Strain identifier

BacDive ID: 14261

Type strain: Yes

Species: Sphingomonas changbaiensis

Strain Designation: V2M44

Strain history: CIP <- 2012, NBRC <- J.Y. Zhang, Chinese Acad. Sci., China: strain V2M44

NCBI tax ID(s): 1219043 (strain), 529705 (species)

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General

@ref: 18080

BacDive-ID: 14261

DSM-Number: 25652

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

description: Sphingomonas changbaiensis V2M44 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from forest soil.

NCBI tax id

NCBI tax idMatching level
1219043strain
529705species

strain history

@refhistory
18080<- NBRC <- CGMCC <- J.-Y. Zhang, Chinese Acad. Sci. (CAS), Beijing; V2M44
118224CIP <- 2012, NBRC <- J.Y. Zhang, Chinese Acad. Sci., China: strain V2M44

doi: 10.13145/bacdive14261.20230509.8.1

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 changbaiensis
  • full scientific name: Sphingomonas changbaiensis Zhang et al. 2010

@ref: 18080

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas changbaiensis

full scientific name: Sphingomonas changbaiensis Zhang et al. 2010

strain designation: V2M44

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29356negative2 µm0.35 µmrod-shapedyes
69480negative99.966
118224negativerod-shapedyes

pigmentation

  • @ref: 29356
  • production: yes

multimedia

  • @ref: 18080
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25652.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18080R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
34726MEDIUM 563 - for Novosphingobium roseaeyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (15.000 g);Yeast extract (2.000 g);Polypeptone (10.000 g)
118224CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
118224CIP Medium 563yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=563

culture temp

@refgrowthtypetemperaturerange
18080positivegrowth28mesophilic
29356positivegrowth20-33
29356positiveoptimum30mesophilic
34726positivegrowth30mesophilic

culture pH

@refabilitytypepH
29356positivegrowth05-08
29356positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29356
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
29356NaClpositivegrowth0-0.1 %
29356NaClpositiveoptimum0.05 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2935617128adipate+carbon source
2935624265gluconate+carbon source
2935617234glucose+carbon source
2935625115malate+carbon source
293564853esculin+hydrolysis
6836925115malate-assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683694853esculin-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11822417632nitrate-reduction
11822416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11822435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
29356acid phosphatase+3.1.3.2
29356alkaline phosphatase+3.1.3.1
29356catalase+1.11.1.6
29356gelatinase+
29356cytochrome oxidase+1.9.3.1
29356urease+3.5.1.5
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6
118224oxidase+
118224catalase+1.11.1.6
118224urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118224-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18080----+-+-------+-+---+
18080---------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18080forest soilChangbai Mountains, Heilongjiang ProvinceChinaCHNAsia
118224Environment, Soil, forestChangbai mountain, northeastChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5983.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_2854;97_3510;98_4442;99_5983&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: EU682685
  • Sequence Identity:
  • Total samples: 1755
  • soil counts: 1044
  • aquatic counts: 499
  • animal counts: 151
  • plant counts: 61

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
180801Risk group (German classification)
1182241Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18080
  • description: Sphingomonas changbaiensis strain V2M44 16S ribosomal RNA gene, partial sequence
  • accession: EU682685
  • length: 1477
  • database: ena
  • NCBI tax ID: 1219043

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas changbaiensis NBRC 104936GCA_000974765contigncbi1219043
66792Sphingomonas changbaiensis NBRC 1049361219043.4wgspatric1219043
66792Sphingomonas changbaiensis NBRC 1049362636415880draftimg1219043

GC content

@refGC-contentmethod
1808065.8thermal denaturation, midpoint method (Tm)
2935665.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.515yes
gram-positiveno97.461no
anaerobicno99.342yes
halophileno93.21no
spore-formingno93.463no
thermophileno93.57yes
glucose-utilyes77.146no
flagellatedno85.503no
aerobicyes88.985yes
glucose-fermentno92.688no

External links

@ref: 18080

culture collection no.: DSM 25652, CGMCC 1.7057, NBRC 104936, CIP 110386

straininfo link

  • @ref: 83420
  • straininfo: 369450

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19656932Sphingomonas changbaiensis sp. nov., isolated from forest soil.Zhang JY, Liu XY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.011486-02009Bacterial Typing Techniques, Base Composition, China, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics/*isolation & purification/physiology, *TreesGenetics
Phylogeny32970222Sphingomonas horti sp. nov., a novel bacterial species isolated from soil of a tomato garden.Akter S, Lee SY, Moon SK, Choi C, Balusamy SR, Siddiqi MZ, Ashrafudoulla M, Huq MAArch Microbiol10.1007/s00203-020-02056-x2020Base Composition, Fatty Acids/analysis, Gardens, Lycopersicon esculentum/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, Sphingomonas/*classification/genetics
Phylogeny33048038Sphingomonas changnyeongensis sp. nov. isolated from the Hapcheon-Changnyeong barrage area in the Nakdong river.Park C, Kim M, Lee BH, Lee KE, Park WInt J Syst Evol Microbiol10.1099/ijsem.0.0045032020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18080Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25652)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25652
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
29356Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2576828776041
34726Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8240
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
68382Automatically annotated from API zym
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
83420Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID369450.1StrainInfo: A central database for resolving microbial strain identifiers
118224Curators of the CIPCollection of Institut Pasteur (CIP 110386)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110386