Strain identifier

BacDive ID: 146

Type strain: Yes

Species: Actinotignum urinale

Strain Designation: R9242

Strain history: CIP <- 2002, CCUG <- Hall, PHLS, Cardiff, UK: strain R9242

NCBI tax ID(s): 1120933 (strain), 190146 (species)

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General

@ref: 6115

BacDive-ID: 146

DSM-Number: 15805

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped

description: Actinotignum urinale R9242 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from urine culture, human female with pyuria.

NCBI tax id

NCBI tax idMatching level
1120933strain
190146species

strain history

@refhistory
6115<- CCUG <- V. Hall
67771<- CCUG <- V Hall
123752CIP <- 2002, CCUG <- Hall, PHLS, Cardiff, UK: strain R9242

doi: 10.13145/bacdive146.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinotignum
  • species: Actinotignum urinale
  • full scientific name: Actinotignum urinale (Hall et al. 2003) Yassin et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Actinobaculum urinale

@ref: 6115

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinotignum

species: Actinotignum urinale

full scientific name: Actinotignum urinale (Hall et al. 2003) Yassin et al. 2015

strain designation: R9242

type strain: yes

Morphology

cell morphology

@refcell shapegram stainmotilityconfidence
67771rod-shaped
67771curved-shaped
67771positive
69480no93.336
69480positive100
123752rod-shapedpositiveno

colony morphology

  • @ref: 123752

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6115PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
33058MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
123752CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
6115positivegrowth37mesophilic
33058positivegrowth37mesophilic
57056positivegrowth37mesophilic
67771positivegrowth37mesophilic
123752positivegrowth30-41
123752nogrowth10psychrophilic
123752nogrowth25mesophilic
123752nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6115anaerobe
57056anaerobe
67771anaerobe
69480anaerobe96.824
123752anaerobe

spore formation

@refspore formationconfidence
67771no
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
123752NaClpositivegrowth0 %
123752NaClnogrowth2 %
123752NaClnogrowth4 %
123752NaClnogrowth6 %
123752NaClnogrowth8 %
123752NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335465327D-xylose-builds acid from
2335428087glycogen-builds acid from
2335415443inulin-builds acid from
2335430849L-arabinose-builds acid from
2335417716lactose-builds acid from
2335417306maltose-builds acid from
2335429864mannitol-builds acid from
2335416634raffinose-builds acid from
2335430911sorbitol-builds acid from
2335428017starch-builds acid from
2335417992sucrose-builds acid from
2335427082trehalose-builds acid from
233544853esculin-hydrolysis
233545291gelatin-hydrolysis
2335417634D-glucose+builds acid from
2335416988D-ribose+builds acid from
23354606565hippurate+hydrolysis
12375216947citrate-carbon source
1237524853esculin-hydrolysis
123752606565hippurate+hydrolysis
12375217632nitrate-reduction
12375216301nitrite-reduction
12375217632nitrate+respiration
6838016199urea+hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

  • @ref: 123752
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
12375235581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
12375215688acetoin-
12375217234glucose-

enzymes

@refvalueactivityec
23354alpha-chymotrypsin-3.4.21.1
23354alpha-fucosidase-3.2.1.51
23354alpha-galactosidase-3.2.1.22
23354arginine dihydrolase-3.5.3.6
23354beta-galactosidase-3.2.1.23
23354catalase-1.11.1.6
23354cystine arylamidase-3.4.11.3
23354cytochrome oxidase-1.9.3.1
23354esterase (C 4)-
23354lipase (C 14)-
23354pyrazinamidase-3.5.1.B15
23354trypsin-3.4.21.4
23354valine 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
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
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
123752oxidase-
123752beta-galactosidase-3.2.1.23
123752alcohol dehydrogenase-1.1.1.1
123752gelatinase-
123752catalase+1.11.1.6
123752gamma-glutamyltransferase-2.3.2.2
123752lysine decarboxylase-4.1.1.18
123752ornithine decarboxylase-4.1.1.17
123752tryptophan deaminase+
123752urease+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
123752--+-----------+-----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6115+-------+-++------+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6115urine culture, human female with pyuriaWorthing, West SussexUnited KingdomGBREurope
57056Human urine,femaleWorthingUnited KingdomGBREurope1995
67771From urine culture, human female with pyuriaWest Sussex, WorthingUnited KingdomGBREurope
123752Human, UrineCardiffUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host#Human
#Host Body Product#Fluids#Urine
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_5354.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_188;96_2596;97_3179;98_3992;99_5354&stattab=map
  • Last taxonomy: Actinotignum urinale subclade
  • 16S sequence: NR_028978
  • Sequence Identity:
  • Total samples: 2282
  • soil counts: 159
  • aquatic counts: 368
  • animal counts: 1702
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61152Risk group (German classification)
1237521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6115Actinobaculum urinalis 16S rRNA gene, strain CCUG 46093TAJ4394531488ena190146
67771Actinotignum urinale strain R9242 16S ribosomal RNA, partial sequenceNR_0289781488nuccore190146

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinobaculum urinale DSM 158051120933.3wgspatric1120933
66792Actinotignum urinale DSM 158052524614758draftimg1120933
67771Actinotignum urinale DSM 15805GCA_000420445scaffoldncbi1120933

GC content

@refGC-contentmethod
2335450.0Thermal denaturation, fluorometry
611550high performance liquid chromatography (HPLC)
6777150.0thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.31no
flagellatedno97.349no
gram-positiveyes93.017yes
anaerobicyes73.132yes
aerobicno95.015yes
halophileyes51.196no
spore-formingno97.215yes
thermophileno98.274yes
glucose-utilyes88.96no
glucose-fermentyes82.987no

External links

@ref: 6115

culture collection no.: KCTC 15231, DSM 15805, CCUG 46093, CIP 107424

straininfo link

  • @ref: 69829
  • straininfo: 23014

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807186Actinobaculum urinale sp. nov., from human urine.Hall V, Collins MD, Hutson RA, Falsen E, Inganas E, Duerden BIInt J Syst Evol Microbiol10.1099/ijs.0.02422-02003Actinomycetaceae/*classification/genetics/isolation & purification, Actinomycetales Infections/*microbiology, Bacterial Typing Techniques, Female, Genes, rRNA, Humans, Molecular Sequence Data, Phenotype, Pyuria/*microbiology, RNA, Ribosomal, 16S/genetics, Reagent Kits, Diagnostic, Sequence Analysis, DNA, Urine/*microbiologyPathogenicity
Phylogeny25406238Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species.Yassin AF, Sproer C, Pukall R, Sylvester M, Siering C, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.069294-02014Actinomycetaceae/*classification/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6115Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15805)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15805
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
23354A. F. Yassin, C. Spröer, R. Pukall, M. Sylvester, C. Siering, P. Schumann10.1099/ijs.0.069294-0Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T (=DSM 19118T), revealing that it does not represent a strain of this speciesIJSEM 65: 615-624 201525406238
33058Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4858
57056Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46093)https://www.ccug.se/strain?id=46093
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
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
69829Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID23014.1StrainInfo: A central database for resolving microbial strain identifiers
123752Curators of the CIPCollection of Institut Pasteur (CIP 107424)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107424