Strain identifier

BacDive ID: 13152

Type strain: Yes

Species: Pseudomonas simiae

Strain Designation: OLi

Strain history: CIP <- 2007 CECT <- 2005, A. l. Vela, Complutense Univ., Madrid, Spain: strain OLi

NCBI tax ID(s): 321846 (species)

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General

@ref: 7751

BacDive-ID: 13152

DSM-Number: 18861

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

description: Pseudomonas simiae OLi is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from lung of female monkey with pneumonitis and pneumonia.

NCBI tax id

  • NCBI tax id: 321846
  • Matching level: species

strain history

@refhistory
7751<- J. F. Fernández-Garayzábal, Veterin. Faculty, Univ. Madrid
122615CIP <- 2007 CECT <- 2005, A. l. Vela, Complutense Univ., Madrid, Spain: strain OLi

doi: 10.13145/bacdive13152.20230509.8.1

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 simiae
  • full scientific name: Pseudomonas simiae Vela et al. 2006

@ref: 7751

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas simiae

full scientific name: Pseudomonas simiae Vela et al. 2006

strain designation: OLi

type strain: yes

Morphology

cell morphology

  • @ref: 122615
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7751NUTRIENT 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
37755MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122615CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7751positivegrowth28mesophilic
37755positivegrowth30mesophilic
59076positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59076aerobe
122615obligate aerobe

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
12261517632nitrate+reduction
12261516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12261535581indoleno

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
122615oxidase+
122615catalase+1.11.1.6
122615urease-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
122615--+--+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7751+--+--+-++++--++-++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic location
7751lung of female monkey (Callithrix geoffroyi) with pneumonitis and pneumoniaCallithrix geoffroyiSpainESPEurope
59076Monkey brain (Callithrix geoffroyi)SpainESPEurope2003Madrid
122615Animal, Monkeys liver with acute bronchopneumonia, bacteraemiaSpainESPEuropeMadrid

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Inflammation
#Host#Mammals#Primates
#Host Body-Site#Oral cavity and airways#Lung

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: AJ936933
  • Sequence Identity:
  • Total samples: 5463
  • soil counts: 555
  • aquatic counts: 976
  • animal counts: 2173
  • plant counts: 1759

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7751yes2Risk group (German classification)
1226151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7751
  • description: Pseudomonas simiae partial 16S rRNA gene, type strain OLiT
  • accession: AJ936933
  • length: 1345
  • database: ena
  • NCBI tax ID: 321846

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas simiae CCUG 50988GCA_900111895scaffoldncbi321846
66792Pseudomonas simiae CCUG 50988GCA_001730615contigncbi321846
66792Pseudomonas simiae strain CCUG 50988321846.11wgspatric321846
66792Pseudomonas simiae strain CCUG 50988321846.20wgspatric321846
66792Pseudomonas simiae DSM 188612663762772draftimg321846
66792Pseudomonas simiae CCUG 509882917126018draftimg321846

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.717no
flagellatedyes81.26no
gram-positiveno98.48no
anaerobicno98.504no
aerobicyes93.785yes
halophileno91.116no
spore-formingno96.42no
glucose-fermentno89.66yes
thermophileno99.82yes
glucose-utilyes93.974no

External links

@ref: 7751

culture collection no.: DSM 18861, CCUG 50988, CECT 7078, CIP 109526

straininfo link

  • @ref: 82360
  • straininfo: 292913

literature

  • topic: Phylogeny
  • Pubmed-ID: 17082409
  • title: Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi).
  • authors: Vela AI, Gutierrez MC, Falsen E, Rollan E, Simarro I, Garcia P, Dominguez L, Ventosa A, Fernandez-Garayzabal JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64378-0
  • year: 2006
  • mesh: Animals, Bacterial Typing Techniques, Callithrix/*microbiology, Carbohydrate Metabolism, Carbon/metabolism, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Female, Gelatinases/analysis, Genes, rRNA, Molecular Sequence Data, Monkey Diseases/*microbiology, Nitrates/metabolism, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phylogeny, Pseudomonas/*classification/cytology/*isolation & purification, Pseudomonas Infections/microbiology/*veterinary, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
7751Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18861)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18861
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
37755Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7279
59076Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50988)https://www.ccug.se/strain?id=50988
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
82360Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292913.1StrainInfo: A central database for resolving microbial strain identifiers
122615Curators of the CIPCollection of Institut Pasteur (CIP 109526)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109526