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Strain identifier

BacDive ID: 24026

Type strain: Yes

Species: Flavobacterium urocaniciphilum

Strain history: D. Fujii strain 95 (=YIT 12746).

NCBI tax ID(s): 1299341 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20573

BacDive-ID: 24026

DSM-Number: 27078

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Flavobacterium urocaniciphilum DSM 27078 is a mesophilic bacterium that was isolated from sludge from wastewater treatment plant associated with a facility, that produces a fermented milk drink.

NCBI tax id

  • NCBI tax id: 1299341
  • Matching level: species

strain history

doi: 10.13145/bacdive24026.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium urocaniciphilum
  • full scientific name: Flavobacterium urocaniciphilum Fujii et al. 2014

@ref: 20573

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium urocaniciphilum

full scientific name: Flavobacterium urocaniciphilum Fujii et al. 2014

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.615

Culture and growth conditions

culture medium

  • @ref: 20573
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
20573positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.031

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 94.157

observation

  • @ref: 67770
  • observation: quinones: MK-6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20573sludge from wastewater treatment plant associated with a facility, that produces a fermented milk drinkSaga Prefecture, Yakult Honsha Co., Ltd.JapanJPNAsia
67770Sludge from a wastewater treatment plant in Saga Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production
#Engineered#Waste#Water treatment plant
#Environmental#Terrestrial#Mud (Sludge)
#Host Body Product#Fluids#Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_27208.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_13493;97_16430;98_20384;99_27208&stattab=map
  • Last taxonomy: Flavobacterium urocaniciphilum subclade
  • 16S sequence: AB795015
  • Sequence Identity:
  • Total samples: 2083
  • soil counts: 418
  • aquatic counts: 1375
  • animal counts: 211
  • plant counts: 79

Safety information

risk assessment

  • @ref: 20573
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20573
  • description: Flavobacterium urocaniciphilum gene for 16S ribosomal RNA, partial sequence
  • accession: AB795015
  • length: 1468
  • database: ena
  • NCBI tax ID: 1299341

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium urocaniciphilum strain DSM 270781299341.3wgspatric1299341
66792Flavobacterium urocaniciphilum DSM 270782693429864draftimg1299341
67770Flavobacterium urocaniciphilum DSM 27078GCA_900110615contigncbi1299341
66792Anaerolineae bacterium UBA8779GCA_003486425scaffoldpatric2052143

GC content

  • @ref: 20573
  • GC-content: 30.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 20573

culture collection no.: DSM 27078, JCM 19142, YIT 12746, BCRC 81228, NRIC 0940

straininfo link

@refpassport
20218http://www.straininfo.net/strains/896378
20218http://www.straininfo.net/strains/896377

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24453232Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena.Fujii D, Nagai F, Watanabe Y, Shirasawa YInt J Syst Evol Microbiol10.1099/ijs.0.054312-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiologyGenetics
Phylogeny26118784Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan.Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VVArch Microbiol10.1007/s00203-015-1128-x2015Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Flavobacterium/*classification/*genetics/isolation & purification, Geologic Sediments/*microbiology, Japan, *Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Vitamin K 2/analysisEnzymology
Phylogeny30355396Flavobacterium sediminis sp. nov., a starch-degrading bacterium isolated from tidal flat sediment.Bae SS, Kim MR, Jung Y, Yang SH, Kwon KK, Baek KInt J Syst Evol Microbiol10.1099/ijsem.0.0030812018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20573Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27078Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27078)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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