftimg1215106
66792Pseudomonas luteola JCM 33522663762783draftimg47886

GC content

  • @ref: 2931
  • GC-content: 55.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
motileyes85.943no
gram-positiveno98.437no
anaerobicno98.296no
aerobicyes92.178no
halophileno92.522no
spore-formingno94.601no
thermophileno99.449yes
glucose-utilyes94.942yes
flagellatedno55.846no
glucose-fermentno88.917yes

External links

@ref: 2931

culture collection no.: DSM 6975, ATCC 43273, IAM 1300, JCM 3352, CCUG 37974, LMG 7041, IAM 13000, CIP 102995, LMG 8814, NBRC 103146

straininfo link

  • @ref: 82256
  • straininfo: 1747

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774686Pseudomonas pachastrellae sp. nov., isolated from a marine sponge.Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova NV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.63176-02005Animals, Bacterial Typing Techniques, DNA, Bacterial, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, Porifera/*microbiology, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny18523186Pseudomonas duriflava sp. nov., isolated from a desert soil.Liu R, Liu H, Feng H, Wang X, Zhang CX, Zhang KY, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.65716-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial, DNA, Ribosomal, *Desert Climate, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny22199212Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil.Feng Z, Zhang J, Huang X, Zhang J, Chen M, Li SInt J Syst Evol Microbiol10.1099/ijs.0.037796-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Herbicides, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2931Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6975)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6975
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
33753Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14742
53991Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37974)https://www.ccug.se/strain?id=37974
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
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
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)
82256Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1747.1StrainInfo: A central database for resolving microbial strain identifiers
120689Curators of the CIPCollection of Institut Pasteur (CIP 102995)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102995