Strain identifier

BacDive ID: 131250

Type strain: Yes

Species: Sphingomonas endophytica

Strain history: S.-K. Tang YIM 65583.

NCBI tax ID(s): 869719 (species)

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General

@ref: 22478

BacDive-ID: 131250

DSM-Number: 101535

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

description: Sphingomonas endophytica DSM 101535 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface sterilized roots of Artemisia annua.

NCBI tax id

  • NCBI tax id: 869719
  • Matching level: species

strain history

@refhistory
22478<- JCM <- J. Li, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China and H.-Y. Huang, Yunnan Univ., Yunnan Institute of Microbiology (YIM), Kunming, China
67770S.-K. Tang YIM 65583.

doi: 10.13145/bacdive131250.20230509.8.1

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 endophytica
  • full scientific name: Sphingomonas endophytica Huang et al. 2012

@ref: 22478

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas endophytica

full scientific name: Sphingomonas endophytica Huang et al. 2012

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30239negative1.8 µm0.55 µmrod-shapedyes
69480yes93.817
69480negative99.854

pigmentation

  • @ref: 30239
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 22478
  • 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
22478positivegrowth28mesophilic
30239positivegrowth12-45
30239positiveoptimum29mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 30239
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

  • @ref: 30239
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30239no
69481no95
69480no99.991

halophily

  • @ref: 30239
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.50 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3023922599arabinose+carbon source
3023917057cellobiose+carbon source
3023928260galactose+carbon source
3023917234glucose+carbon source
3023917716lactose+carbon source
3023917306maltose+carbon source
3023937684mannose+carbon source
3023916634raffinose+carbon source
3023926546rhamnose+carbon source
3023917992sucrose+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
30239catalase+1.11.1.6
30239gelatinase+
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
22478-----+-++++-++---+--+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
22478surface sterilized roots of Artemisia annuaArtemisia annuaYunnan provinceChinaCHNAsia
67770Tissue of Aremisia annua L. in Yunnan providenceAremisia annuaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_1314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_761;97_887;98_1039;99_1314&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: HM629444
  • Sequence Identity:
  • Total samples: 877
  • soil counts: 153
  • aquatic counts: 128
  • animal counts: 324
  • plant counts: 272

Safety information

risk assessment

  • @ref: 22478
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22478
  • description: Sphingomonas endophytica strain YIM 65583 16S ribosomal RNA gene, partial sequence
  • accession: HM629444
  • length: 1412
  • database: ena
  • NCBI tax ID: 869719

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas endophytica DSM 101535GCA_014199415scaffoldncbi869719
66792Sphingomonas endophytica strain DSM 101535869719.5wgspatric869719
66792Sphingomonas endophytica DSM 1015352828434831draftimg869719

GC content

@refGC-contentmethod
3023963.3
6777063.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
flagellatedno88.8no
gram-positiveno97.086yes
anaerobicno99.281yes
aerobicyes95.399no
halophileno93.704yes
spore-formingno95.078yes
glucose-utilyes91.245yes
thermophileno98.442no
motileyes69.757no
glucose-fermentno89.573yes

External links

@ref: 22478

culture collection no.: DSM 101535, CCTCC AA 209035, JCM 17394, YIM 65583

straininfo link

  • @ref: 89695
  • straininfo: 403660

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21873515Sphingomonas endophytica sp. nov., isolated from Artemisia annua L.Huang HY, Li J, Zhao GZ, Zhu WY, Yang LL, Tang HY, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.031484-02011Artemisia annua/*microbiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sphingomonas/*classification/genetics/*isolation & purification/physiology, Temperature, Ubiquinone/analysisGenetics
Phylogeny30010528Sphingomonas aeria sp. nov., isolated from air.Xue H, Piao CG, Wang XZ, Lin CL, Guo MW, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0029102018*Air Microbiology, Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
22478Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101535Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101535)
30239Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172658128776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89695Reimer, 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-ID403660.1