Strain identifier

BacDive ID: 178

Type strain: Yes

Species: Actinomyces urogenitalis

Strain history: CIP <- 2000, CCUG <- 1997, Gen. Diagn., PHL, Göteborg, Sweden

NCBI tax ID(s): 525246 (strain), 103621 (species)

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General

@ref: 5819

BacDive-ID: 178

DSM-Number: 15434

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

description: Actinomyces urogenitalis DSM 15434 is a microaerophile, mesophilic, Gram-positive human pathogen that was isolated from human vaginal secretion.

NCBI tax id

NCBI tax idMatching level
525246strain
103621species

strain history

@refhistory
5819<- CCUG <- PHL, Göteborg
123755CIP <- 2000, CCUG <- 1997, Gen. Diagn., PHL, Göteborg, Sweden

doi: 10.13145/bacdive178.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinomyces
  • species: Actinomyces urogenitalis
  • full scientific name: Actinomyces urogenitalis Nikolaitchouk et al. 2000

@ref: 5819

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces urogenitalis

full scientific name: Actinomyces urogenitalis Nikolaitchouk et al. 2000 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23113positiverod-shapedno
69480no93.228
69480positive100
123755positiverod-shapedno

colony morphology

  • @ref: 123755

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5819BHI/2 MEDIUM (DSMZ Medium 217)yeshttps://mediadive.dsmz.de/medium/217Name: BHI/2 MEDIUM (DSMZ Medium 217) Composition: Brain heart infusion 37.0 g/l Casein hydrolysate 10.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
5819COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
36438MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123755CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
5819positivegrowth37mesophilic
36438positivegrowth37mesophilic
54404positivegrowth37mesophilic
123755positivegrowth25-41
123755nogrowth10psychrophilic
123755nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5819microaerophile
23113facultative anaerobe
54404microaerophile
69480anaerobe92.084
123755facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.993

halophily

@refsaltgrowthtested relationconcentration
123755NaClpositivegrowth2-4 %
123755NaClnogrowth6 %
123755NaClnogrowth8 %
123755NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2311323456cyclodextrin-builds acid from
2311328087glycogen-builds acid from
2311330911sorbitol-builds acid from
2311333954tagatose-builds acid from
231135291gelatin-hydrolysis
23113606565hippurate-hydrolysis
2311318333D-arabitol+builds acid from
2311317634D-glucose+builds acid from
2311316634raffinose+builds acid from
2311365327D-xylose+builds acid from
2311317716lactose+builds acid from
2311317306maltose+builds acid from
231136731melezitose+builds acid from
2311317992sucrose+builds acid from
2311327082trehalose+builds acid from
2311318333D-arabitol+fermentation
2311365327D-xylose+fermentation
231136731melezitose+fermentation
231134853esculin+hydrolysis
2311317632nitrate+reduction
2311330849L-arabinose+/-builds acid from
2311329864mannitol+/-builds acid from
23113320055methyl beta-D-glucopyranoside+/-builds acid from
2311333942ribose+/-builds acid from
2311315688acetoin+/-other
12375516947citrate-carbon source
1237554853esculin+hydrolysis
123755606565hippurate-hydrolysis
12375517632nitrate+reduction
12375516301nitrite-reduction
12375517632nitrate+respiration
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 123755
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
12375535581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
12375515688acetoin-
12375517234glucose+

enzymes

@refvalueactivityec
23113acid phosphatase-3.1.3.2
23113alkaline phosphatase+/-3.1.3.1
23113alpha-fucosidase-3.2.1.51
23113alpha-galactosidase+/-3.2.1.22
23113alpha-galactosidase+3.2.1.22
23113alpha-glucosidase+3.2.1.20
23113alpha-mannosidase+/-3.2.1.24
23113arginine dihydrolase-3.5.3.6
23113beta-glucosidase+3.2.1.21
23113beta-glucuronidase-3.2.1.31
23113catalase-1.11.1.6
23113chymotrypsin-3.4.4.5
23113cystine arylamidase+/-3.4.11.3
23113esterase (C 4)-
23113esterase lipase (C 8)-
23113leucine arylamidase+3.4.11.1
23113lipase (C 14)-
23113pyrazinamidase-3.5.1.B15
23113pyroglutamic acid arylamidase+
23113pyrrolidonyl arylamidase+3.4.19.3
23113trypsin-3.4.21.4
23113urease-3.5.1.5
23113valine arylamidase+
68382alpha-fucosidase-3.2.1.51
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
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68379catalase-1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
123755oxidase-
123755beta-galactosidase-3.2.1.23
123755alcohol dehydrogenase-1.1.1.1
123755gelatinase-
123755amylase+
123755DNase-
123755caseinase-3.4.21.50
123755catalase-1.11.1.6
123755tween esterase-
123755gamma-glutamyltransferase-2.3.2.2
123755lecithinase-
123755lipase-
123755lysine decarboxylase-4.1.1.18
123755ornithine decarboxylase-4.1.1.17
123755phenylalanine ammonia-lyase-4.3.1.24
123755protease-
123755tryptophan deaminase-
123755urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
54404+-+--++++---+++-+++--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
54404-----++-----++-++++-
123755-+++-+++----++-+++--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
5819--++-+++-+++--+--++++++/-+++/---+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123755+--+--+-+++++--++-+---+--------+--++-----------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
5819human vaginal secretionGöteborgSwedenSWEEurope
23113vaginal secretion of 33 year old woman
54404Human vaginal secretion,33-yr-old subjectGöteborgSwedenSWEEurope1997-11-07
123755Human, Vaginal secretionGöteborgSwedenSWEEurope1997

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids
#Host#Human#Female
#Host Body-Site#Urogenital tract#Vagina
#Host Body Product#Urogenital tract#Vaginal secretion

taxonmaps

  • @ref: 69479
  • File name: preview.99_4259.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_2145;97_2588;98_3208;99_4259&stattab=map
  • Last taxonomy: Actinomyces urogenitalis subclade
  • 16S sequence: AJ243791
  • Sequence Identity:
  • Total samples: 10333
  • soil counts: 88
  • aquatic counts: 132
  • animal counts: 10078
  • plant counts: 35

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
5819yes, in single cases1Risk group (German classification)
1237552Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5819
  • description: Actinomyces urogenitalis 16S rRNA gene
  • accession: AJ243791
  • length: 1423
  • database: ena
  • NCBI tax ID: 103621

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces urogenitalis DSM 15434GCA_000159035scaffoldncbi525246
66792Actinomyces urogenitalis DSM 15434525246.3wgspatric525246
66792Actinomyces urogenitalis DSM 15434643886015draftimg525246

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno57no
motileno91.421yes
flagellatedno96.936yes
gram-positiveyes96.717no
anaerobicno91.775no
halophileno87.671no
spore-formingno95.185no
thermophileno93.886no
glucose-utilyes87.41no
aerobicno90.917yes
glucose-fermentyes85.385yes

External links

@ref: 5819

culture collection no.: DSM 15434, CCUG 38702, CIP 106421

straininfo link

  • @ref: 69860
  • straininfo: 51192

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10939672Characterization of Actinomyces isolates from samples from the human urogenital tract: description of Actinomyces urogenitalis sp. nov.Nikolaitchouk N, Hoyles L, Falsen E, Grainger JM, Collins MDInt J Syst Evol Microbiol10.1099/00207713-50-4-16492000Actinomyces/chemistry/*classification/genetics, Adult, Aged, Bacterial Proteins/analysis, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Female, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Urogenital System/*microbiologyPathogenicity
Phylogeny34252022Characterization of isolates of members of the genus Actinomyces from Marmota himalayana: description of Actinomyces faecalis sp. nov., Actinomyces respiraculi sp. nov., and Actinomyces trachealis sp. nov.Zhou J, Zhang S, Zhang G, Yang J, Lai XH, Pu J, Jin D, Lu S, Huang Y, Zhu W, Huang Y, Xu M, Lei W, Cheng Y, Liu L, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0048752021Actinomyces/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Marmota/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5819Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15434)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15434
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
23113N Nikolaitchouk, L Hoyles, E Falsen, J M Grainger, M D Collins10.1099/00207713-50-4-1649Characterization of Actinomyces isolates from samples from the human urogenital tract: description of Actinomyces urogenitalis sp. nov.IJSEM 50: 1649-1654 200010939672
36438Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18550
54404Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38702)https://www.ccug.se/strain?id=38702
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
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)
69860Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID51192.1StrainInfo: A central database for resolving microbial strain identifiers
123755Curators of the CIPCollection of Institut Pasteur (CIP 106421)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106421