Streptomyces xanthochromogenes (DSM 40111, ATCC 19818, CBS 571.68)

Name: Streptomyces xanthochromogenes (DSM 40111, ATCC 19818, CBS 571.68)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16128

Type strain

Culture col. no. DSM 40111 ATCC 19818 CBS 571.68 DSM 2015 IFO 12828 13 more

NCBI tax ID(s) 67384

Special Collections DSMZ JCM KCTC Wink compendium

History <- E.B. Shirling, ISP <- T. Niida, Meiji Seika Kaisha Ltd., 689 KCC S-0215 <-- Y. Okami (NIHJ 196) <-- Meiji Seika Kaisha, Ltd.; 689.

Links

Streptomyces xanthochromogenes DSM 40111 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:50:46

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces xanthochromogenes

Full scientific name Streptomyces xanthochromogenes Arishima et al. 1956 (Approved Lists 1980)

Synonyms (1)

Streptomyces michiganensis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	98.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9322	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9322	positive	growth	28	mesophilic
18537	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Compound production

@ref	Compound
9322	xanthicin (anti-fungal)
67770	Xanthicin

Halophily

@ref	Salt	Growth	Tested relation	Concentration
18537	NaCl	positive	maximum	5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18537	22599 ChEBI	arabinose	-
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
18537	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
18537	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
18537	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
18537	29864 ChEBI	mannitol	-
18537	17268 ChEBI	myo-inositol	-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
18537	16634 ChEBI	raffinose	-
18537	26546 ChEBI	rhamnose	-
18537	17992 ChEBI	sucrose	-
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
18537	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
18537	-	-	-	-	-	-	-	-	-	+	-	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.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
9322	soil		Japan	JPN	Asia
67770	Soil	Kawaji, Tochigi Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18537	1	German classification According to TRBA 466
9322	1	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
66792	ASM1465045v1 assembly for Streptomyces xanthochromogenes JCM 4612	scaffold	GCA_014650455	67384.3	8109608033	67384	65.79

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces xanthochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4612	D44264	120	67384
20218	Streptomyces xanthochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 12828	AB184176	1469	67384
20218	Streptomyces xanthochromogenes strain NRRL B-5410T 16S ribosomal RNA gene, partial sequence	DQ442559	1473	67384
124043	Streptomyces xanthochromogenes strain JCM 4612 16S ribosomal RNA gene, partial sequence.	MT760584	714	67384

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Streptomyces xanthochromogenes JCM 4612
NCBI: GCA_014650455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	75.20	no
125439	motility	BacteriaNetⓘ	no	84.30	no
125439	gram_stain	BacteriaNetⓘ	positive	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces xanthochromogenes JCM 4612
NCBI: GCA_014650455.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.79	no
125438	anaerobic	anaerobicⓘ	no	95.77	no
125438	aerobic	aerobicⓘ	yes	83.33	no
125438	spore-forming	spore-formingⓘ	yes	89.62	no
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	86.69	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Streptomycetes as platform for biotechnological production processes of drugs.	Barbuto Ferraiuolo S, Cammarota M, Schiraldi C, Restaino OF.	Appl Microbiol Biotechnol	10.1007/s00253-020-11064-2	2021
	Gut Microbial Metabolite Pravastatin Attenuates Intestinal Ischemia/Reperfusion Injury Through Promoting IL-13 Release From Type II Innate Lymphoid Cells via IL-33/ST2 Signaling.	Deng F, Hu JJ, Yang X, Sun QS, Lin ZB, Zhao BC, Yao ZW, Luo SD, Chen ZL, Liu Y, Yan ZZ, Li C, Liu WF, Liu KX.	Front Immunol	10.3389/fimmu.2021.704836	2021
Phylogeny	Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region.	Pan HU, Zhou J, Dawa Z, Dai Y, Zhang Y, Yang H, Wang C, Liu H, Zhou H, Lu X, Tian Y.	Pol J Microbiol	10.33073/pjm-2021-008	2021
Phylogeny	A Novel Genus of Actinobacterial Tectiviridae.	Caruso SM, deCarvalho TN, Huynh A, Morcos G, Kuo N, Parsa S, Erill I.	Viruses	10.3390/v11121134	2019
	Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy.	Swiecimska M, Golinska P, Goodfellow M.	Front Microbiol	10.3389/fmicb.2022.1054384	2022
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 .
#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 )

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Streptomyces xanthochromogenes (DSM 40111, ATCC 19818, CBS 571.68)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Compound production

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014650455

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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