Strain identifier

BacDive ID: 190

Type strain: Yes

Species: Actinomyces johnsonii

Strain Designation: genospecies WVA 963, genospecies(serotype) WVA 963

Strain history: <- DSM <- CCUG <- P Pienta, ATCC <- LH Moore, VPI D135D-26 <- WEC Moore

NCBI tax ID(s): 544581 (species)

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General

@ref: 16664

BacDive-ID: 190

DSM-Number: 23038

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Actinomyces johnsonii genospecies WVA 963 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from gingival crevice of a healthy child.

NCBI tax id

  • NCBI tax id: 544581
  • Matching level: species

strain history

@refhistory
16664<- CCUG <- P. Pienta, ATCC <- L. H. Moore; VPI D135D-26 <- W.E.C. Moore
67770CCUG 34287 <-- ATCC 49338 <-- L. H. Moore VPI D135D-26 <-- W. E. C. Moore.
67771<- DSM <- CCUG <- P Pienta, ATCC <- LH Moore, VPI D135D-26 <- WEC Moore

doi: 10.13145/bacdive190.20230509.8.1

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 johnsonii
  • full scientific name: Actinomyces johnsonii Henssge et al. 2009

@ref: 16664

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces johnsonii

full scientific name: Actinomyces johnsonii Henssge et al. 2009

strain designation: genospecies WVA 963, genospecies(serotype) WVA 963

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
67771positive
69480no95.802
69480positive100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16664PYG 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
16664COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
16664positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16664anaerobe
67771anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.981

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16664--++-++---++--+---+-++-+-----

Isolation, sampling and environmental information

isolation

@refsample type
16664gingival crevice of a healthy child
52033Human gingival crevice
67770Gingival crevice of a healthy child
67771From gingival crevice of a healthy child

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Gingiva
#Host#Human#Child

taxonmaps

  • @ref: 69479
  • File name: preview.99_569.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_361;97_405;98_464;99_569&stattab=map
  • Last taxonomy: Actinomyces johnsonii subclade
  • 16S sequence: X81063
  • Sequence Identity:
  • Total samples: 16172
  • soil counts: 225
  • aquatic counts: 417
  • animal counts: 15456
  • plant counts: 74

Safety information

risk assessment

  • @ref: 16664
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomyces johnsonii partial 16S rRNA gene, strain VPI D135D-26HF5583781534ena544581
20218Actinomyces sp. 16S rRNA geneX810631417ena29317
16664Actinomyces johnsonii strain WVA 963 16S ribosomal RNA gene, partial sequenceEU667411480ena544581
67771Actinomyces johnsonii gene for 16S ribosomal RNA, partial sequenceAB5459331522ena544581

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces johnsonii strain CCUG 34287544581.4wgspatric544581
67770Actinomyces johnsonii CCUG 34287TGCA_008693165contigncbi544581
67771Actinomyces johnsonii CCUG 34287GCA_006546835scaffoldncbi544581

GC content

@refGC-content
1666467.0
6777067

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno81no
gram-positiveyes95.469yes
anaerobicno69.093yes
halophileno86.143no
spore-formingno92.389no
glucose-utilyes88.176no
thermophileno95.622yes
aerobicno91.91yes
motileno90.346no
flagellatedno96.084no
glucose-fermentyes83.513no

External links

@ref: 16664

culture collection no.: DSM 23038, ATCC 49338, CCUG 34287, KCTC 15157, VPI D135D-26, JCM 16129

straininfo link

  • @ref: 69872
  • straininfo: 42430

literature

  • topic: Phylogeny
  • Pubmed-ID: 19244431
  • title: Emended description of Actinomyces naeslundii and descriptions of Actinomyces oris sp. nov. and Actinomyces johnsonii sp. nov., previously identified as Actinomyces naeslundii genospecies 1, 2 and WVA 963.
  • authors: Henssge U, Do T, Radford DR, Gilbert SC, Clark D, Beighton D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000950-0
  • year: 2009
  • mesh: Actinomyces/*classification/genetics/isolation & purification/physiology, Actinomycosis/*microbiology, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Blood/microbiology, Cerebrospinal Fluid/microbiology, DNA, Bacterial/analysis, Humans, Molecular Sequence Data, Mouth/*microbiology, Phenotype, Plague/microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16664Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23038)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23038
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
52033Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34287)https://www.ccug.se/strain?id=34287
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
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)
69872Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42430.1StrainInfo: A central database for resolving microbial strain identifiers