Strain identifier

BacDive ID: 14265

Type strain: Yes

Species: Sphingomonas xinjiangensis

Strain Designation: 10-1-84

Strain history: CIP <- 2012, CCTCC <- Wuhan Univ., Wuhan, China: strain 10-1-84

NCBI tax ID(s): 643568 (species)

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General

@ref: 18278

BacDive-ID: 14265

DSM-Number: 26736

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

description: Sphingomonas xinjiangensis 10-1-84 is a mesophilic, Gram-negative bacterium that was isolated from desert sand.

NCBI tax id

  • NCBI tax id: 643568
  • Matching level: species

strain history

@refhistory
18278<- NRRL
123989CIP <- 2012, CCTCC <- Wuhan Univ., Wuhan, China: strain 10-1-84

doi: 10.13145/bacdive14265.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas xinjiangensis
  • full scientific name: Sphingomonas xinjiangensis An et al. 2011

@ref: 18278

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas xinjiangensis

full scientific name: Sphingomonas xinjiangensis An et al. 2011

strain designation: 10-1-84

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.943
123989negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18278NUTRIENT 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
41594MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123989CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
18278positivegrowth28mesophilic
41594positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no96
69480no99.987

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

metabolite production

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

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18278+----+-++++-+++--+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
18278desert sandXingjiang ProvinceChinaCHNAsia
123989Environment, Sand sampleDesert of XinjiangChinaCHNAsia2007

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy
#Condition#Xerophilic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
182781Risk group (German classification)
1239891Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18278
  • description: Sphingomonas xinjiangensis strain 10-1-84 16S ribosomal RNA gene, partial sequence
  • accession: FJ754464
  • length: 1442
  • database: ena
  • NCBI tax ID: 643568

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas xinjiangensis DSM 26736GCA_014199255contigncbi643568
66792Sphingomonas xinjiangensis strain DSM 26736643568.3wgspatric643568
66792Sphingomonas xinjiangensis DSM 267362828373550draftimg643568

GC content

  • @ref: 18278
  • GC-content: 63.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
gram-positiveno96.913no
anaerobicno99.463no
halophileno97.101no
spore-formingno94.586no
glucose-utilyes92.019no
thermophileno97.991yes
flagellatedno90.196no
aerobicyes91.56no
motileyes66.657no
glucose-fermentno90.024yes

External links

@ref: 18278

culture collection no.: DSM 26736, CCTCC AB 208035, NRRL B-51332, CIP 110458

straininfo link

  • @ref: 83423
  • straininfo: 400638

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20817834Sphingomonas xinjiangensis sp. nov., isolated from desert sand.An H, Xu M, Dai J, Wang Y, Cai F, Qi H, Peng F, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.021147-02010DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Desert Climate, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purificationGenetics
Phylogeny26163005Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field.Sukweenadhi J, Kim YJ, Kang CH, Farh Mel-A, Nguyen NL, Hoang VA, Choi ES, Yang DCArch Microbiol10.1007/s00203-015-1134-z2015Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Panax/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/*physiologyTranscriptome
Phylogeny28792375Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0020102017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrocarbons/metabolism, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
18278Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26736)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26736
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
41594Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8319
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
83423Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400638.1StrainInfo: A central database for resolving microbial strain identifiers
123989Curators of the CIPCollection of Institut Pasteur (CIP 110458)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110458