Actinomyces johnsonii (DSM 23038, ATCC 49338, CCUG 34287)

Name: Actinomyces johnsonii (DSM 23038, ATCC 49338, CCUG 34287)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 190

Type strain

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

Culture col. no. DSM 23038 ATCC 49338 CCUG 34287 KCTC 15157 genospecies WVA 963 3 more

NCBI tax ID(s) 544581

Special Collections DSMZ CCUG JCM KCTC

Links

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

Gram-positive anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 42430

DSM 23038,KCTC 15157,ATCC 49338,CCUG 34287,JCM 16129

@ref 20215

Last LPSN update 2025-12-16 09:46:48

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Actinomycetales

Family Actinomycetaceae

Genus Actinomyces

Species Actinomyces johnsonii

Full scientific name Actinomyces johnsonii Henssge et al. 2009

BacDive ID	Other strains from **Actinomyces johnsonii** (1)	Type strain
147641	A. johnsonii CCUG 33932

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	positive
125439	positive	96.5
125438		93.375
125438	positive	90.26

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16664	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: 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
16664	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16664	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16664	anaerobe
67771	anaerobe
125439	anaerobe	90.9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	+	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	+		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
16664	-	-	+	+	-	+	+	-	-	-	+	+	-	-	+	-	-	-	+	-	+	+	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Host Body-Site	#Oral cavity and airways	#Gingiva
#Host	#Human	#Child

Isolation

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

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16664	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM869316v1 assembly for Actinomyces johnsonii CCUG 34287T	contig	GCA_008693165	544581.5		544581	70.44
67771	ASM654683v1 assembly for Actinomyces johnsonii CCUG 34287	scaffold	GCA_006546835	544581.4	8053452152	544581	69.51
124043	ASM3129661v1 assembly for Actinomyces johnsonii CCUG 34287	contig	GCA_031296615	544581.8		544581	68.78

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinomyces johnsonii partial 16S rRNA gene, strain VPI D135D-26	HF558378	1534	544581
20218	Actinomyces sp. 16S rRNA gene	X81063	1417	29317
16664	Actinomyces johnsonii strain WVA 963 16S ribosomal RNA gene, partial sequence	EU667411	480	544581
67771	Actinomyces johnsonii gene for 16S ribosomal RNA, partial sequence	AB545933	1522	544581

GC content

@ref	GC-content (mol%)
16664	67.0
67770	67

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinomyces johnsonii CCUG 34287
NCBI: GCA_006546835

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	76.20	no
125439	motility	BacteriaNetⓘ	no	76.70	no
125439	gram_stain	BacteriaNetⓘ	positive	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomyces johnsonii strain CCUG 34287
PATRIC: 544581.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.26	yes
125438	anaerobic	anaerobicⓘ	no	71.68	yes
125438	spore-forming	spore-formingⓘ	no	74.82	no
125438	aerobic	aerobicⓘ	no	77.49	no
125438	thermophilic	thermophileⓘ	no	94.03	yes
125438	flagellated	motile2+ⓘ	no	93.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Evidence for recombination between a sialidase (nanH) of Actinomyces naeslundii and Actinomyces oris, previously named 'Actinomyces naeslundii genospecies 1 and 2'.	Do T, Henssge U, Gilbert SC, Clark D, Beighton D.	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01336.x	2008
	Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.	Liu L, Li M, Qin Y, Liu Y, Li M, Lian B, Guo R, Xiao Y, Yin C.	Sci Rep	10.1038/s41598-025-07357-z	2025
	Linking oral microbiota to periodontitis and hypertension unveils that Filifactor alocis aggravates hypertension via infiltration of interferon-gamma⁺ T cells.	Zhang J, Chen B-Y, Zhi M-F, Lin W-Z, Li Y-L, Ye H-L, Xu S, Zhu H, Zhou L-J, Du L-J, Meng X-Q, Liu Y, Feng Q, Duan S-Z.	mSystems	10.1128/msystems.00084-25	2025
	Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.	Bruno JS, Heidrich V, Restini FCF, Alves TMMT, Miranda-Silva W, Knebel FH, Coser EM, Inoue LT, Asprino PF, Camargo AA, Fregnani ER.	mSphere	10.1128/msphere.00257-25	2025
	Longitudinal Microbiome Changes in Supragingival Biofilm Transcriptomes Induced by Orthodontics.	Babikow E, Ghaltakhchyan N, Livingston T, Qu Y, Liu C, Hoxie A, Sulkowski T, Bocklage C, Marsh A, Phillips ST, Mitchell KB, Ribeiro AA, Jackson TH, Roach J, Wu D, Divaris K, Jacox LA.	JDR Clin Trans Res	10.1177/23800844231199393	2024
	Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.	Kirdok E, Kashuba N, Damlien H, Manninen MA, Nordqvist B, Kjellstrom A, Jakobsson M, Lindberg AM, Stora J, Persson P, Andersson B, Aravena A, Gotherstrom A.	Sci Rep	10.1038/s41598-023-48762-6	2024
	Microbiomes Detected by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing among HIV-Infected and Uninfected Patients with Pulmonary Infection.	Tan Y, Chen Z, Zeng Z, Wu S, Liu J, Zou S, Wang M, Liang K.	Microbiol Spectr	10.1128/spectrum.00005-23	2023
	Clinical identification and microbiota analysis of Chlamydia psittaci- and Chlamydia abortus- pneumonia by metagenomic next-generation sequencing.	Xie G, Hu Q, Cao X, Wu W, Dai P, Guo W, Wang O, Wei L, Ren R, Li Y.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1157540	2023
	The Main Bacterial Communities Identified in the Sites Affected by Periimplantitis: A Systematic Review.	Iusan SAL, Lucaciu OP, Petrescu NB, Mirica IC, Toc DA, Albu S, Costache C.	Microorganisms	10.3390/microorganisms10061232	2022
	Activity of five antimicrobial peptides against periodontal as well as non-periodontal pathogenic strains.	Enigk K, Jentsch H, Rodloff AC, Eschrich K, Stingu CS.	J Oral Microbiol	10.1080/20002297.2020.1829405	2020
Genetics	Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.	Zeybel M, Arif M, Li X, Altay O, Yang H, Shi M, Akyildiz M, Saglam B, Gonenli MG, Yigit B, Ulukan B, Ural D, Shoaie S, Turkez H, Nielsen J, Zhang C, Uhlen M, Boren J, Mardinoglu A.	Adv Sci (Weinh)	10.1002/advs.202104373	2022
	Human microbiome in post-acute COVID-19 syndrome (PACS).	Fallah A, Sedighian H, Kachuei R, Fooladi AAI.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100324	2025
	Omics community detection using multi-resolution clustering.	Rahnavard A, Chatterjee S, Sayoldin B, Crandall KA, Tekola-Ayele F, Mallick H.	Bioinformatics	10.1093/bioinformatics/btab317	2021
	Oral Microbiota in Children with Cleft Lip and Palate: A Systematic Review.	Switala J, Sycinska-Dziarnowska M, Spagnuolo G, Wozniak K, Mankowska K, Szyszka-Sommerfeld L.	J Clin Med	10.3390/jcm12185867	2023
	Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing.	Mussano F, Ferrocino I, Gavrilova N, Genova T, Dell'Acqua A, Cocolin L, Carossa S.	BMC Oral Health	10.1186/s12903-018-0520-8	2018
Genetics	Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders.	Manghi P, Filosi M, Zolfo M, Casten LG, Garcia-Valiente A, Mattevi S, Heidrich V, Golzato D, Perini S, Thomas AM, Montalbano S, Cancellieri S, Waldron L, Hall JB, Xu S, Volfovsky N, Green Snyder L, Feliciano P, Asnicar F, Valles-Colomer M, Michaelson JJ, Segata N, Domenici E.	Nat Commun	10.1038/s41467-024-53934-7	2024
	Functional dysbiosis within dental plaque microbiota in cleft lip and palate patients.	Funahashi K, Shiba T, Watanabe T, Muramoto K, Takeuchi Y, Ogawa T, Izumi Y, Sekizaki T, Nakagawa I, Moriyama K.	Prog Orthod	10.1186/s40510-019-0265-1	2019
	Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents.	Pang L, Wang Y, Ye Y, Zhou Y, Zhi Q, Lin H.	Front Cell Infect Microbiol	10.3389/fcimb.2021.740981	2021
	The Impact of Long-Term Macrolide Exposure on the Gut Microbiome and Its Implications for Metabolic Control.	Choo JM, Martin AM, Taylor SL, Sun E, Mobegi FM, Kanno T, Richard A, Burr LD, Lingman S, Martin M, Keating DJ, Mason AJ, Rogers GB.	Microbiol Spectr	10.1128/spectrum.00831-23	2023
	Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus.	Li Y, Qian F, Cheng X, Wang D, Wang Y, Pan Y, Chen L, Wang W, Tian Y.	Microbiol Spectr	10.1128/spectrum.03796-22	2023
	Molecular subgroup of periodontitis revealed by integrated analysis of the microbiome and metabolome in a cross-sectional observational study.	Na HS, Kim S, Kim S, Yu Y, Kim SY, Kim HJ, Lee JY, Lee JH, Chung J.	J Oral Microbiol	10.1080/20002297.2021.1902707	2021
Genetics	Investigating the demographic history of Japan using ancient oral microbiota.	Eisenhofer R, Kanzawa-Kiriyama H, Shinoda KI, Weyrich LS.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2019.0578	2020
	Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection.	Xie G, Zhao B, Wang X, Bao L, Xu Y, Ren X, Ji J, He T, Zhao H.	Infect Dis Ther	10.1007/s40121-021-00476-w	2021
	MALDI-TOF MS and 16S RNA Identification of Culturable Gastric Microbiota: Variability Associated with the Presence of Helicobacter pylori.	Troncoso C, Pavez M, Cerda A, Oporto M, Villarroel D, Hofmann E, Rios E, Sierralta A, Copelli L, Barrientos L.	Microorganisms	10.3390/microorganisms8111763	2020
Pathogenicity	Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation.	Plachokova AS, Andreu-Sanchez S, Noz MP, Fu J, Riksen NP.	Int J Mol Sci	10.3390/ijms22115876	2021
Enzymology	Is the Oral Microbiome Associated with Blood Pressure in Older Women?	Gordon JH, LaMonte MJ, Genco RJ, Zhao J, Li L, Hovey KM, Tsompana M, Buck MJ, Andrews CA, Mcskimming DI, Zheng W, Sun Y, Wactawski-Wende J.	High Blood Press Cardiovasc Prev	10.1007/s40292-019-00322-8	2019
	Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS.	Stingu CS, Borgmann T, Rodloff AC, Vielkind P, Jentsch H, Schellenberger W, Eschrich K.	J Oral Microbiol	10.3402/jom.v7.26110	2015
Genetics	Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children.	Al-Hebshi NN, Baraniya D, Chen T, Hill J, Puri S, Puri S, Tellez M, Hasan NA, Colwell RR, Ismail A.	J Oral Microbiol	10.1080/20002297.2018.1557986	2019
	Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.	Kang Y, Sun B, Chen Y, Lou Y, Zheng M, Li Z.	mSphere	10.1128/msphere.00162-21	2021
	Intraindividual variation in core microbiota in peri-implantitis and periodontitis.	Maruyama N, Maruyama F, Takeuchi Y, Aikawa C, Izumi Y, Nakagawa I.	Sci Rep	10.1038/srep06602	2014
Enzymology	Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory.	Schulthess B, Bloemberg GV, Zbinden R, Bottger EC, Hombach M.	J Clin Microbiol	10.1128/jcm.02399-13	2014
Phylogeny	Application of MLST and pilus gene sequence comparisons to investigate the population structures of Actinomyces naeslundii and Actinomyces oris.	Henssge U, Do T, Gilbert SC, Cox S, Clark D, Wickstrom C, Ligtenberg AJ, Radford DR, Beighton D.	PLoS One	10.1371/journal.pone.0021430	2011
Genetics	Genome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity.	Tian X, Teo WFA, Wee WY, Yang Y, Ahmed H, Jakubovics NS, Choo SW, Tan GYA.	BMC Genomics	10.1186/s12864-023-09831-2	2023
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
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Actinomyces johnsonii (DSM 23038, ATCC 49338, CCUG 34287)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_008693165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media