Strain identifier

BacDive ID: 14182

Type strain: Yes

Species: Sphingobium amiense

Strain Designation: YT

Strain history: CIP <- 2003, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain YT <- Y. Takahara

NCBI tax ID(s): 135719 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6275

BacDive-ID: 14182

DSM-Number: 16289

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

description: Sphingobium amiense YT is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from river sediment.

NCBI tax id

  • NCBI tax id: 135719
  • Matching level: species

strain history

@refhistory
6275<- H. Ohta, University Ami-machi, Japan; YT
116330CIP <- 2003, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain YT <- Y. Takahara

doi: 10.13145/bacdive14182.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium amiense
  • full scientific name: Sphingobium amiense Ushiba et al. 2003

@ref: 6275

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium amiense

full scientific name: Sphingobium amiense Ushiba et al. 2003

strain designation: YT

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480negative99.993
116330negativeno

pigmentation

  • @ref: 116330
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6275CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
6275TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
40728MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116330CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6275positivegrowth28mesophilic
40728positivegrowth30mesophilic
116330positivegrowth25-30mesophilic
116330nogrowth5psychrophilic
116330nogrowth10psychrophilic
116330nogrowth37mesophilic
116330nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116330
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.88

halophily

@refsaltgrowthtested relationconcentration
116330NaClpositivegrowth0-2 %
116330NaClnogrowth4 %
116330NaClnogrowth6 %
116330NaClnogrowth8 %
116330NaClnogrowth10 %

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
11633016947citrate-carbon source
1163304853esculin-hydrolysis
11633017632nitrate-reduction
11633016301nitrite-reduction
11633017632nitrate-respiration

antibiotic resistance

  • @ref: 116330
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11633035581indoleno

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
116330oxidase+
116330beta-galactosidase+3.2.1.23
116330alcohol dehydrogenase-1.1.1.1
116330gelatinase-
116330amylase+
116330DNase-
116330caseinase-3.4.21.50
116330catalase+1.11.1.6
116330tween esterase-
116330lecithinase-
116330lipase-
116330lysine decarboxylase-4.1.1.18
116330ornithine decarboxylase-4.1.1.17
116330tryptophan deaminase-
116330urease-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
116330-+---+--++++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6275--------+-++-++--+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6275river sedimentIbarakiJapanJPNAsia
116330Environment, River sediment sampleIbarakiJapanJPNAsia1999

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7507.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_774;97_3571;98_5499;99_7507&stattab=map
  • Last taxonomy: Sphingobium amiense
  • 16S sequence: AB047364
  • Sequence Identity:
  • Total samples: 133
  • soil counts: 6
  • aquatic counts: 60
  • animal counts: 7
  • plant counts: 60

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62751Risk group (German classification)
1163301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6275
  • description: Sphingomonas sp. YT gene for 16S rRNA
  • accession: AB047364
  • length: 1448
  • database: ena
  • NCBI tax ID: 135719

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium amiense DSM 16289GCA_003967075completencbi135719
66792Sphingobium amiense strain DSM 16289135719.3wgspatric135719
66792Sphingobium amiense DSM 162892843241807completeimg135719

GC content

  • @ref: 6275
  • GC-content: 66.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileyes58.557no
flagellatedno85.848no
gram-positiveno96.953no
anaerobicno98.736no
aerobicyes90.502no
halophileno96.824no
spore-formingno94.344no
thermophileno97.239yes
glucose-utilyes89.153yes
glucose-fermentno92.371yes

External links

@ref: 6275

culture collection no.: DSM 16289, CIP 107839, IAM 15006, JCM 11777

straininfo link

  • @ref: 83345
  • straininfo: 128017

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657143Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment.Ushiba Y, Takahara Y, Ohta HInt J Syst Evol Microbiol10.1099/ijs.0.02581-02003Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Geologic Sediments/microbiology, Japan, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny19651722Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil.Bala K, Sharma P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.010868-02009Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, Hexachlorocyclohexane/*metabolism, India, Insecticides/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soil Pollutants/*metabolism, Sphingomonadaceae/*classification/genetics/*metabolismMetabolism
Phylogeny19651723Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil.Liang Q, Lloyd-Jones GInt J Syst Evol Microbiol10.1099/ijs.0.008144-02009Base Composition, Base Sequence, DNA, Bacterial/chemistry, Hydrocarbons, Aromatic/*metabolism, Industrial Waste, Molecular Sequence Data, New Zealand, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Soil Pollutants/*metabolism, Sphingomonadaceae/*classification/genetics/*metabolismMetabolism
Phylogeny22561591Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.040105-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Fresh Water, Molecular Sequence Data, Myristic Acids/analysis, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, *Water MicrobiologyGenetics
Metabolism30518740Comparative Analysis of the Genetic Basis of Branched Nonylphenol Degradation by Sphingobium amiense DSM 16289(T) and Sphingobium cloacae JCM 10874(T).Ootsuka M, Nishizawa T, Hasegawa M, Kurusu Y, Ohta HMicrobes Environ10.1264/jsme2.ME180772018Bacterial Proteins/genetics/*metabolism, Escherichia coli/genetics/metabolism, Genes, Bacterial/genetics, Genome, Bacterial/*genetics, Phenols/*metabolism, Plasmids, Recombinant Proteins/genetics/metabolism, Sphingomonadaceae/*genetics/metabolism, Substrate SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6275Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16289)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16289
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
40728Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5394
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
83345Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128017.1StrainInfo: A central database for resolving microbial strain identifiers
116330Curators of the CIPCollection of Institut Pasteur (CIP 107839)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107839