Name: Actinomyces johnsonii genospecies WVA 963
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 190

Type strain:

Species: Actinomyces johnsonii

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

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

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

NCBI tax ID(s): 544581 (species)

SI-ID 42430

ATCC 49338, CCUG 34287, JCM 16129

Other strains from Actinomyces johnsonii

A. johnsonii CCUG 33932

Section

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

Gram-positive
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Actinomycetales*
	Family	*Actinomycetaceae*
	Genus	*Actinomyces*
	Species	**Actinomyces johnsonii**
	Full Scientific Name (LPSN)	Actinomyces johnsonii Henssge et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	no Confidence in %95.802

Information on culture and growth conditions Culture and growth conditions

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Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #16664]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #16664]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16664]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.981

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	+	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	+	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	+		* from API rID32A
[Ref.: #68380]	proline-arylamidase	+	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	+		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #16664]	12772	-	-	+	+	-	+	+	-	-	-	+	+	-	-	+	-	-	-	+	-	+	+	-	+	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16664]	Sample type/isolated from	gingival crevice of a healthy child

[Ref.: #52033]	Sample type/isolated from	Human gingival crevice

[Ref.: #67770]	Sample type/isolated from	Gingival crevice of a healthy child

[Ref.: #67771]	Sample type/isolated from	From gingival crevice of a healthy child
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X81063 (>99% sequence identity) for Actinomyces johnsonii subclade from Microbeatlas

Aquatic Samples	417
Soil Samples	225
Animal Samples	15456
Plant Samples	74
Total Samples	16172

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

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Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16664]	Actinomyces johnsonii strain WVA 963 16S ribosomal RNA gene, partial sequence	EU667411	480	ENA	544581 tax ID
[Ref.: #67771]	Actinomyces johnsonii gene for 16S ribosomal RNA, partial sequence	AB545933	1522	ENA	544581 tax ID
[Ref.: #20218]	Actinomyces sp. 16S rRNA gene	X81063	1417	ENA	29317 tax ID	*
[Ref.: #20218]	Actinomyces johnsonii partial 16S rRNA gene, strain VPI D135D-26	HF558378	1534	ENA	544581 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Actinomyces johnsonii CCUG 34287T	GCA_008693165	contig	GenBank	544581 tax ID
[Ref.: #67771]	Actinomyces johnsonii CCUG 34287	GCA_006546835	scaffold	GenBank	544581 tax ID
[Ref.: #66792]	Actinomyces johnsonii strain CCUG 34287	544581.4	wgs	PATRIC	544581 tax ID	*

[Ref.: #16664]	GC-content	67.0 mol%
[Ref.: #67770]	GC-content	67 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Actinomyces johnsonii CCUG 34287 NCBI: GCA_006546835.1
[Ref.: #69481]	spore-forming	no	81	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Actinomyces johnsonii strain CCUG 34287 PATRIC: 544581.4
[Ref.: #69480]	gram-positive	yes	95.469	yes
[Ref.: #69480]	anaerobic	no	69.093	yes
[Ref.: #69480]	halophile	no	86.143	no
[Ref.: #69480]	spore-forming	no	92.389	no
[Ref.: #69480]	glucose-util	yes	88.176	no
[Ref.: #69480]	thermophile	no	95.622	yes
[Ref.: #69480]	aerobic	no	91.91	yes
[Ref.: #69480]	motile	no	90.346	no
[Ref.: #69480]	flagellated	no	96.084	no
[Ref.: #69480]	glucose-ferment	yes	83.513	no

Availability in culture collections External links

[Ref.: #16664]

Culture collection no.

DSM 23038, ATCC 49338, CCUG 34287, KCTC 15157, VPI D135D-26, JCM 16129

[Ref.: #69872]

SI-ID 42430

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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.	Henssge U, Do T, Radford DR, Gilbert SC, Clark D, Beighton D	Int J Syst Evol Microbiol	10.1099/ijs.0.000950-0	2009	*

References

#16664

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23038

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#52033 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 34287

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68380

Automatically annotated from API rID32A .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#69872

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID42430.1 )

* These data were automatically processed and therefore are not curated

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Actinomyces johnsonii CCUG 34287

Actinomyces johnsonii strain CCUG 34287

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