Strain identifier

BacDive ID: 23284

Type strain: Yes

Species: Sphingopyxis italica

Strain Designation: SC13E-971

Strain history: <- V. Jurado, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain; SC13E-971 <- L. Laiz, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain

NCBI tax ID(s): 1129133 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 19367

BacDive-ID: 23284

DSM-Number: 25229

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

description: Sphingopyxis italica SC13E-971 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tuff from a catacomb wall.

NCBI tax id

  • NCBI tax id: 1129133
  • Matching level: species

strain history

  • @ref: 19367
  • history: <- V. Jurado, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain; SC13E-971 <- L. Laiz, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain

doi: 10.13145/bacdive23284.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingopyxis
  • species: Sphingopyxis italica
  • full scientific name: Sphingopyxis italica Alias-Villegas et al. 2013

@ref: 19367

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingopyxis

species: Sphingopyxis italica

full scientific name: Sphingopyxis italica Alias-Villegas et al. 2013

strain designation: SC13E-971

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30877negative1.5 µm0.7 µmrod-shapedyes
69480negative99.975

pigmentation

  • @ref: 30877
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19367
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19367positivegrowth25mesophilic
30877positivegrowth10-30
30877positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
30877positivegrowth4.5-8.5alkaliphile
30877positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30877
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30877no
69481no100
69480no99.981

halophily

  • @ref: 30877
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

observation

  • @ref: 30877
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3087722599arabinose+carbon source
3087717234glucose+carbon source
3087725115malate+carbon source
3087717306maltose+carbon source
3087737684mannose+carbon source
30877506227N-acetylglucosamine+carbon source
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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
30877alkaline phosphatase+3.1.3.1
30877catalase+1.11.1.6
30877cytochrome oxidase+1.9.3.1
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 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
19367-----+-++++-++---+--+

Isolation, sampling and environmental information

isolation

  • @ref: 19367
  • sample type: tuff (volcanic rock) from a catacomb wall
  • geographic location: Rome, Roman catacombs of Saint Callixtus
  • country: Italy
  • origin.country: ITA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Volcanic

Safety information

risk assessment

  • @ref: 19367
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19367
  • description: Sphingopyxis italica partial 16S rRNA gene, type strain CS13E-S71T
  • accession: HE648058
  • length: 1411
  • database: ena
  • NCBI tax ID: 1129133

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingopyxis italica DSM 25229GCA_011926545scaffoldncbi1129133
66792Sphingopyxis italica strain DSM 252291129133.3wgspatric1129133
66792Sphingopyxis italica DSM 252292828641578draftimg1129133

GC content

@refGC-contentmethod
1936765.7high performance liquid chromatography (HPLC)
3087765.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes73.349no
flagellatedno84.142no
gram-positiveno96.624yes
anaerobicno99.559no
aerobicyes95.203no
halophileno93.827no
spore-formingno93.809no
thermophileno98.028no
glucose-utilyes86.292yes
glucose-fermentno93.195yes

External links

@ref: 19367

culture collection no.: DSM 25229, CECT 8016

straininfo link

  • @ref: 87505
  • straininfo: 390295

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23264504Sphingopyxis italica sp. nov., isolated from Roman catacombs.Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.046573-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny28613148Sphingopyxis solisilvae sp. nov., isolated from forest soil.Chaudhary DK, Dahal RH, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0018692017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19367Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25229)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25229
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
30877Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2720728776041
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
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
87505Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID390295.1StrainInfo: A central database for resolving microbial strain identifiers