Name: Streptomyces californicus DSM 40058
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 15492

Type strain:

Species: Streptomyces californicus

Culture col. no.: DSM 40058, ATCC 11896, ATCC 19734, ATCC 3312, CBS 125.20, CBS 354.53, CBS 473.68, ETH 10212, IFO 12750, IFO 3386, IMET 40261, IMRU 3312, IMRU 3313, ISP 5058, JCM 4015, JCM 4567, KCC S-0015, KCC S-0567, NBRC 12750, NBRC 3386, NRRL B-1221, NRRL B-2098, RIA 1015, RIA 63, BCRC 13688, CCM 3016, CGMCC 4.0570, HUT 6049, IFM 1070, KCTC 19939, KCTC 19957, LMG 19309, NBIMCC 1036, NCAIM B.01475, NRRL ISP-5058, VKM Ac-575, VTT E-991421

Strain history: KCC S-0015 <-- T. Yamaguchi (IAM 0003) <-- ATCC 3312 <-- IMRU 3312.

NCBI tax ID(s): 67351 (species)

SI-ID 38299

LMG 19309, ATCC 19734, ATCC 3312, CCRC 13688, DSM 40058, HUT 6049, IFO 12750, IFO 3386, IMET 40261, JCM 4015, JCM 4567, NRRL B-1221, NRRL B-2098, VKM Ac-575, ATCC 11896, NRRL 1221, CCM 3016, CBS 473.68, CBS 125.20, CBS 354.53, AS 4.0570, NBRC 12750, NBRC 3386, NCAIM B.01475, BCRC 13688, ICMP 232, KCTC 19939, KCTC 19957, NBIMCC 1036, ATCC 201410, CGMCC 4.0570, VTT E-991421

Section

Streptomyces californicus DSM 40058 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production
spore-forming
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	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces californicus**
	Full Scientific Name (LPSN)	Streptomyces californicus (Waksman and Curtis 1916) Waksman and Henrici 1948 (Approved Lists 1980)

	Synonym	"Actinomyces* californicus"*
	Synonym	Streptomyces floridae

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %92.84

[Ref.: #19804]	Multicellular complex forming ability	yes
[Ref.: #19804]	Multicellular complex name	Aerial Mycelium
[Ref.: #19804]	Multicellular complex color	Grey
[Ref.: #19804]	Medium Name (multicellularity)	ISP 2

[Ref.: #19804]	Multicellular complex forming ability	yes
[Ref.: #19804]	Multicellular complex name	Aerial Mycelium
[Ref.: #19804]	Multicellular complex color	Grey
[Ref.: #19804]	Medium Name (multicellularity)	ISP 3

[Ref.: #19804]	Multicellular complex forming ability	yes
[Ref.: #19804]	Multicellular complex name	Aerial Mycelium
[Ref.: #19804]	Multicellular complex color	Grey
[Ref.: #19804]	Medium Name (multicellularity)	ISP 4

[Ref.: #19804]	Multicellular complex forming ability	yes
[Ref.: #19804]	Multicellular complex name	Aerial Mycelium
[Ref.: #19804]	Multicellular complex color	Grey
[Ref.: #19804]	Medium Name (multicellularity)	ISP 5

[Ref.: #19804]	Multicellular complex forming ability	yes
[Ref.: #19804]	Multicellular complex name	Aerial Mycelium
[Ref.: #19804]	Multicellular complex color	Grey
[Ref.: #19804]	Medium Name (multicellularity)	ISP 6

[Ref.: #19804]	Multicellular complex forming ability	yes
[Ref.: #19804]	Multicellular complex name	Aerial Mycelium
[Ref.: #19804]	Multicellular complex color	Grey
[Ref.: #19804]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9241]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #9241]

Culture medium growth

[Ref.: #9241]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9241]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #9241]	growth	28 °C
[Ref.: #19804]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #9241]	Temperature range	mesophilic
[Ref.: #19804]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #19804]	Spore description	Formation of spore chains: rectiflixibilis, spore surface: smooth
[Ref.: #19804]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #9241]	Name of produced compound	viomycin
[Ref.: #20216]	Name of produced compound	Griseorhodin
[Ref.: #20216]	Name of produced compound	Sideromycin

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #19804]	arabinose ChEBI	+
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19804]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #19804]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19804]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #19804]	mannitol ChEBI	+
[Ref.: #19804]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #19804]	raffinose ChEBI	-
[Ref.: #19804]	rhamnose ChEBI	-
[Ref.: #19804]	sucrose ChEBI	-
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19804]	xylose ChEBI	+
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	+	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #19804]	517	+	+	+	-	-	-	+	+	-	+	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #9241]	Sample type/isolated from	soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB184755 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	286
Soil Samples	2441
Animal Samples	1009
Plant Samples	294
Total Samples	4030

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

[Ref.: #9241]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19804]	Biosafety level	1	Risk group (German classification)

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Streptomyces californicus strain IFO 12750 16S ribosomal RNA gene, partial sequence	AY999837	1419	ENA	67281 tax ID	*
[Ref.: #20218]	Streptomyces californicus strain DSM 40058 16S ribosomal RNA gene, partial sequence	AY999845	1420	ENA	67281 tax ID	*
[Ref.: #20218]	Streptomyces californicus gene for 16S rRNA, partial sequence, strain: NBRC 12750	AB184116	1480	ENA	67281 tax ID	*
[Ref.: #20218]	Streptomyces californicus strain DSM 40058 16S ribosomal RNA gene, partial sequence	GU383162	779	ENA	67281 tax ID	*
[Ref.: #20218]	Streptomyces californicus gene for 16S rRNA, partial sequence, strain: NBRC 3386	AB184755	1477	ENA	67281 tax ID	*
[Ref.: #20218]	Streptomyces californicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4567	D44236	120	ENA	67281 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Streptomyces californicus NRRL B-1221	GCA_000715715	scaffold	GenBank	67351 tax ID
[Ref.: #67770]	Streptomyces californicus NRRL B-2098	GCA_000717645	contig	GenBank	67351 tax ID
[Ref.: #67770]	Streptomyces californicus NRRL ISP-5058	GCA_000716065	scaffold	GenBank	67351 tax ID
[Ref.: #66792]	Streptomyces californicus strain FDAARGOS_1209	67351.14	complete	PATRIC	67351 tax ID	*

[Ref.: #67770]	GC-content	70 mol%	fluorimetric
[Ref.: #67770]	GC-content	72.7 mol%	genome sequence analysis

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: Streptomyces californicus strain FDAARGOS_1209 strain Not applicable PATRIC: 67351.14
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces californicus strain FDAARGOS_1209 strain Not applicable PATRIC: 67351.14
[Ref.: #69480]	gram-positive	yes	92.835	no
[Ref.: #69480]	anaerobic	no	99.046	no
[Ref.: #69480]	halophile	no	93.853	no
[Ref.: #69480]	spore-forming	yes	94.516	yes
[Ref.: #69480]	glucose-util	yes	88.292	no
[Ref.: #69480]	thermophile	no	98.67	no
[Ref.: #69480]	flagellated	no	98.049	no
[Ref.: #69480]	motile	no	94.27	no
[Ref.: #69480]	aerobic	yes	93.559	no
[Ref.: #69480]	glucose-ferment	no	85.047	yes

Availability in culture collections External links

[Ref.: #9241]

Culture collection no.

DSM 40058, ATCC 11896, ATCC 19734, ATCC 3312, CBS 125.20, CBS 354.53, CBS 473.68, ETH 10212, IFO 12750, IFO 3386, IMET 40261, IMRU 3312, IMRU 3313, ISP 5058, JCM 4015, JCM 4567, KCC S-0015, KCC S-0567, NBRC 12750, NBRC 3386, NRRL B-1221, NRRL B-2098, RIA 1015, RIA 63, BCRC 13688, CCM 3016, CGMCC 4.0570, HUT 6049, IFM 1070, KCTC 19939, KCTC 19957, LMG 19309, NBIMCC 1036, NCAIM B.01475, NRRL ISP-5058, VKM Ac-575, VTT E-991421

[Ref.: #84579]

SI-ID 38299

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces sundarbansensis sp. nov., an actinomycete that produces 2-allyloxyphenol.	Arumugam M, Mitra A, Pramanik A, Saha M, Gachhui R, Mukherjee J	Int J Syst Evol Microbiol	10.1099/ijs.0.028258-0	2010	*

References

#9241

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40058

#19804

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#20216

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) .

#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 )

#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;

#68368

Automatically annotated from API 20E .

#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 )

#84579

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-ID38299.1 )

* These data were automatically processed and therefore are not curated

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Streptomyces californicus strain FDAARGOS_1209 strain Not applicable

Streptomyces californicus strain FDAARGOS_1209 strain Not applicable

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