Strain identifier

BacDive ID: 135453

Type strain: No

Species: Sphingopyxis terrae

Strain history: CIP <- 1994, CCUG <- JCM <- E. Yabuuchi, Osaka, Japan <- R. Mamiya

NCBI tax ID(s): 33052 (species)

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General

@ref: 34575

BacDive-ID: 135453

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

description: Sphingopyxis terrae CIP 104253 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from Sterile water used before surgery.

NCBI tax id

  • NCBI tax id: 33052
  • Matching level: species

strain history

@refhistory
67770GIFU 11456 <-- R. Mamiya.
34575CIP <- 1994, CCUG <- JCM <- E. Yabuuchi, Osaka, Japan <- R. Mamiya

doi: 10.13145/bacdive135453.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingopyxis
  • species: Sphingopyxis terrae
  • full scientific name: Sphingopyxis terrae (Takeuchi et al. 1993) Takeuchi et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas terrae

@ref: 34575

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingopyxis

species: Sphingopyxis terrae

type strain: no

Morphology

cell morphology

  • @ref: 34575
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34575MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
34575CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperature
34575positivegrowth30
67770positivegrowth30
34575positivegrowth30-37
34575nogrowth5
34575nogrowth41
34575nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 34575
  • oxygen tolerance: obligate aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3457516947citrate+carbon source
3457517632nitrate-reduction
3457516301nitrite-reduction
34575132112sodium thiosulfate-builds gas from
6836917306maltose+assimilation
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-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

antibiotic resistance

  • @ref: 34575
  • 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
3457535581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
34575oxidase+
34575beta-galactosidase+3.2.1.23
34575alcohol dehydrogenase-1.1.1.1
34575gelatinase+/-
34575amylase+
34575DNase+
34575caseinase-3.4.21.50
34575catalase+1.11.1.6
34575lipase+
34575lysine decarboxylase-4.1.1.18
34575ornithine decarboxylase-4.1.1.17
34575phenylalanine ammonia-lyase+4.3.1.24
34575urease-3.5.1.5
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-chymotrypsin-3.4.21.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
65627-+-+-++---++-+++++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
65627-----+-++++-++---++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
34575+++++-+++++++++++++-+++-+------+--++-----+-------+---+-----+---------------+---++-------+++--+----+

Isolation, sampling and environmental information

isolation

@refsample type
67770Sterile water used before surgery
34575Environment, Water, used before surgery

Safety information

risk assessment

  • @ref: 34575
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Sphingomonas sp. JCM 7513 gene for 16S ribosomal RNA, partial sequence
  • accession: LC504028
  • length: 1411
  • database: nuccore
  • NCBI tax ID: 28214

GC content

  • @ref: 67770
  • GC-content: 64.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 34575

culture collection no.: CIP 104253, CCUG 27293, GIFU 11456, IFO 10924, JCM 7513, LMG 10924, IAM 14272, IFO 15103, NBRC 15103

straininfo link

  • @ref: 92811
  • straininfo: 4986

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
34575Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104253Collection of Institut Pasteur (CIP 104253)
65627Curators of the CCUGhttps://www.ccug.se/strain?id=27293Culture Collection University of Gothenburg (CCUG) (CCUG 27293)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
92811Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID4986.1