Strain identifier

BacDive ID: 14267

Type strain: Yes

Species: Sphingomonas jinjuensis

Strain Designation: YC6723

Strain history: CIP <- 2012, DSMZ <- Y.R. Chung, GSNU Gyeongsang Nat. Univ., Jinju, Korea: strain YC6723 <- Z. Aslam

NCBI tax ID(s): 535907 (species)

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General

@ref: 15717

BacDive-ID: 14267

DSM-Number: 21457

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

description: Sphingomonas jinjuensis YC6723 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of a rice field under conventional practice.

NCBI tax id

  • NCBI tax id: 535907
  • Matching level: species

strain history

@refhistory
15717<- Y. R. Chung, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; YC6723 <- Z. Aslam
67771<- YR Chung, Kyeongsang Univ.
120353CIP <- 2012, DSMZ <- Y.R. Chung, GSNU Gyeongsang Nat. Univ., Jinju, Korea: strain YC6723 <- Z. Aslam

doi: 10.13145/bacdive14267.20230509.8.1

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 jinjuensis
  • full scientific name: Sphingomonas jinjuensis Chung et al. 2011

@ref: 15717

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas jinjuensis

full scientific name: Sphingomonas jinjuensis Chung et al. 2011

strain designation: YC6723

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
67771negative
69480negative99.951
120353negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15717NUTRIENT 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
33358MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120353CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
15717positivegrowth30mesophilic
33358positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.998

observation

  • @ref: 67771
  • observation: quinones: Q-10

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15717-----+-+++--++------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15717rhizosphere of a rice field under conventional practiceJinjuRepublic of KoreaKORAsia
67771From rice fieldJinjuRepublic of KoreaKORAsia
120353Environment, Rhizosphere of a rice field under conventional practiceJinjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_127451.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_49771;97_64080;98_85462;99_127451&stattab=map
  • Last taxonomy: Sphingomonas jinjuensis subclade
  • 16S sequence: EU707561
  • Sequence Identity:
  • Total samples: 47
  • aquatic counts: 7
  • animal counts: 19
  • plant counts: 21

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157171Risk group (German classification)
1203531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15717
  • description: Sphingomonas jinjuensis strain YC6723 16S ribosomal RNA gene, partial sequence
  • accession: EU707561
  • length: 1375
  • database: ena
  • NCBI tax ID: 535907

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas jinjuensis YC6723GCA_014197105scaffoldncbi535907
66792Sphingomonas jinjuensis DSM 214572830075706draftimg535907

GC content

  • @ref: 15717
  • GC-content: 61.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
flagellatedno90.453no
gram-positiveno96.687yes
anaerobicno99.499no
aerobicyes94.157yes
halophileno93.06no
spore-formingno95.797no
glucose-utilyes93.006no
thermophileno97.26no
motileyes70.54no
glucose-fermentno90.643yes

External links

@ref: 15717

culture collection no.: DSM 21457, CIP 110411, KCTC 22477

straininfo link

  • @ref: 83424
  • straininfo: 378358

literature

  • topic: Phylogeny
  • Pubmed-ID: 21057052
  • title: Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.).
  • authors: Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO, Chung YR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.023846-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Oryza/growth & development, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/*isolation & purification/physiology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
15717Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21457)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21457
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
33358Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8267
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
83424Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID378358.1StrainInfo: A central database for resolving microbial strain identifiers
120353Curators of the CIPCollection of Institut Pasteur (CIP 110411)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110411