Strain identifier

BacDive ID: 17416

Type strain: Yes

Species: Ancylobacter koreensis

Strain history: CIP <- 2006, IAM <- W.-T. Im: strain Jip08

NCBI tax ID(s): 266121 (species)

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General

@ref: 7542

BacDive-ID: 17416

DSM-Number: 18406

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

description: Ancylobacter koreensis DSM 18406 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stem of rice straw.

NCBI tax id

  • NCBI tax id: 266121
  • Matching level: species

strain history

@refhistory
7542<- KAIST, Republic of Korea <- W.-T. Im; Jip08
375372006, IAM
67770IAM 15215 <-- W.-T. Im Jip08.
67771<- ST Lee, KAIST
120489CIP <- 2006, IAM <- W.-T. Im: strain Jip08

doi: 10.13145/bacdive17416.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Xanthobacteraceae
  • genus: Ancylobacter
  • species: Ancylobacter koreensis
  • full scientific name: Ancylobacter koreensis (Im et al. 2006) Doronina et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Starkeya koreensis

@ref: 7542

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Starkeya

species: Starkeya koreensis

full scientific name: Starkeya koreensis Im et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
120489negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7542R2A 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
37537MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
120489CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7542positivegrowth30mesophilic
37537positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12048917632nitrate-reduction
12048916301nitrite-reduction

metabolite production

  • @ref: 120489
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120489oxidase+
120489catalase+1.11.1.6
120489urease+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
120489--++-++-+-------+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7542stem of rice strawDaejonRepublic of KoreaKORAsia
67770Rice strawDaejeonRepublic of KoreaKORAsia
67771From rotten rice strawRepublic of KoreaKORAsia
120489Food, Rice strawRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7033.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_2984;97_3669;98_5167;99_7033&stattab=map
  • Last taxonomy: Starkeya
  • 16S sequence: AB681299
  • Sequence Identity:
  • Total samples: 2051
  • soil counts: 522
  • aquatic counts: 773
  • animal counts: 291
  • plant counts: 465

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75421Risk group (German classification)
1204891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Starkeya koreensis gene for 16S rRNA, partial sequence, strain: NBRC 100963AB6812991410ena266121
7542Starkeya koreensis gene for 16S rRNA, partial sequenceAB1668771406ena266121

GC content

@refGC-contentmethod
754269
6777069high performance liquid chromatography (HPLC)

External links

@ref: 7542

culture collection no.: DSM 18406, IAM 15215, KCTC 12212, NBRC 100963, Jip 08, JCM 21669, CIP 109384

straininfo link

  • @ref: 86412
  • straininfo: 232746

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012571Starkeya koreensis sp. nov., isolated from rice straw.Im WT, Aslam Z, Lee M, Ten LN, Yang DC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64093-02006Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny36462112Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter.Doronina NV, Chemodurova AA, Grouzdev DS, Koziaeva VV, Agafonova NV, Shi W, Wu L, Kaparullina ENAntonie Van Leeuwenhoek10.1007/s10482-022-01788-82022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18406)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18406
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37537Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7119
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
86412Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232746.1StrainInfo: A central database for resolving microbial strain identifiers
120489Curators of the CIPCollection of Institut Pasteur (CIP 109384)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109384