Name: Kitasatospora misakiensis IPCR 7617
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 15413

Type strain:

Species: Kitasatospora misakiensis

Strain Designation: IPCR 7617

Culture col. no.: DSM 40222, ATCC 23938, CBS 278.65, CBS 922.68, IFO 12891, ISP 5222, JCM 4062, JCM 4653, NBRC 12891, NRRL B-2923, RIA 1166, BCRC 13799, CGMCC 4.1437, IFM 1195, KCTC 19951, NCIMB 9852, NRRL ISP-5222, VKM Ac-625

Strain history: KCC S-0062 <-- G. Nakamura 7617 (=1755).

NCBI tax ID(s): 67330 (species)

SI-ID 14119

LMG 19369, ATCC 23938, DSM 40222, IFO 12891, JCM 4062, JCM 4653, NCIMB 9852, NRRL B-2923, VKM Ac-625, CBS 922.68, CBS 278.65, AS 4.1437, NBRC 12891, BCRC 13799, CCRC 13799, KCTC 19951, NCIB 9852, CGMCC 4.1437

Special Collections

Section

When using BacDive for research please cite our paper

Kitasatospora misakiensis IPCR 7617 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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Kitasatospora*
	Species	**Kitasatospora misakiensis**
	Full Scientific Name (LPSN)	Kitasatospora misakiensis (Nakamura 1961) Labeda et al. 2017

Synonym

Streptomyces misakiensis

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %100
[Ref.: #125438]	Gram stain	positive Confidence in %90.531

[Ref.: #125439]	Motility	no Confidence in %91.2
[Ref.: #125438]	Motility	no Confidence in %93

[Ref.: #19425]	Colony color	Light red
[Ref.: #19425]	Incubation period	10-14 days
[Ref.: #19425]	Cultivation medium used	ISP 2

[Ref.: #19425]	Colony color	Yellow red
[Ref.: #19425]	Incubation period	10-14 days
[Ref.: #19425]	Cultivation medium used	ISP 3

[Ref.: #19425]	Colony color	Yellow
[Ref.: #19425]	Incubation period	10-14 days
[Ref.: #19425]	Cultivation medium used	ISP 4

[Ref.: #19425]	Colony color	Brown
[Ref.: #19425]	Incubation period	10-14 days
[Ref.: #19425]	Cultivation medium used	ISP 5

[Ref.: #19425]	Colony color	Brown
[Ref.: #19425]	Incubation period	10-14 days
[Ref.: #19425]	Cultivation medium used	ISP 6

[Ref.: #19425]	Colony color	Brown red
[Ref.: #19425]	Incubation period	10-14 days
[Ref.: #19425]	Cultivation medium used	ISP 7

[Ref.: #19425]	Multicellular complex forming ability	yes
[Ref.: #19425]	Multicellular complex name	Aerial Mycelium
[Ref.: #19425]	Multicellular complex color	Grey
[Ref.: #19425]	Medium Name (multicellularity)	ISP 2

[Ref.: #19425]	Multicellular complex forming ability	yes
[Ref.: #19425]	Multicellular complex name	Aerial Mycelium
[Ref.: #19425]	Multicellular complex color	Light grey
[Ref.: #19425]	Medium Name (multicellularity)	ISP 3

[Ref.: #19425]	Multicellular complex forming ability	yes
[Ref.: #19425]	Multicellular complex name	Aerial Mycelium
[Ref.: #19425]	Multicellular complex color	Grey
[Ref.: #19425]	Medium Name (multicellularity)	ISP 4

[Ref.: #19425]	Multicellular complex forming ability	yes
[Ref.: #19425]	Multicellular complex name	Aerial Mycelium
[Ref.: #19425]	Multicellular complex color	Grey
[Ref.: #19425]	Medium Name (multicellularity)	ISP 5

[Ref.: #19425]	Multicellular complex forming ability	no
[Ref.: #19425]	Medium Name (multicellularity)	ISP 6

[Ref.: #19425]	Multicellular complex forming ability	yes
[Ref.: #19425]	Multicellular complex name	Aerial Mycelium
[Ref.: #19425]	Multicellular complex color	Grey
[Ref.: #19425]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9279]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #9279]

Culture medium composition

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[Ref.: #19425]

Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 7

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #9279]	growth	28 °C
[Ref.: #19425]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %99.5

[Ref.: #19425]	Spore description	Formation of spore chains: rectiflixibilis, spore surface: smooth
[Ref.: #19425]	Ability of spore formation	yes
[Ref.: #125439]	Ability of spore formation	yes Confidence in %97.3

[Ref.: #9279]	Name of produced compound	tubermycin A
[Ref.: #9279]	Name of produced compound	tubermycin B
[Ref.: #9279]	Name of produced compound	tubermycin A, B
[Ref.: #20216]	Name of produced compound	Tubermycin A
[Ref.: #20216]	Name of produced compound	Tubermycin B
[Ref.: #67770]	Name of produced compound	Tubermycins A and B

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #19425]	arabinose ChEBI	-
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19425]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #19425]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #19425]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #19425]	mannitol ChEBI	-
[Ref.: #19425]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #19425]	raffinose ChEBI	-
[Ref.: #19425]	rhamnose ChEBI	-
[Ref.: #19425]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19425]	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.: #19425]	289	+	+	+	+	+	-	+	-	-	+	-	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.: #9279]	Sample type/isolated from	soil
[Ref.: #9279]	Country	Japan
[Ref.: #9279]	Country ISO 3 Code	JPN
[Ref.: #9279]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Misaki, Kanagawa 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.: #9279]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19425]	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.: #9279]	Streptomyces misakiensis gene for 16S rRNA, partial sequence, strain:IFO 12891	AB217605	1473	GenBank ENA	67330 tax ID
[Ref.: #20218]	Streptomyces misakiensis strain DSM 40222 16S ribosomal RNA gene, partial sequence	AY999839	1420	GenBank ENA	67330 tax ID	*
[Ref.: #20218]	Streptomyces misakiensis gene for 16S rRNA, partial sequence	AB122749	564	GenBank ENA	67330 tax ID	*
[Ref.: #20218]	Streptomyces misakiensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4653	D44287	120	GenBank ENA	67330 tax ID	*
[Ref.: #20218]	Streptomyces misakiensis 16S rRNA gene, type strain LMG 19369	AJ781325	1476	GenBank ENA	67330 tax ID	*
[Ref.: #20218]	Streptomyces misakiensis gene for 16S rRNA, partial sequence, strain: NBRC 12891	AB184223	1473	GenBank ENA	67330 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Kitasatospora misakiensis NRRL B-2923	GCA_000715585	contig	GenBank ENA	67330 tax ID

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Kitasatospora misakiensis NRRL B-2923 NCBI: GCA_000715585.2
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	90.531	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	98.894	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.025	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	89.34	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	93	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Kitasatospora misakiensis NRRL B-2923 NCBI: GCA_000715585
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	97.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	91.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	100
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.5

Availability in culture collections External links

[Ref.: #9279]

Culture collection no.

DSM 40222, ATCC 23938, CBS 278.65, CBS 922.68, IFO 12891, ISP 5222, JCM 4062, JCM 4653, NBRC 12891, NRRL B-2923, RIA 1166, BCRC 13799, CGMCC 4.1437, IFM 1195, KCTC 19951, NCIMB 9852, NRRL ISP-5222, VKM Ac-625

[Ref.: #84502]

SI-ID 14119

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces polygonati sp. nov., an endophytic actinomycete isolated from a root of Polygonatum odoratum (Mill.).	Guo S, Liu C, Liu S, Guan X, Guo L, Jia F, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.000906	2016	*

References

#9279

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40222

#19425

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68368

Automatically annotated from API 20E .

#84502

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-ID14119.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Kitasatospora misakiensis NRRL B-2923

Kitasatospora misakiensis NRRL B-2923

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