Strain identifier

BacDive ID: 24049

Type strain: Yes

Species: Olleya namhaensis

Strain Designation: WT-MY15

Strain history: <- JH Yoon, KRIBB, Korea

NCBI tax ID(s): 1144750 (species)

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General

@ref: 21092

BacDive-ID: 24049

DSM-Number: 28881

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

description: Olleya namhaensis WT-MY15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from wood fallen into coastal sea.

NCBI tax id

  • NCBI tax id: 1144750
  • Matching level: species

strain history

@refhistory
21092<- KCTC <- J.-H. Yoon and et al., Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon
67771<- JH Yoon, KRIBB, Korea

doi: 10.13145/bacdive24049.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Olleya
  • species: Olleya namhaensis
  • full scientific name: Olleya namhaensis Lee et al. 2013

@ref: 21092

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Olleya

species: Olleya namhaensis

full scientific name: Olleya namhaensis Lee et al. 2013

strain designation: WT-MY15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
30778negative2 µm0.35 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative
69480negative99.995

colony morphology

  • @ref: 62644
  • incubation period: 2 days

pigmentation

  • @ref: 30778
  • production: yes

multimedia

  • @ref: 21092
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28881.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 21092
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21092positivegrowth28mesophilic
30778positivegrowth04-30
30778positiveoptimum25mesophilic
62644positivegrowth20psychrophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
30778positivegrowth5.5-8
30778positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30778aerobe
62644aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

  • @ref: 30778
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 2 %

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

  • @ref: 30778
  • Chebi-ID: 4853
  • metabolite: esculin
  • utilization activity: +
  • kind of utilization tested: hydrolysis

enzymes

@refvalueactivityec
30778acid phosphatase+3.1.3.2
30778alkaline phosphatase+3.1.3.1
30778catalase+1.11.1.6
30778gelatinase+
30778cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21092wood fallen into coastal seaSouth Sea, coast at WandoRepublic of KoreaKORAsia
62644Wood fall in seawaterWando Island,South SeaRepublic of KoreaKORAsia2011
67771From the coast at Wando, an island of South KoreaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Host Body Product#Plant#Timber

taxonmaps

  • @ref: 69479
  • File name: preview.99_37799.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_1385;97_1649;98_27779;99_37799&stattab=map
  • Last taxonomy: Olleya namhaensis subclade
  • 16S sequence: JQ327134
  • Sequence Identity:
  • Total samples: 1529
  • soil counts: 50
  • aquatic counts: 1447
  • animal counts: 20
  • plant counts: 12

Safety information

risk assessment

  • @ref: 21092
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21092
  • description: Olleya namhaensis strain WT-MY15 16S ribosomal RNA gene, partial sequence
  • accession: JQ327134
  • length: 1441
  • database: ena
  • NCBI tax ID: 1144750

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Olleya namhaensis DSM 28881GCA_900114005contigncbi1144750
66792Olleya namhaensis strain DSM 288811144750.3wgspatric1144750
66792Olleya namhaensis DSM 288812693429874draftimg1144750

GC content

  • @ref: 21092
  • GC-content: 42.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.771no
flagellatedno93.164no
gram-positiveno98.244yes
anaerobicno99.331no
aerobicyes92.972no
halophileno73.459no
spore-formingno95.838no
glucose-utilyes87.807no
thermophileno99.213yes
glucose-fermentno91.957no

External links

@ref: 21092

culture collection no.: DSM 28881, CCUG 61507, KCTC 23673

straininfo link

  • @ref: 88021
  • straininfo: 399758

literature

  • topic: Phylogeny
  • Pubmed-ID: 22904221
  • title: Olleya namhaensis sp. nov., isolated from wood falls, and emended description of the genus Olleya Mancuso Nichols et al. 2005 emend. Lee et al. 2010.
  • authors: Lee MH, Jung YT, Park S, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.044131-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Wood/*microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21092Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28881Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28881)
30778Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172710928776041
62644Curators of the CCUGhttps://www.ccug.se/strain?id=61507Culture Collection University of Gothenburg (CCUG) (CCUG 61507)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88021Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399758.1