Name: Streptomyces xanthochromogenes DSM 40111
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16128

Type strain:

Species: Streptomyces xanthochromogenes

Culture col. no.: DSM 40111, ATCC 19818, CBS 571.68, DSM 2015, IFO 12828, ISP 5111, JCM 4215, JCM 4612, KCC S-0215, NBRC 12828, NIHJ 196, RIA 1098, BCRC 11876, CGMCC 4.1435, KCTC 19954, NRRL B-5410, VKM Ac-1071

Strain history: KCC S-0215 <-- Y. Okami (NIHJ 196) <-- Meiji Seika Kaisha, Ltd.; 689.

NCBI tax ID(s): 67384 (species)

SI-ID 13364

LMG 19366, ATCC 19818, CCRC 11876, DSM 2015, DSM 40111, IFO 12828, JCM 4215, JCM 4612, NRRL B-5410, VKM Ac-1071, AS 4.1435, NBRC 12828, BCRC 11876, KCTC 19954, CGMCC 4.1435, CBS 571.68

Section

Streptomyces xanthochromogenes DSM 40111 is a spore-forming, mesophilic bacterium that was isolated from soil.

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 xanthochromogenes**
	Full Scientific Name (LPSN)	Streptomyces xanthochromogenes Arishima et al. 1956 (Approved Lists 1980)

Synonym

Streptomyces michiganensis

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %93.131

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9322]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #9322]

Culture medium growth

[Ref.: #9322]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9322]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #9322]	growth	28 °C
[Ref.: #18537]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #9322]	Temperature range	mesophilic
[Ref.: #18537]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #9322]	Name of produced compound	xanthicin (anti-fungal)
[Ref.: #67770]	Name of produced compound	Xanthicin

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #18537]		NaCl		maximum	5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #18537]	arabinose ChEBI	-
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #18537]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #18537]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #18537]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #18537]	mannitol ChEBI	-
[Ref.: #18537]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #18537]	raffinose ChEBI	-
[Ref.: #18537]	rhamnose ChEBI	-
[Ref.: #18537]	sucrose ChEBI	-
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #18537]	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.: #18537]	97	-	-	-	-	-	-	-	-	-	+	-	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.	not determinedn.d.

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

[Ref.: #9322]	Sample type/isolated from	soil
[Ref.: #9322]	Country	Japan
[Ref.: #9322]	Country ISO 3 Code	JPN
[Ref.: #9322]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kawaji, Tochigi Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #18537]	Biosafety level	1	German classification
[Ref.: #9322]	Biosafety level	1	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.: #20218]	Streptomyces xanthochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4612	D44264	120	ENA	67384 tax ID	*
[Ref.: #20218]	Streptomyces xanthochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 12828	AB184176	1469	ENA	67384 tax ID	*
[Ref.: #20218]	Streptomyces xanthochromogenes strain NRRL B-5410T 16S ribosomal RNA gene, partial sequence	DQ442559	1473	ENA	67384 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Streptomyces xanthochromogenes JCM 4612	GCA_014650455	scaffold	GenBank	67384 tax ID	*
[Ref.: #66792]	Streptomyces xanthochromogenes strain JCM 4612	67384.3	wgs	PATRIC	67384 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: Streptomyces xanthochromogenes JCM 4612 NCBI: GCA_014650455.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces xanthochromogenes JCM 4612 NCBI: GCA_014650455.1
[Ref.: #69480]	flagellated	no	98.1	no
[Ref.: #69480]	gram-positive	yes	87.991	no
[Ref.: #69480]	anaerobic	no	98.935	no
[Ref.: #69480]	aerobic	yes	90.051	no
[Ref.: #69480]	halophile	no	93.351	no
[Ref.: #69480]	spore-forming	yes	95.589	no
[Ref.: #69480]	glucose-util	yes	88.168	no
[Ref.: #69480]	thermophile	no	99.143	yes
[Ref.: #69480]	motile	no	93.428	no
[Ref.: #69480]	glucose-ferment	no	88.843	no

Availability in culture collections External links

[Ref.: #9322]

Culture collection no.

DSM 40111, ATCC 19818, CBS 571.68, DSM 2015, IFO 12828, ISP 5111, JCM 4215, JCM 4612, KCC S-0215, NBRC 12828, NIHJ 196, RIA 1098, BCRC 11876, CGMCC 4.1435, KCTC 19954, NRRL B-5410, VKM Ac-1071

[Ref.: #85193]

SI-ID 13364

Literature:

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Strain Improvement of Streptomyces xanthochromogenes RIA 1098 for Enhanced Pravastatin Production at High Compactin Concentrations.	Dzhavakhiya VV, Voinova TM, Glagoleva EV, Petukhov DV, Ovchinnikov AI, Kartashov MI, Kuznetsov BB, Skryabin KG	Indian J Microbiol	10.1007/s12088-015-0537-5	2015	*
Phylogeny	Streptomyces genisteinicus sp. nov., a novel genistein-producing actinomycete isolated from a Chinese medicinal plant and proposal of Streptomyces michiganensis Corbaz et al. 1957 as a later heterotypic synonym of Streptomyces xanthochromogenes Arishima et al. 1956.	Hu S, Li K, Wang Y, Guo Y, Zhou M, Tang X, Gao J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004954	2021	*
Phylogeny	Streptomyces hundungensis sp. nov., a novel actinomycete with antifungal activity and plant growth promoting traits.	Nimaichand S, Tamrihao K, Yang LL, Zhu WY, Zhang YG, Li L, Tang SK, Ningthoujam DS, Li WJ	J Antibiot (Tokyo)	10.1038/ja.2012.119	2013	*

References

#9322

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40111

#18537

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 )

#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 .

#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 )

#85193

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-ID13364.1 )

* These data were automatically processed and therefore are not curated

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