Strain identifier

BacDive ID: 360

Type strain: Yes

Species: Pigmentiphaga daeguensis

Strain Designation: K110

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 414049 (species)

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General

@ref: 16713

BacDive-ID: 360

DSM-Number: 23373

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

description: Pigmentiphaga daeguensis K110 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from wastewater from a dye works.

NCBI tax id

  • NCBI tax id: 414049
  • Matching level: species

strain history

@refhistory
16713<- KCTC <- J. H. Yoon, KRIBB
67770J.-H. Yoon K110.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive360.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Pigmentiphaga
  • species: Pigmentiphaga daeguensis
  • full scientific name: Pigmentiphaga daeguensis Yoon et al. 2007

@ref: 16713

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Pigmentiphaga

species: Pigmentiphaga daeguensis

full scientific name: Pigmentiphaga daeguensis Yoon et al. 2007

strain designation: K110

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23274negative0.7-2.5 µm0.3-0.6 µmrod-shapedno
67771negative

colony morphology

  • @ref: 23274
  • colony size: 1-2 mm
  • colony color: yellowish white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TSA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16713TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23274Trypticase Soy Agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
16713positivegrowth28mesophilic
23274positivegrowth15-46
23274nogrowth10psychrophilic
23274nogrowth47thermophilic
23274positiveoptimum37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
23274positiveoptimum7.0-8.0
23274positivegrowth5.0-9.0alkaliphile
23274nogrowth4.5
23274nogrowth9.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23274aerobe
67771aerobe

spore formation

  • @ref: 23274
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
23274NaClpositivemaximum5 %
23274NaClpositiveoptimum0.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23274168082-dehydro-D-gluconate-assimilation
23274174265-dehydro-D-gluconate-assimilation
2327427613amygdalin-assimilation
2327427689decanoate-assimilation
2327417108D-arabinose-assimilation
2327418333D-arabitol-assimilation
2327428847D-fucose-assimilation
2327462318D-lyxose-assimilation
2327416443D-tagatose-assimilation
2327432528turanose-assimilation
2327416813galactitol-assimilation
2327417113erythritol-assimilation
232744853esculin-assimilation
2327428066gentiobiose-assimilation
2327417754glycerol-assimilation
2327428087glycogen-assimilation
2327415443inulin-assimilation
2327418403L-arabitol-assimilation
2327418287L-fucose-assimilation
2327465328L-xylose-assimilation
2327417716lactose-assimilation
232746731melezitose-assimilation
23274320061methyl alpha-D-glucopyranoside-assimilation
2327443943methyl alpha-D-mannoside-assimilation
2327474863methyl beta-D-xylopyranoside-assimilation
2327418401phenylacetate-assimilation
2327416634raffinose-assimilation
2327427922sorbose-assimilation
2327428017starch-assimilation
2327417151xylitol-assimilation
2327417128adipate+assimilation
2327425115malate+assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2327427902tetracyclineyesyes
232743393carbenicillinyesyes

enzymes

@refvalueactivityec
23274arginine dihydrolase+/-3.5.3.6
23274lysine decarboxylase-4.1.1.18
23274ornithine decarboxylase-4.1.1.17
23274tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16713wastewater from a dye worksDaeguRepublic of KoreaKORAsia
60985Wastewater from a dye worksRepublic of KoreaKORAsia
67770Wastewater from a dye works
67771From wastewaterRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_40308.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1835;97_16214;98_20090;99_40308&stattab=map
  • Last taxonomy: Pigmentiphaga
  • 16S sequence: EF100696
  • Sequence Identity:
  • Total samples: 7339
  • soil counts: 1825
  • aquatic counts: 3532
  • animal counts: 1092
  • plant counts: 890

Safety information

risk assessment

  • @ref: 16713
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16713
  • description: Pigmentiphaga daeguensis strain K110 16S ribosomal RNA gene, partial sequence
  • accession: EF100696
  • length: 1486
  • database: ena
  • NCBI tax ID: 414049

GC content

  • @ref: 16713
  • GC-content: 67.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 16713

culture collection no.: DSM 23373, JCM 14330, KCTC 12838, CCUG 56486

straininfo link

  • @ref: 70040
  • straininfo: 309474

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551027
  • title: Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga.
  • authors: Yoon JH, Kang SJ, Kim W, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64901-0
  • year: 2007
  • mesh: Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Base Composition, Coloring Agents, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Hypotonic Solutions, Industrial Waste, Korea, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction/methods, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Repetitive Sequences, Nucleic Acid/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride, Spores, Bacterial, Temperature, Ubiquinone/analysis, Waste Disposal, Fluid, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16713Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23373)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23373
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
23274Jung-Hoon Yoon, So-Jung Kang, Wonyong Kim, Tae-Kwang Oh10.1099/ijs.0.64901-0Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus PigmentiphagaIJSEM 57: 1188-1191 200717551027
60985Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56486)https://www.ccug.se/strain?id=56486
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
70040Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309474.1StrainInfo: A central database for resolving microbial strain identifiers