Strain identifier

BacDive ID: 14220

Type strain: Yes

Species: Sphingomonas parapaucimobilis

Strain Designation: OH 3807

Strain history: CIP <- 2000, CCM <- GIFU <- H. Yamanaka: strain OH 3807

NCBI tax ID(s): 1219049 (strain), 28213 (species)

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General

@ref: 3168

BacDive-ID: 14220

DSM-Number: 7463

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative

description: Sphingomonas parapaucimobilis OH 3807 is an aerobe, Gram-negative bacterium that was isolated from urine.

NCBI tax id

NCBI tax idMatching level
28213species
1219049strain

strain history

@refhistory
3168<- JCM <- GIFU <- H. Yamanaka
67770GIFU 11387 <-- Y. Yamanaka OH 3807.
121573CIP <- 2000, CCM <- GIFU <- H. Yamanaka: strain OH 3807

doi: 10.13145/bacdive14220.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas parapaucimobilis
  • full scientific name: Sphingomonas parapaucimobilis Yabuuchi et al. 1990

@ref: 3168

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas parapaucimobilis

full scientific name: Sphingomonas parapaucimobilis Yabuuchi et al. 1990

strain designation: OH 3807

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121573negativerod-shapedyes
69480negative95.639

pigmentation

  • @ref: 121573
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3168CASO 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
35211MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121573CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
3168positivegrowth28
35211positivegrowth30
48700positivegrowth30
67770positivegrowth30
121573positivegrowth25-37
121573nogrowth5
121573nogrowth10
121573nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
48700aerobe
121573obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

  • @ref: 121573
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

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
12157316947citrate+carbon source
1215734853esculin+hydrolysis
12157317632nitrate+reduction
12157316301nitrite-reduction
12157317632nitrate-respiration

antibiotic resistance

  • @ref: 121573
  • 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
12157335581indoleno

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
121573oxidase-
121573alcohol dehydrogenase-1.1.1.1
121573gelatinase+/-
121573amylase-
121573DNase-
121573caseinase-3.4.21.50
121573catalase+1.11.1.6
121573tween esterase-
121573lecithinase-
121573lipase-
121573lysine decarboxylase-4.1.1.18
121573ornithine decarboxylase-4.1.1.17
121573protease-
121573tryptophan deaminase-
121573urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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-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
48700-+---++---++-+-+++--
121573-++++++++-++-++-++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
48700+----+-++++-++---++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121573++-++-+++++++--++-+-+++--+-----+-----------------+---++----++------------------++---------+-------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3168urineJapanJPNAsia
48700Urine
67770Urine
121573UrineJapanJPNAsia

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_2706.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_761;97_956;98_1125;99_2706&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AB680767
  • Sequence Identity:
  • Total samples: 2473
  • soil counts: 167
  • aquatic counts: 518
  • animal counts: 1394
  • plant counts: 394

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31682Risk group (German classification)
1215731Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas parapaucimobilis 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGQ907188729nuccore28213
20218Sphingomonas parapaucimobilis 16S ribosomal RNA, partial sequenceD38424156nuccore28213
20218Sphingomonas parapaucimobilis gene for 16S rRNA, partial sequenceD137241418nuccore28213
20218Sphingomonas parapaucimobilis gene for 16S rRNAD845251388nuccore28213
20218Sphingomonas parapaucimobilis partial 16S rRNA geneX727211408nuccore28213
20218Sphingomonas parapaucimobilis gene for 16S rRNA, partial sequence, strain: NBRC 15100AB6807671416nuccore28213

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas parapaucimobilis NBRC 151001219049.3wgspatric1219049
66792Sphingomonas parapaucimobilis NBRC 151002630968314draftimg1219049
67770Sphingomonas parapaucimobilis NBRC 15100GCA_000787715contigncbi1219049

GC content

  • @ref: 3168
  • GC-content: 64.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno95.639no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.502yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.029no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.395no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.288no
69480flagellatedmotile2+Ability to perform flagellated movementyes66.858no

External links

@ref: 3168

culture collection no.: DSM 7463, ATCC 51231, GIFU 11387, IAM 14268, JCM 7510, NCIMB 13745, CCUG 27291, LMG 10923, BCRC 17635, CCM 4599, CIP 106724, IFO 15100, NBRC 15100

straininfo link

  • @ref: 83379
  • straininfo: 4984

literature

  • topic: Phylogeny
  • Pubmed-ID: 2111872
  • title: Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas.
  • authors: Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H
  • journal: Microbiol Immunol
  • DOI: 10.1111/j.1348-0421.1990.tb00996.x
  • year: 1990
  • mesh: Base Composition, Base Sequence, Cluster Analysis, DNA, Bacterial/isolation & purification, Fatty Acids/analysis, Flavobacterium/*classification/genetics/growth & development, Glycosphingolipids/*analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Phenotype, Pseudomonas/*classification/genetics/growth & development, Pseudomonas aeruginosa/classification/genetics/growth & development, RNA, Ribosomal/*analysis, RNA, Ribosomal, 16S/*analysis/isolation & purification
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3168Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7463)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7463
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
35211Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18886
48700Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27291)https://www.ccug.se/strain?id=27291
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)
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
83379Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4984.1StrainInfo: A central database for resolving microbial strain identifiers
121573Curators of the CIPCollection of Institut Pasteur (CIP 106724)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106724