Name: Actinomyces timonensis 7400942
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 193

Type strain:

Species: Actinomyces timonensis

Strain Designation: 7400942

Culture col. no.: KCTC 15137, DSM 23838, CCUG 55928, CSUR P35

Strain history: <- CCUG <- V Roux,Timone Hospital, Marseille, France

NCBI tax ID(s): 521393 (strain), 1288391 (species)

SI-ID 398734

DSM 23838, CCUG 55928

Other strains from Actinomyces timonensis

A. timonensis CCUG 44994
A. timonensis CCUG 44999
A. timonensis CCUG 45116
A. timonensis CCUG 45117
A. timonensis CCUG 45118

Section

Actinomyces timonensis 7400942 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human aspirate.

Gram-positive
rod-shaped
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 timonensis**
	Full Scientific Name (LPSN)	Actinomyces timonensis Renvoise et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29427]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29427]	Cell length	1-3.2 µm

[Ref.: #29427]	Cell width	0.3-0.5 µm

[Ref.: #29427]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #29427]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.674

[Ref.: #29427]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17395]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #17395]

Culture medium growth

[Ref.: #17395]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17395]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17395]	growth	37 °C
[Ref.: #29427]	growth	25-37 °C
[Ref.: #29427]	optimum	37 °C
[Ref.: #60798]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #17395]	Temperature range	mesophilic
[Ref.: #29427]	Temperature range	mesophilic
[Ref.: #60798]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29427]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #17395]	Oxygen tolerance	anaerobe
[Ref.: #29427]	Oxygen tolerance	anaerobe
[Ref.: #60798]	Oxygen tolerance	microaerophile
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #29427]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29427]		NaCl		growth	0-1	%
[Ref.: #29427]		NaCl		optimum	0-1	%

	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.: #29427]	fructose ChEBI	+	carbon source
[Ref.: #29427]	galactose ChEBI	+	carbon source
[Ref.: #29427]	glucose ChEBI	+	carbon source
[Ref.: #29427]	glycerol ChEBI	+	carbon source
[Ref.: #29427]	glycogen ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #29427]	maltose ChEBI	+	carbon source
[Ref.: #29427]	mannitol ChEBI	+	carbon source
[Ref.: #29427]	mannose ChEBI	+	carbon source
[Ref.: #29427]	melibiose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #29427]	raffinose ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #29427]	ribose ChEBI	+	carbon source
[Ref.: #29427]	salicin ChEBI	+	carbon source
[Ref.: #29427]	sucrose ChEBI	+	carbon source
[Ref.: #29427]	trehalose ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	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-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.: #17395]	12777	-	-	+	+	+/-	+	+	-	-	-	+	+	-	-	-	-	-	-	+	-	+	+	-	+	+	-	-	-	-

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

[Ref.: #17395]	Sample type/isolated from	human aspirate
[Ref.: #17395]	Geographic location (country and/or sea, region)	Marseille, Timone hospital
[Ref.: #17395]	Country	France
[Ref.: #17395]	Country ISO 3 Code	FRA
[Ref.: #17395]	Continent	Europe

[Ref.: #60798]	Sample type/isolated from	Human aspirate,13-yr-old girl
[Ref.: #60798]	Sampling date	2007-02-01
[Ref.: #60798]	Geographic location (country and/or sea, region)	Marseille,Timone hospital
[Ref.: #60798]	Country	France
[Ref.: #60798]	Country ISO 3 Code	FRA
[Ref.: #60798]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From human clinical osteo-articular sample(human aspirate), 13-yr-old girl
[Ref.: #67771]	Geographic location (country and/or sea, region)	Timone hospital, Marseille
[Ref.: #67771]	Country	France
[Ref.: #67771]	Country ISO 3 Code	FRA
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Fluids	#Aspirate

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU484334 (>99% sequence identity) for Actinomyces timonensis subclade from Microbeatlas

Aquatic Samples	60
Soil Samples	40
Animal Samples	2878
Plant Samples	22
Total Samples	3000

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

[Ref.: #17395]

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.: #17395]	Actinomyces timonensis DSM 23838 16S ribosomal RNA gene, partial sequence	EU484334	1464	ENA	521393 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Actinomyces timonensis DSM 23838 7400942	GCA_000295095	scaffold	GenBank	521393 tax ID
[Ref.: #66792]	Actinomyces timonensis DSM 23838 strain 7400942	521393.3	wgs	PATRIC	521393 tax ID	*
[Ref.: #66792]	Actinomyces timonensis 7400942, CCUG 55928	2548877015	draft	JGI IMG/M	521393 tax ID	*

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 timonensis DSM 23838 7400942 NCBI: GCA_000295095.1
[Ref.: #69481]	spore-forming	no	70	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Actinomyces timonensis DSM 23838 strain 7400942 PATRIC: 521393.3
[Ref.: #69480]	gram-positive	yes	96.038	no
[Ref.: #69480]	anaerobic	no	90.751	no
[Ref.: #69480]	halophile	no	89.719	yes
[Ref.: #69480]	spore-forming	no	92.897	yes
[Ref.: #69480]	glucose-util	yes	87.177	yes
[Ref.: #69480]	aerobic	no	93.632	yes
[Ref.: #69480]	thermophile	no	94.878	yes
[Ref.: #69480]	motile	no	92.677	yes
[Ref.: #69480]	flagellated	no	97.365	yes
[Ref.: #69480]	glucose-ferment	yes	78.628	no

Availability in culture collections External links

[Ref.: #17395]

Culture collection no.

KCTC 15137, DSM 23838, CCUG 55928, CSUR P35

[Ref.: #69876]

SI-ID 398734

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinomyces lilanjuaniae sp. nov., isolated from the faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau.	Li J, Lu S, Yang J, Pu J, Lai XH, Jin D, Tian Z, Dong K, Zhang S, Lei W, Zhu W, Zhang G, Ren Z, Wu X, Huang Y, Wang S, Meng X, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003649	2019	*
Genetics	Draft genome sequences of Actinomyces timonensis strain 7400942T and its prophage.	Gorlas A, Gimenez G, Raoult D, Roux V	J Bacteriol	10.1128/JB.01730-12	2012	*
Phylogeny	Actinomyces timonensis sp. nov., isolated from a human clinical osteo-articular sample.	Renvoise A, Raoult D, Roux V	Int J Syst Evol Microbiol	10.1099/ijs.0.012914-0	2009	*

References

#17395

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23838

#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 )

#29427

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25833 (see below)

#60798 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55928

#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) .

#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 )

#69876

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-ID398734.1 )

#25833

IJSEM 1516 2010 ( DOI 10.1099/ijs.0.012914-0 , PubMed 19684313 )

* These data were automatically processed and therefore are not curated

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Actinomyces timonensis DSM 23838 7400942

Actinomyces timonensis DSM 23838 strain 7400942

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