Strain identifier

BacDive ID: 13072

Type strain: Yes

Species: Pseudomonas rhodesiae

Strain history: CIP <- 1995, Med. Univ., Lille, France: strain CFML 92-111

NCBI tax ID(s): 76760 (species)

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General

@ref: 5223

BacDive-ID: 13072

DSM-Number: 14020

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

description: Pseudomonas rhodesiae CCUG 38732 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from natural mineral water.

NCBI tax id

  • NCBI tax id: 76760
  • Matching level: species

strain history

@refhistory
5223<- CIP <- Med. Univ., Lille; CFML92-111
67770DSM 14020 <-- CIP 104664 <-- Med. Univ., Lille, France; CFML 92-111.
122217CIP <- 1995, Med. Univ., Lille, France: strain CFML 92-111

doi: 10.13145/bacdive13072.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas rhodesiae
  • full scientific name: Pseudomonas rhodesiae Coroler et al. 1997

@ref: 5223

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas rhodesiae

full scientific name: Pseudomonas rhodesiae Coroler et al. 1997

type strain: yes

Morphology

cell morphology

  • @ref: 122217
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5223R2A 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
34626MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122217CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
5223positivegrowth30mesophilic
34626positivegrowth30mesophilic
67770positivegrowth30mesophilic
122217positivegrowth5-37
122217nogrowth41thermophilic
122217nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122217
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122217NaClpositivegrowth0-6 %
122217NaClnogrowth8 %
122217NaClnogrowth10 %

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
12221716947citrate+carbon source
1222174853esculin-hydrolysis
12221717632nitrate+reduction
12221716301nitrite-reduction
12221715882phenol+degradation
12221717632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12221735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
12221715688acetoin-

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
122217oxidase+
122217beta-galactosidase-3.2.1.23
122217alcohol dehydrogenase+1.1.1.1
122217gelatinase-
122217amylase-
122217DNase-
122217caseinase+3.4.21.50
122217catalase+1.11.1.6
122217tween esterase-
122217lysine decarboxylase-4.1.1.18
122217ornithine decarboxylase-4.1.1.17
122217phenylalanine ammonia-lyase+4.3.1.24
122217tryptophan deaminase-
122217urease+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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122217-+++-++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5223+--+--+-+++++-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122217+++++--+-----------+++----+----+++--+--+---++---++++-++++--++-+++------+++-+++++++-++---+++++++++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
5223natural mineral waterFranceFRAEurope
54423Water,natural mineral water
67770Natural mineral waters
122217Environment, Natural mineral water1992

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_168.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_168&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AF064459
  • Sequence Identity:
  • Total samples: 5463
  • soil counts: 555
  • aquatic counts: 976
  • animal counts: 2173
  • plant counts: 1759

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52231Risk group (German classification)
1222171Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas rhodesiae gene for 16S rRNA, strain: CIP 104664AB0214101501ena76760
20218Pseudomonas rhodesiae 16S ribosomal RNA gene, complete sequenceAF0644591522ena76760

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas rhodesiae strain DSM 1402076760.14wgspatric76760
66792Pseudomonas rhodesiae LMG 177642639763190draftimg76760
67770Pseudomonas rhodesiae DSM 14020GCA_007858255contigncbi76760
66792Pseudomonas rhodesiae CIP104664GCA_024169765contigncbi76760
66792Pseudomonas rhodesiae LMG 17764GCA_900105575chromosomencbi76760

GC content

  • @ref: 67770
  • GC-content: 61
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.925no
glucose-fermentno91.412no
flagellatedyes81.041no
gram-positiveno98.185no
anaerobicno98.208no
aerobicyes95.841no
halophileno89.484no
spore-formingno95.874no
thermophileno99.872yes
glucose-utilyes94.067no

External links

@ref: 5223

culture collection no.: CCUG 38732, LMG 17764, CCM 4734, JCM 11940, DSM 14020, CIP 104664, NCIMB 13509, CFML 92-111

straininfo link

  • @ref: 82282
  • straininfo: 11213

literature

  • topic: Phylogeny
  • Pubmed-ID: 12361251
  • title: Pseudomonas grimontii sp. nov.
  • authors: Baida N, Yazourh A, Singer E, Izard D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-5-1497
  • year: 2002
  • mesh: DNA, Bacterial/genetics, Fresh Water/microbiology, Microscopy, Electron, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/metabolism, Terminology as Topic
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5223Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14020)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14020
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
34626Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16597
54423Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38732)https://www.ccug.se/strain?id=38732
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
82282Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11213.1StrainInfo: A central database for resolving microbial strain identifiers
122217Curators of the CIPCollection of Institut Pasteur (CIP 104664)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104664