Strain identifier

BacDive ID: 168

Type strain: Yes

Species: Schaalia radingae

Strain Designation: APL1

Strain history: CIP <- 1997, DSM <- J. Würst: strain APL1

NCBI tax ID(s): 131110 (species)

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General

@ref: 3502

BacDive-ID: 168

DSM-Number: 9169

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

description: Schaalia radingae APL1 is an anaerobe, mesophilic bacterium that was isolated from perianal abscess.

NCBI tax id

  • NCBI tax id: 131110
  • Matching level: species

strain history

@refhistory
3502<- J. Wüst, APL1
122117CIP <- 1997, DSM <- J. Würst: strain APL1

doi: 10.13145/bacdive168.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Schaalia
  • species: Schaalia radingae
  • full scientific name: Schaalia radingae (Wüst et al. 1995) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces radingae

@ref: 3502

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Schaalia

species: Schaalia radingae

full scientific name: Schaalia radingae (Wüst et al. 1995) Nouioui et al. 2018

strain designation: APL1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.179
69480100positive
122117nopositiverod-shaped

colony morphology

  • @ref: 122117

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3502COLUMBIA 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
39275MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122117CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
3502positivegrowth37mesophilic
39275positivegrowth37mesophilic
122117positivegrowth25-41
122117nogrowth10psychrophilic
122117nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe98.15
122117facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
122117NaClnogrowth0 %
122117NaClnogrowth2 %
122117NaClnogrowth4 %
122117NaClnogrowth6 %
122117NaClnogrowth8 %
122117NaClnogrowth10 %

murein

  • @ref: 3502
  • murein short key: A11.55
  • type: A5alpha L-Lys(L-Orn)-L-Lys-D-Glu

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
122117esculin-hydrolysis4853
122117hippurate-hydrolysis606565
122117nitrate-reduction17632
122117nitrite-reduction16301
122117nitrate+respiration17632
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose+fermentation16988
68379D-xylose+fermentation65327
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose-fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose-fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

@refChebi-IDmetaboliteproduction
12211735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
12211715688acetoin-
12211717234glucose-

enzymes

@refvalueactivityec
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
68380glutamyl-glutamate arylamidase-
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
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
122117oxidase-
122117beta-galactosidase+3.2.1.23
122117alcohol dehydrogenase+1.1.1.1
122117gelatinase-
122117amylase-
122117DNase-
122117caseinase-3.4.21.50
122117catalase-1.11.1.6
122117tween esterase-
122117gamma-glutamyltransferase-2.3.2.2
122117lecithinase-
122117lipase-
122117lysine decarboxylase+4.1.1.18
122117ornithine decarboxylase-4.1.1.17
122117phenylalanine ammonia-lyase-4.3.1.24
122117tryptophan deaminase-
122117urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    65612C14:02.414
    65612C16:027.816
    65612C18:018.918
    65612C16:1 ω7c3.215.819
    65612C18:1 ω9c17.417.769
    65612C18:2 ω6,9c/C18:0 ANTE30.417.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
65612-+---++++---+++-+-+--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122117-+++-++---++++-+++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122117+-++++---++++---+---+---++++-++---+----++--++-+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
3502--++-++------+---++-++-++/-+/-+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3502perianal abscessSwitzerlandCHEEurope
122117Perianal abscess

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Gastrointestinal tract
#Host Body-Site#Other#Abscess

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
35022Risk group (German classification)
1221172Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3502
  • description: Actinomyces radingae 16S rRNA gene, starin APL1
  • accession: X78719
  • length: 1429
  • database: ena
  • NCBI tax ID: 131110

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Schaalia radingae DSM 9169GCA_900106055chromosomencbi131110
66792Actinomyces radingae strain DSM 9169131110.4completepatric131110
66792Schaalia radingae DSM 91692630968294draftimg131110

GC content

  • @ref: 3502
  • GC-content: 60
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno93.42no
gram-positiveyes94.21no
anaerobicyes53.914no
halophileno87.367no
spore-formingno94.104no
glucose-utilyes84.658no
aerobicno93.173no
flagellatedno97.061no
thermophileno89.343no
glucose-fermentyes84.839yes

External links

@ref: 3502

culture collection no.: DSM 9169, ATCC 51856, CCUG 32394, CIP 105358

straininfo link

  • @ref: 69850
  • straininfo: 7936

literature

  • topic: Phylogeny
  • Pubmed-ID: 7534464
  • title: Assignment of Actinomyces pyogenes-like (CDC coryneform group E) bacteria to the genus Actinomyces as Actinomyces radingae sp. nov. and Actinomyces turicensis sp. nov.
  • authors: Wust J, Stubbs S, Weiss N, Funke G, Collins MD
  • journal: Lett Appl Microbiol
  • DOI: 10.1111/j.1472-765x.1995.tb01290.x
  • year: 1995
  • mesh: Actinomyces/chemistry/classification/*genetics, Amino Acid Sequence, Fatty Acids/analysis, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
3502Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9169)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9169
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
39275Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17369
65612Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32394)https://www.ccug.se/strain?id=32394
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
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
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
69850Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7936.1StrainInfo: A central database for resolving microbial strain identifiers
122117Curators of the CIPCollection of Institut Pasteur (CIP 105358)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105358