Strain identifier

BacDive ID: 356

Type strain: Yes

Species: Oligella ureolytica

Strain Designation: C379

Strain history: CIP <- 1988, LMG <- 1982, CCUG <- 1972, R. Weaver, CDC: strain C379

NCBI tax ID(s): 1122619 (strain), 90244 (species)

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General

@ref: 7461

BacDive-ID: 356

DSM-Number: 18253

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, motile, rod-shaped, human pathogen

description: Oligella ureolytica C379 is a microaerophile, mesophilic, Gram-negative human pathogen that was isolated from human urine.

NCBI tax id

NCBI tax idMatching level
90244species
1122619strain

strain history

@refhistory
7461<- CCUG <- R. E. Weaver, CDC
123746CIP <- 1988, LMG <- 1982, CCUG <- 1972, R. Weaver, CDC: strain C379

doi: 10.13145/bacdive356.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Oligella
  • species: Oligella ureolytica
  • full scientific name: Oligella ureolytica Rossau et al. 1987

@ref: 7461

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Oligella

species: Oligella ureolytica

full scientific name: Oligella ureolytica Rossau et al. 1987

strain designation: C379

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityflagellum arrangementconfidence
23272negative1 µmrod-shapedyesperitrichous
69480yes91.911
69480negative99.999

colony morphology

  • @ref: 23272
  • type of hemolysis: gamma

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18253_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18253_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18253_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18253_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7461COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
40525MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123746CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7461positivegrowth37mesophilic
23272nogrowth42thermophilic
40525positivegrowth30mesophilic
44381positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7461microaerophile
44381microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

  • @ref: 23272
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 4.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2327215963ribitol-builds acid from
2327215824D-fructose-builds acid from
2327217634D-glucose-builds acid from
2327265327D-xylose-builds acid from
2327217306maltose-builds acid from
2327232382(R)-mandelate-carbon source
23272165672-aminobenzoate-carbon source
23272168082-dehydro-D-gluconate-carbon source
23272307613-aminobenzoate-carbon source
23272879973-aminobutyrate-carbon source
23272178364-aminobenzoate-carbon source
23272391504-oxopentanoate-carbon source
23272174265-dehydro-D-gluconate-carbon source
2327227856acetamide-carbon source
2327222210aconitate-carbon source
2327217128adipate-carbon source
2327215963ribitol-carbon source
2327227613amygdalin-carbon source
2327218305arbutin-carbon source
2327278208azelaate-carbon source
2327240538benzylamine-carbon source
2327216958beta-alanine-carbon source
2327217750betaine-carbon source
2327243799butan-1-amine-carbon source
2327227689decanoate-carbon source
2327225646octanoate-carbon source
2327217057cellobiose-carbon source
2327230719citraconate-carbon source
2327216919creatine-carbon source
2327217108D-arabinose-carbon source
2327218403D-arabitol-carbon source
2327215824D-fructose-carbon source
2327228847D-fucose-carbon source
2327212936D-galactose-carbon source
232728391D-gluconate-carbon source
2327217315D-glucosamine-carbon source
2327217634D-glucose-carbon source
2327262318D-lyxose-carbon source
2327216899D-mannitol-carbon source
2327216024D-mannose-carbon source
2327216988D-ribose-carbon source
2327216443D-tagatose-carbon source
2327230927D-tartrate-carbon source
2327216296D-tryptophan-carbon source
2327265327D-xylose-carbon source
2327233871glycerate-carbon source
2327216813galactitol-carbon source
2327217113erythritol-carbon source
232724853esculin-carbon source
2327216000ethanolamine-carbon source
2327215862ethylamine-carbon source
2327228066gentiobiose-carbon source
2327215428glycine-carbon source
2327228087glycogen-carbon source
2327229805glycolate-carbon source
2327232362heptanoate-carbon source
2327218295histamine-carbon source
2327215443inulin-carbon source
2327230803isophthalate-carbon source
2327228683kynurenine-carbon source
2327230849L-arabinose-carbon source
2327218403L-arabitol-carbon source
2327216467L-arginine-carbon source
2327216349L-citrulline-carbon source
2327217561L-cysteine-carbon source
2327218287L-fucose-carbon source
2327215971L-histidine-carbon source
2327218019L-lysine-carbon source
2327216643L-methionine-carbon source
2327215729L-ornithine-carbon source
2327217295L-phenylalanine-carbon source
2327262345L-rhamnose-carbon source
2327217115L-serine-carbon source
2327217266L-sorbose-carbon source
2327216857L-threonine-carbon source
2327216828L-tryptophan-carbon source
2327217895L-tyrosine-carbon source
2327265328L-xylose-carbon source
2327217716lactose-carbon source
2327218300maleic acid-carbon source
2327215792malonate-carbon source
2327217306maltose-carbon source
232726731melezitose-carbon source
2327228053melibiose-carbon source
2327230928meso-tartrate-carbon source
23272320061methyl alpha-D-glucopyranoside-carbon source
2327243943methyl alpha-D-mannoside-carbon source
2327274863methyl beta-D-xylopyranoside-carbon source
23272506227N-acetylglucosamine-carbon source
2327232361nonanoate-carbon source
2327230623oxalate-carbon source
2327274848pentan-1-amine-carbon source
2327217563phthalate-carbon source
2327217774pimelate-carbon source
2327217148putrescine-carbon source
2327216634raffinose-carbon source
2327217814salicin-carbon source
2327215611sarcosine-carbon source
2327241865sebacic acid-carbon source
2327230911sorbitol-carbon source
2327215746spermine-carbon source
2327228017starch-carbon source
232729300suberic acid-carbon source
2327217992sucrose-carbon source
2327230043terephthalate-carbon source
2327227082trehalose-carbon source
2327216765tryptamine-carbon source
2327232528turanose-carbon source
2327216199urea-carbon source
2327217151xylitol-carbon source
2327232800(S)-mandelic acid-growth
23272283402-aminobutyrate-growth
23272194752-aminopentanoic acid-growth
23272161933-hydroxybenzoate-growth
2327216865gamma-aminobutyric acid-growth
23272158875-aminovaleric acid-growth
232723565cetrimide-growth
2327216947citrate-growth
2327215588D-malate-growth
2327248944isobutyrate-growth
2327216977L-alanine-growth
2327229991L-aspartate-growth
2327217191L-isoleucine-growth
2327215603L-leucine-growth
2327218347L-norleucine-growth
2327216414L-valine-growth
2327218401phenylacetate-growth
2327218123trigonelline-growth
2327227856acetamide-hydrolysis
2327216991dna-hydrolysis
232724853esculin-hydrolysis
232725291gelatin-hydrolysis
2327228017starch-hydrolysis
2327253426tween 80-hydrolysis
2327215589L-malate+carbon source
23272309162-oxoglutarate+carbon source
23272370543-hydroxybutyrate+carbon source
2327230089acetate+carbon source
2327216150benzoate+carbon source
2327229806fumarate+carbon source
2327229985L-glutamate+carbon source
2327224996lactate+carbon source
2327215361pyruvate+carbon source
2327230031succinate+carbon source
23272178794-hydroxybenzoate+growth
2327215570D-alanine+growth
2327217859glutaric acid+growth
2327248942isovalerate+growth
2327217240itaconate+growth
2327217203L-proline+growth
2327230924L-tartrate+growth
2327236986mesaconate+growth
2327217272propionate+growth
2327231011valerate+growth
2327217632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

antibiotic resistance

  • @ref: 23272
  • ChEBI: 17334
  • metabolite: penicillin
  • is antibiotic: yes
  • is resistant: yes

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
23272Acid phosphatase-3.1.3.2
23272Alkaline phosphatase-3.1.3.1
23272alpha-chymotrypsin-3.4.21.1
23272alpha-fucosidase-3.2.1.51
23272alpha-galactosidase-3.2.1.22
23272alpha-glucosidase-3.2.1.20
23272alpha-mannosidase-3.2.1.24
23272beta-galactosidase-3.2.1.23
23272beta-glucoronidase-3.2.1.31
23272beta-glucosidase-3.2.1.21
23272cystine arylamidase-3.4.11.3
23272esterase (C 4)+
23272esterase lipase (C 8)+
23272leucine arylamidase+3.4.11.1
23272lipase (C 14)-
23272N-acetyl-beta-glucosaminidase-3.2.1.52
23272naphthol-AS-BI-phosphohydrolase-
23272trypsin-3.4.21.4
23272urease+3.5.1.5
23272valine arylamidase-
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    44381C14:05.614
    44381C15:0215
    44381C16:02816
    44381C17:01.817
    44381C18:01.118
    44381C12:0 ALDE ?110.915
    44381C13:1 at 12-13112.931
    44381C14:0 3OH/C16:1 ISO I5.415.485
    44381C16:0 3OH2.817.52
    44381C16:1 ω7c1.115.819
    44381C17:1 ISO I/C16:0 DMA0.616.481
    44381C17:1 ω6c0.716.862
    44381C18:1 ω7c /12t/9t48.517.824
    44381Unidentified0.417.706
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
44381-+---+--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
44381+---+------------+--+
7461+---+------------++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7461human urineLouisianaUSAUSANorth America
44381Human urineLouisianaUSAUSANorth America1971
123746Human, UrineLouisianaUnited States of AmericaUSANorth America1971

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6680.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1726;97_3878;98_4926;99_6680&stattab=map
  • Last taxonomy: Oligella ureolytica subclade
  • 16S sequence: AJ251912
  • Sequence Identity:
  • Total samples: 4938
  • soil counts: 382
  • aquatic counts: 756
  • animal counts: 3610
  • plant counts: 190

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
7461yes, in single cases1Risk group (German classification)
1237461Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Oligella ureolytica 16S ribosomal RNA gene, partial sequenceAF2271641477ena1122619
20218Oligella ureolytica 16S rRNA gene, partialAJ247261457ena1122619
7461Oligella ureolytica 16S rRNA gene, strain LMG 6519AJ2519121489ena1122619

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oligella ureolytica DSM 18253GCA_000373745scaffoldncbi1122619
66792Oligella ureolytica NCTC11997GCA_900454285contigncbi90244
66792Oligella ureolytica DSM 182531122619.3wgspatric1122619
66792Oligella ureolytica strain FDAARGOS_87290244.6completepatric90244
66792Oligella ureolytica strain NCTC1199790244.3wgspatric90244
66792Oligella ureolytica NCTC 119972808606647draftimg90244
66792Oligella ureolytica DSM 182532515154154draftimg1122619

GC content

  • @ref: 23272
  • GC-content: 46-47
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.089yes
flagellatedno55.546no
gram-positiveno98.291yes
anaerobicno95.598yes
halophileno80.871no
spore-formingno94.858no
thermophileno98.407no
glucose-utilno85.76no
aerobicno62.332yes
glucose-fermentno88.942no

External links

@ref: 7461

culture collection no.: DSM 18253, ATCC 43534, CCM 4583, CCUG 1465Aa, CDC C379, CIP 103114, LMG 6519, NCTC 11997, CCUG 1465 A, CCUG 1465

straininfo link

  • @ref: 70036
  • straininfo: 3727

literature

  • topic: Pathogenicity
  • Pubmed-ID: 23880127
  • title: Plants traditionally used individually and in combination to treat sexually transmitted infections in northern Maputaland, South Africa: antimicrobial activity and cytotoxicity.
  • authors: Naidoo D, van Vuuren SF, van Zyl RL, de Wet H
  • journal: J Ethnopharmacol
  • DOI: 10.1016/j.jep.2013.07.018
  • year: 2013
  • mesh: Anti-Infective Agents/administration & dosage/pharmacology/*therapeutic use/toxicity, Cell Survival/drug effects, Drug Synergism, Drug Therapy, Combination, HEK293 Cells, Humans, *Medicine, African Traditional, Microbial Sensitivity Tests, Plant Extracts/administration & dosage/pharmacology/*therapeutic use/toxicity, Plants, Medicinal/*chemistry, Sexually Transmitted Diseases/*drug therapy/*microbiology, South Africa, Treatment Outcome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7461Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18253)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18253
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23272R. Rossau, K. Kersters, E. Falsen, E. Jantzen, P. Segers, A. Union, L. Nehls, J. De Ley10.1099/00207713-37-3-198Oligella, a New Genus Including Oligella urethralis comb. nov. (Formerly Moraxella urethralis) and Oligella ureolytica sp. nov. (Formerly CDC Group IVe): Relationship to Taylorella equigenitalis and Related TaxaIJSEM 37: 198-210 1987
40525Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14876
44381Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1465 A)https://www.ccug.se/strain?id=1465
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
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
70036Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3727.1StrainInfo: A central database for resolving microbial strain identifiers
123746Curators of the CIPCollection of Institut Pasteur (CIP 103114)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103114