Strain identifier

BacDive ID: 140996

Type strain: Yes

Species: Umboniibacter caenipelagi

Strain Designation: SCTF-16

Strain history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

NCBI tax ID(s): 1943576 (species)

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General

@ref: 67683

BacDive-ID: 140996

DSM-Number: 112598

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, ovoid-shaped, colony-forming

description: Umboniibacter caenipelagi SCTF-16 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from tidal flat sediment, Seocheon, Yellow Sea, South Korea.

NCBI tax id

  • NCBI tax id: 1943576
  • Matching level: species

strain history

@refhistory
67683<- NBRC; NBRC 112760 <- J. H. Yoon, Sungkyunkwan University, Suwon; SCTF-16
67771<- Jung-Hoon YOON, Sungkyunkwan Univ.

doi: 10.13145/bacdive140996.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Cellvibrionaceae
  • genus: Umboniibacter
  • species: Umboniibacter caenipelagi
  • full scientific name: Umboniibacter caenipelagi Park et al. 2017

@ref: 67683

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cellvibrionales

family: Cellvibrionaceae

genus: Umboniibacter

species: Umboniibacter caenipelagi

full scientific name: Umboniibacter caenipelagi Park et al. 2017

strain designation: SCTF-16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43882negative0.5-10.0 µm0.2-0.4 µmovoid-shapedno
43882rod-shaped

colony morphology

  • @ref: 43882
  • colony size: 1.0-1.5 mm
  • colony color: greyish yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43882Marine agar (MA)yes
67683MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://mediadive.dsmz.de/medium/514fName: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) Composition: NaCl 19.4 g/l Agar 15.0 g/l MgCl2 8.8 g/l 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
43882positiveoptimum30mesophilic
43882positivegrowth10-40
43882nogrowth4psychrophilic
43882nogrowth45thermophilic
67683positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
43882positiveoptimum7.0-7.5
43882positivegrowth6
43882nogrowth5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43882aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
43882NaClpositiveoptimum2 %(w/v)
43882NaClpositivegrowth0-6 %(w/v)

observation

@refobservation
43882Mg2+ ions are required for growth
43882quinone Q-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4388230089acetate-carbon source
4388216150benzoate-carbon source
4388217057cellobiose-carbon source
4388216947citrate-carbon source
4388215824D-fructose-carbon source
4388212936D-galactose-carbon source
4388217634D-glucose-carbon source
4388216024D-mannose-carbon source
4388265327D-xylose-carbon source
4388215740formate-carbon source
4388230849L-arabinose-carbon source
4388229985L-glutamate-carbon source
43882maltose hydrate-carbon source
4388215361pyruvate-carbon source
4388217814salicin-carbon source
4388217992sucrose-carbon source
4388227082trehalose-carbon source
43882casein-hydrolysis
438825291gelatin-hydrolysis
4388217368hypoxanthine-hydrolysis
4388217895L-tyrosine-hydrolysis
4388216199urea-hydrolysis
4388215318xanthine-hydrolysis
4388215589L-malate+carbon source
4388230031succinate+carbon source
438824853esculin+hydrolysis
4388228017starch+hydrolysis
4388253426tween 80+hydrolysis
4388217632nitrate+reduction
6836917128adipate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
683695291gelatin-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
438823393carbenicillinyesyes100 µg (disc)
4388217833gentamicinyesyes30 µg (disc)
438827507neomycinyesyes30 µg (disc)
4388228368novobiocinyesyes5 µg (disc)
4388216869oleandomycinyesyes15 µg (disc)
438828309polymyxin byesyes100 Unit (disc)
4388227902tetracyclineyesyes30 µg (disc)
4388217698chloramphenicolyesyes100 µg (disc)
438826104kanamycinyesyes30 µg (disc)
4388217076streptomycinyesyes50 µg (disc)
4388228971ampicillinyesyes10 µg (disc)
438826472lincomycinyesyes15 µg (disc)
4388218208penicillin gyesyes20 Unit (disc)
43882124991cefalotinyesyes30 µg (disc)

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
43882catalase+1.11.1.6
43882cytochrome oxidase+1.9.3.1
43882alkaline phosphatase+3.1.3.1
43882esterase Lipase (C 8)+
43882leucine arylamidase+3.4.11.1
43882valine arylamidase+
43882cystine arylamidase+3.4.11.3
43882trypsin+3.4.21.4
43882alpha-chymotrypsin+3.4.21.1
43882naphthol-AS-BI-phosphohydrolase+
43882N-acetyl-beta-glucosaminidase+3.2.1.52
43882esterase (C 4)-
43882lipase (C 14)-
43882acid phosphatase-3.1.3.2
43882alpha-galactosidase-3.2.1.22
43882beta-galactosidase-3.2.1.23
43882beta-glucuronidase-3.2.1.31
43882alpha-glucosidase-3.2.1.20
43882beta-glucosidase-3.2.1.21
43882alpha-mannosidase-3.2.1.24
43882alpha-fucosidase-3.2.1.51
68369cytochrome oxidase+1.9.3.1
68369gelatinase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43882C10:01.8
    43882C10:0 3OH2.9
    43882C11:01.8
    43882C11:0 3OH4.3
    43882C12:05.1
    43882C12:0 3OH2.2
    43882C13:012.5
    43882C14:07.5
    43882C15:1ω6c2.7
    43882C15:1ω8c2.3
    43882C16:08.6
    43882C16:1ω7c / C16:1ω6c23.8
    43882C17:02.5
    43882C17:1ω6c1.3
    43882C17:1ω8c8.2
    43882C18:1ω7c7.5
    43882C9:01.6
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 30
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
67683+----+-+------------+
67683---++---++----++-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperature
43882tidal flat sediment, Seocheon, Yellow Sea, South KoreaSeocheon, Yellow SeaRepublic of KoreaKORAsiaMarine agar 221625
67683tial flat sedimentnear SeocheonRepublic of KoreaKORAsia
67771From mud flatSeocheon-gunRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_19111.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_235;96_9760;97_11761;98_14453;99_19111&stattab=map
  • Last taxonomy: Umboniibacter
  • 16S sequence: KY560466
  • Sequence Identity:
  • Total samples: 2908
  • soil counts: 52
  • aquatic counts: 2706
  • animal counts: 128
  • plant counts: 22

Safety information

risk assessment

  • @ref: 67683
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 43882
  • description: 16S rRNA gene sequence
  • accession: KY560466
  • database: nuccore

GC content

  • @ref: 43882
  • GC-content: 50
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 67683

culture collection no.: KCTC 52628, NBRC 112760, DSM 112598

straininfo link

  • @ref: 96825
  • straininfo: 405135

literature

  • topic: Phylogeny
  • Pubmed-ID: 28820102
  • title: Umboniibacter caenipelagi sp. nov., isolated from a tidal flat.
  • authors: Park S, Choi SJ, Park JM, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002056
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43882Sooyeon Park, Su Jung Choi, Ji-Min Park, Jung-Hoon YoonUmboniibacter caenipelagi sp. nov., isolated from a tidal flat10.1099/ijsem.0.002056IJSEM 67: 2959-2963 201728820102
67683Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-112598Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 112598)
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96825Reimer, 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-ID405135.1