Strain identifier

BacDive ID: 13014

Type strain: No

Species: Stutzerimonas degradans

Strain Designation: 419

Strain history: CIP <- 2002, CCUG <- ICPB <- R.Y. Stanier: strain 419 <- N.J. Palleroni

NCBI tax ID(s): 203192 (species), 316 (species)

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General

@ref: 12679

BacDive-ID: 13014

DSM-Number: 50238

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, human pathogen

description: Stutzerimonas degradans 419 is an obligate aerobe, mesophilic, Gram-negative human pathogen that was isolated from soil, enrichment with L--tartrate.

NCBI tax id

NCBI tax idMatching level
203192species
316species

strain history

@refhistory
12679<- ICPB <- R.Y. Stanier; 419 <- N.J. Palleroni
123335CIP <- 2002, CCUG <- ICPB <- R.Y. Stanier: strain 419 <- N.J. Palleroni

doi: 10.13145/bacdive13014.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Stutzerimonas
  • species: Stutzerimonas degradans
  • full scientific name: Stutzerimonas degradans Gomila et al. 2022

@ref: 12679

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas stutzeri

full scientific name: Pseudomonas stutzeri (Lehmann and Neumann 1896) Sijderius 1946

strain designation: 419

type strain: no

Morphology

cell morphology

@refgram stainconfidencemotilitycell shape
69480negative100
6948097.801yes
123335negativeyesrod-shaped

pigmentation

  • @ref: 123335
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12679REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 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
38223MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123335CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12679positivegrowth30mesophilic
38223positivegrowth30mesophilic
123335positivegrowth10-41
123335nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123335
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.978

halophily

@refsaltgrowthtested relationconcentration
123335NaClpositivegrowth0-6 %
123335NaClnogrowth8 %
123335NaClnogrowth10 %

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
12333516947citrate+carbon source
1233354853esculin-hydrolysis
12333517632nitrate+reduction
12333516301nitrite+reduction
12333517632nitrate+respiration

antibiotic resistance

  • @ref: 123335
  • 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
12333535581indoleno

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
123335oxidase+
123335beta-galactosidase-3.2.1.23
123335alcohol dehydrogenase-1.1.1.1
123335gelatinase-
123335amylase+
123335DNase-
123335caseinase-3.4.21.50
123335catalase+1.11.1.6
123335tween esterase+
123335lecithinase-
123335lipase-
123335lysine decarboxylase-4.1.1.18
123335ornithine decarboxylase-4.1.1.17
123335protease-
123335tryptophan deaminase-
123335urease-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
68382cystine arylamidase-3.4.11.3
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
56398--++-+-----+--------
123335--++-++-+--+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
56398+-------+----+-+-++-+
12679+-------+----+-+-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123335+--------++--------------------+-------------+---++--+-------------+-----+-+++-+++++---++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12679soil, enrichment with L-(+)-tartrateBerkeleyUSAUSANorth America
56398Soil,enrichment with L-(+)-tartrateUSAUSANorth America
123335Environment, Soil, enrichment

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5087.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_148;99_5087&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: U26416
  • Sequence Identity:
  • Total samples: 1328
  • soil counts: 220
  • aquatic counts: 520
  • animal counts: 534
  • plant counts: 54

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12679yes, in single cases1Risk group (German classification)
1233351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pseudomonas stutzeri strain DSM 50238 16S rRNA gene
  • accession: U26416
  • length: 1456
  • database: ena
  • NCBI tax ID: 316

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stutzerimonas degradans DSM 50238GCA_002891015contigncbi2968968
66792Pseudomonas stutzeri strain DSM 50238316.373wgspatric316
66792Pseudomonas stutzeri strain FDAARGOS_876316.578completepatric316
66792Stutzerimonas degradans DSM 50238GCA_024448505contigncbi2968968

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.927no
anaerobicno97.331no
halophileno81.747no
spore-formingno95.861no
glucose-utilyes84.544yes
motileyes89.679no
flagellatedyes85.543no
aerobicyes87.557no
thermophileno99.344yes
glucose-fermentno91.492yes

External links

@ref: 12679

culture collection no.: DSM 50238, ATCC 17832, ICPB 2737-419, CCUG 44596 A, LMG 14935, CIP 107692, CCUG 44596

straininfo link

  • @ref: 82224
  • straininfo: 8272

literature

  • topic: Metabolism
  • Pubmed-ID: 17473886
  • title: Identification of siderophores of Pseudomonas stutzeri.
  • authors: Zawadzka AM, Vandecasteele FP, Crawford RL, Paszczynski AJ
  • journal: Can J Microbiol
  • DOI: 10.1139/w06-077
  • year: 2006
  • mesh: Bacterial Outer Membrane Proteins/genetics/metabolism, Chromatography, High Pressure Liquid, Deferoxamine/chemistry/metabolism, Ferric Compounds/chemistry/metabolism, Gas Chromatography-Mass Spectrometry, Molecular Structure, Oligopeptides/chemistry/metabolism, Pseudomonas stutzeri/classification/genetics/*metabolism, Receptors, Cell Surface/genetics/metabolism, Siderophores/chemistry/*metabolism, Spectrometry, Mass, Electrospray Ionization, Tandem Mass Spectrometry
  • topic2: Proteome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12679Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50238)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50238
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
38223Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5155
56398Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44596 A)https://www.ccug.se/strain?id=44596
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
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)
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
82224Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8272.1StrainInfo: A central database for resolving microbial strain identifiers
123335Curators of the CIPCollection of Institut Pasteur (CIP 107692)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107692