Strain identifier

BacDive ID: 5701

Type strain: Yes

Species: Chryseobacterium ureilyticum

Strain Designation: F-Fue-04IIIaaaa

Strain history: CIP <- 2010, CCUG <- 2006, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain F-Fue-04IIIaaaa

NCBI tax ID(s): 373668 (species)

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

@ref: 7345

BacDive-ID: 5701

DSM-Number: 18017

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

description: Chryseobacterium ureilyticum F-Fue-04IIIaaaa is an aerobe, mesophilic, Gram-negative bacterium that was isolated from steel surface of a beer-bottling plant.

NCBI tax id

  • NCBI tax id: 373668
  • Matching level: species

strain history

@refhistory
7345<- A. Lipski, School of Biology/Chemistry, Univ. Osnabrück, Germany; F-Fue-04IIIaaaa <- P. Herzog
123745CIP <- 2010, CCUG <- 2006, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain F-Fue-04IIIaaaa

doi: 10.13145/bacdive5701.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium ureilyticum
  • full scientific name: Chryseobacterium ureilyticum Herzog et al. 2008

@ref: 7345

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium ureilyticum

full scientific name: Chryseobacterium ureilyticum Herzog et al. 2008 emend. Montero-Calasanz et al. 2014

strain designation: F-Fue-04IIIaaaa

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilitycell shapeconfidence
31941negative1.4 µm0.7 µmno
32348negative2 µm0.7 µmnorod-shaped
69480no91.998
69480negative99.989
123745negativenorod-shaped

pigmentation

@refproduction
32348yes
31941yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7345TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
39840MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123745CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7345positivegrowth28mesophilic
31941positivegrowth15-42
32348positivegrowth25-30mesophilic
31941positiveoptimum28.5mesophilic
39840positivegrowth30mesophilic
59589positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31941positivegrowth5.5-8.5alkaliphile
31941positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32348aerobe
31941aerobe
59589aerobe
123745obligate aerobe

spore formation

@refspore formationconfidence
31941no
32348no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
32348NaClpositivegrowth<2 %
31941NaClpositivegrowth0-0.9 %
31941NaClpositiveoptimum0.45 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31941581435-dehydro-D-gluconate+carbon source
3194122599arabinose+carbon source
3194133984fucose+carbon source
3194124265gluconate+carbon source
3194117234glucose+carbon source
3194117306maltose+carbon source
3194137684mannose+carbon source
3194128053melibiose+carbon source
31941506227N-acetylglucosamine+carbon source
3194126271proline+carbon source
3194126546rhamnose+carbon source
3194117814salicin+carbon source
3194130911sorbitol+carbon source
3234817234glucose+carbon source
3234817306maltose+carbon source
323484853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12374517632nitrate-reduction
12374516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3234835581indoleyes
12374535581indoleno

metabolite tests

  • @ref: 32348
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31941catalase+1.11.1.6
31941cytochrome oxidase+1.9.3.1
31941urease+3.5.1.5
32348catalase+1.11.1.6
32348gelatinase+
32348cytochrome oxidase+1.9.3.1
32348urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
123745oxidase+
123745catalase+1.11.1.6
123745urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123745-+-+-++-+-++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123745+/----------+-+---------+/--+/--+/-+---+------+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
7345steel surface of a beer-bottling plantGermanyDEUEurope
59589Steel surface of a beer bottling plantGermanyDEUEurope2004-07-01
123745Steel surface of a beer bottling plantGermanyDEUEuropeOsnabrück2006

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Bottled, canned, packed food
#Engineered#Food production#Fermented
#Engineered#Industrial#Engineered product
#Engineered#Industrial#Plant (Factory)
#Engineered#Food production#Beverage

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73451Risk group (German classification)
1237451Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7345
  • description: Chryseobacterium ureilyticum partial 16S rRNA gene, type strain F-Fue-04IIIaaaaT
  • accession: AM232806
  • length: 1472
  • database: ena
  • NCBI tax ID: 373668

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium ureilyticum DSM 18017GCA_900156735contigncbi373668
66792Chryseobacterium ureilyticum strain DSM 18017373668.4wgspatric373668
66792Chryseobacterium ureilyticum DSM 180172681813509draftimg373668

GC content

@refGC-content
3234836.4
3194148.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.687yes
anaerobicno99.531yes
halophileno93.879yes
spore-formingno93.491yes
glucose-utilyes86.632yes
aerobicyes92.101no
motileno90.474no
flagellatedno95.273no
thermophileno99.821yes
glucose-fermentno92.787no

External links

@ref: 7345

culture collection no.: DSM 18017, CCUG 52546, CIP 110146

straininfo link

  • @ref: 75183
  • straininfo: 377001

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175677Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants.Herzog P, Winkler I, Wolking D, Kampfer P, Lipski AInt J Syst Evol Microbiol10.1099/ijs.0.65362-02008Bacterial Typing Techniques, *Beer, Biofilms/growth & development, Chryseobacterium/chemistry/classification/genetics/*isolation & purification, Fatty Acids/analysis, Genotype, *Industrial Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, SteelGenetics
Phylogeny22115847Chryseobacterium oncorhynchi sp. nov., isolated from rainbow trout (Oncorhynchus mykiss).Zamora L, Fernandez-Garayzabal JF, Palacios MA, Sanchez-Porro C, Svensson-Stadler LA, Dominguez L, Moore ER, Ventosa A, Vela AISyst Appl Microbiol10.1016/j.syapm.2011.10.0022011Animals, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gills/microbiology, Liver/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oncorhynchus mykiss/*microbiology, Oxidoreductases/metabolism, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny22268076Chryseobacterium viscerum sp. nov., isolated from diseased fish.Zamora L, Vela AI, Palacios MA, Sanchez-Porro C, Svensson-Stadler LA, Dominguez L, Moore ERB, Ventosa A, Fernandez-Garayzabal JFInt J Syst Evol Microbiol10.1099/ijs.0.036699-02012Animals, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Fish Diseases/microbiology, Gills/microbiology, Liver/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oncorhynchus mykiss/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24958763Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer.Venil CK, Nordin N, Zakaria ZA, Ahmad WAInt J Syst Evol Microbiol10.1099/ijs.0.063594-02014Artocarpus/*microbiology, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30372407Chryseobacterium phosphatilyticum sp. nov., a phosphate-solubilizing endophyte isolated from cucumber (Cucumis sativus L.) root.Jeong JJ, Sang MK, Lee DW, Choi IG, Kim KDInt J Syst Evol Microbiol10.1099/ijsem.0.0030912018Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/isolation & purification, Cucumis sativus/*microbiology, DNA, Bacterial/genetics, Endophytes/classification/isolation & purification, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phosphates, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7345Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18017)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18017
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
31941Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2819728776041
32348Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2857928776041
39840Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7972
59589Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52546)https://www.ccug.se/strain?id=52546
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75183Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377001.1StrainInfo: A central database for resolving microbial strain identifiers
123745Curators of the CIPCollection of Institut Pasteur (CIP 110146)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110146