Strain identifier

BacDive ID: 14256

Type strain: Yes

Species: Sphingomonas sanxanigenens

Strain Designation: NX02

Strain history: CIP <- 2012, DSMZ <- R. Liu, Nankai Univ., China <- S. Zhang, Nankai Univ., China: strain NX02

NCBI tax ID(s): 1123269 (strain), 397260 (species)

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General

@ref: 8232

BacDive-ID: 14256

DSM-Number: 19645

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

description: Sphingomonas sanxanigenens NX02 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from cornfield soil.

NCBI tax id

NCBI tax idMatching level
1123269strain
397260species

strain history

@refhistory
8232<- R. Liu, College of Life Science, Nankai University <- S. Zhang, College of Life Science, Nankai University
122484CIP <- 2012, DSMZ <- R. Liu, Nankai Univ., China <- S. Zhang, Nankai Univ., China: strain NX02

doi: 10.13145/bacdive14256.20230509.8.1

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 sanxanigenens
  • full scientific name: Sphingomonas sanxanigenens Huang et al. 2009

@ref: 8232

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas sanxanigenens

full scientific name: Sphingomonas sanxanigenens Huang et al. 2009

strain designation: NX02

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidencemotility
28879negative1.75 µm0.75 µmrod-shaped
69480negative99.807
122484negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8232REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
39797MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122484CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8232positivegrowth28mesophilic
28879positiveoptimum29mesophilic
39797positivegrowth30mesophilic

culture pH

  • @ref: 28879
  • ability: positive
  • type: optimum
  • pH: 7.25

Physiology and metabolism

spore formation

@refspore formationconfidence
28879no
69481no99
69480no99.891

halophily

  • @ref: 28879
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.025 %

observation

  • @ref: 28879
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2887922599arabinose+carbon source
2887917057cellobiose+carbon source
2887923652dextrin+carbon source
2887928260galactose+carbon source
288795291gelatin+carbon source
2887917234glucose+carbon source
2887937684mannose+carbon source
2887928053melibiose+carbon source
2887951850methyl pyruvate+carbon source
2887916634raffinose+carbon source
2887917992sucrose+carbon source
2887927082trehalose+carbon source
2887927248urocanic acid+carbon source
288794853esculin+hydrolysis
2887917632nitrate+reduction
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
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
28879catalase+1.11.1.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8232-------++++--++--++-+
8232--------+++--++--++-+
8232-----+-++++--++--++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8232cornfield soilXinhe CountyChinaCHNAsia
122484Environment, Cornfield soilXinheChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2216.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1204;97_1421;98_1729;99_2216&stattab=map
  • Last taxonomy: Sphingomonas sanxanigenens
  • 16S sequence: DQ789172
  • Sequence Identity:
  • Total samples: 580
  • soil counts: 135
  • aquatic counts: 340
  • animal counts: 85
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82321Risk group (German classification)
1224841Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8232
  • description: Sphingomonas sanxanigenens strain NX02 16S ribosomal RNA gene, partial sequence
  • accession: DQ789172
  • length: 1480
  • database: ena
  • NCBI tax ID: 397260

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas sanxanigenens DSM 19645 = NX02GCA_000512205completencbi1123269
66792Sphingomonas sanxanigenens DSM 19645 = NX021123269.5completepatric1123269
66792Sphingomonas sanxanigenens DSM 19645 = NX021123269.18plasmidpatric1123269
66792Sphingomonas sanxanigenens DSM 196452574179733draftimg1123269
66792Sphingomonas sanxanigenens DSM 19645, NX022558860262completeimg1123269

GC content

  • @ref: 8232
  • GC-content: 66.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno70.072no
motileno70.072no
flagellatedno95.274no
flagellatedno95.274no
gram-positiveno97.477yes
gram-positiveno97.477yes
anaerobicno99.129no
anaerobicno99.129no
halophileno94.474yes
halophileno94.474yes
spore-formingno91.718yes
spore-formingno91.718yes
thermophileno98.907no
thermophileno98.907no
glucose-utilyes91.015yes
glucose-utilyes91.015yes
aerobicyes93.09no
aerobicyes93.09no
glucose-fermentno92.83yes
glucose-fermentno92.83yes

External links

@ref: 8232

culture collection no.: DSM 19645, CGMCC 1.6417, CIP 110406

straininfo link

  • @ref: 83415
  • straininfo: 362326

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329595Sphingomonas sanxanigenens sp. nov., isolated from soil.Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RLInt J Syst Evol Microbiol10.1099/ijs.0.000257-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny24198054Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge.Felfoldi T, Vengring A, Marialigeti K, Andras J, Schumann P, Toth EMInt J Syst Evol Microbiol10.1099/ijs.0.053736-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, Molecular Sequence Data, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny27374123Sphingomonaszeicaulis sp. nov., an endophytic bacterium isolated from maize root.Gao JL, Sun P, Wang XM, Cheng S, Lv F, Qiu TL, Yuan M, Sun JGInt J Syst Evol Microbiol10.1099/ijsem.0.0012622016Bacterial Typing Techniques, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Spiro Compounds, Ubiquinone/chemistry, Zea mays/*microbiologyTranscriptome
Phylogeny31418668Sphingomonas gilva sp. nov., isolated from mountain soil.Zhu D, Niu Y, Liu D, Wang G, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0036452019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8232Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19645)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19645
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
28879Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2531928776041
39797Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8262
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
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
83415Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362326.1StrainInfo: A central database for resolving microbial strain identifiers
122484Curators of the CIPCollection of Institut Pasteur (CIP 110406)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110406