Strain identifier

BacDive ID: 14244

Type strain: Yes

Species: Sphingomonas yunnanensis

Strain history: CIP <- 2013, KCTC <- strain YIM 003

NCBI tax ID(s): 310400 (species)

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General

@ref: 6682

BacDive-ID: 14244

DSM-Number: 17000

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

description: Sphingomonas yunnanensis DSM 17000 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from plate contamination.

NCBI tax id

  • NCBI tax id: 310400
  • Matching level: species

strain history

@refhistory
6682<- W.-J-. Li, Yunnan Univ.; YIM 003
124019CIP <- 2013, KCTC <- strain YIM 003

doi: 10.13145/bacdive14244.20230509.8.1

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 yunnanensis
  • full scientific name: Sphingomonas yunnanensis Zhang et al. 2005

@ref: 6682

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas yunnanensis

full scientific name: Sphingomonas yunnanensis Zhang et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31504negative0.9 µm0.55 µmrod-shapedyes
124019negativerod-shapedno

pigmentation

  • @ref: 31504
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6682NUTRIENT 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
36540MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
124019CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
124019CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
6682positivegrowth28mesophilic
31504positivegrowth28mesophilic
31504positiveoptimum28mesophilic
36540positivegrowth30mesophilic

culture pH

@refabilitytypepH
31504positivegrowth7-7.5
31504positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 31504
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31504
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31504NaClpositivegrowth0-1 %
31504NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3150423652dextrin+carbon source
3150428757fructose+carbon source
3150428260galactose+carbon source
3150417234glucose+carbon source
3150417716lactose+carbon source
3150415792malonate+carbon source
3150437684mannose+carbon source
31504506227N-acetylglucosamine+carbon source
3150433942ribose+carbon source
3150418222xylose+carbon source
315044853esculin+hydrolysis
3150417632nitrate+reduction

enzymes

@refvalueactivityec
31504alpha-galactosidase+3.2.1.22
31504catalase+1.11.1.6
31504cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6682plate contaminationChinaCHNAsia
124019Environment, SoilChinaCHNAsiaYunnan

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Engineered#Laboratory#Lab enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_17341.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_761;97_887;98_5182;99_17341&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AY894691
  • Sequence Identity:
  • Total samples: 242
  • soil counts: 47
  • aquatic counts: 29
  • animal counts: 48
  • plant counts: 118

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66821Risk group (German classification)
1240191Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31504
  • description: Sphingomonas yunnanensis strain YIM 003 16S ribosomal RNA gene, partial sequence
  • accession: AY894691
  • length: 1415
  • database: nuccore
  • NCBI tax ID: 310400

GC content

  • @ref: 31504
  • GC-content: 67.5

External links

@ref: 6682

culture collection no.: DSM 17000, CCTCC AB 204064, KCTC 12346, YIM 003, CIP 110397

straininfo link

  • @ref: 83403
  • straininfo: 134965

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280497Sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate.Zhang YQ, Chen YG, Li WJ, Tian XP, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63697-02005Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Bacterial/chemistry/isolation & purification, Fatty Acids/chemistry/*metabolism, Genes, rRNA, Gentian Violet, Hydrogen-Ion Concentration, Molecular Sequence Data, Phenazines, RNA, Ribosomal, 16S/analysis/genetics, Sphingomonas/classification/cytology/*isolation & purification/physiologyCultivation
Phylogeny21221931Sphingomonas ginsenosidimutans sp. nov., with ginsenoside converting activity.Choi TE, Liu QM, Yang JE, Sun S, Kim SY, Yi TH, Im WTJ Microbiol10.1007/s12275-010-0469-z2011Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/isolation & purification/*metabolism/physiology, Temperature, beta-Glucosidase/metabolismMetabolism
Phylogeny21742816Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample.Luo YR, Tian Y, Huang X, Kwon K, Yang SH, Seo HS, Kim SJ, Zheng TLInt J Syst Evol Microbiol10.1099/ijs.0.033530-02011Bacterial Typing Techniques, Biodegradation, Environmental, China, DNA, Bacterial/genetics, Molecular Sequence Data, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/*isolation & purification/metabolism, *Water MicrobiologyGenetics
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6682Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17000)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17000
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
31504Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780228776041
36540Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8252
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
83403Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134965.1StrainInfo: A central database for resolving microbial strain identifiers
124019Curators of the CIPCollection of Institut Pasteur (CIP 110397)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110397