Spirilliplanes yamanashiensis (DSM 44325, IFO 15828, NBRC 15828)

Name: Spirilliplanes yamanashiensis (DSM 44325, IFO 15828, NBRC 15828)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8028

Type strain

Strain Designation YU 127-1

Culture col. no. DSM 44325 IFO 15828 NBRC 15828 YU 127-1 VKM Ac-1993 2 more

NCBI tax ID(s) 42233

Special Collections DSMZ JCM Wink compendium

History <- IFO IFO 15828 <-- M. Hayakawa YU127-1.

Links

Spirilliplanes yamanashiensis YU 127-1 is a bacterium that was isolated from soil sample.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 50567

DSM 44325,IFO 15828,JCM 10032,HUT 6596,VKM Ac-1993,NBRC 15828

@ref 20215

Last LPSN update 2026-02-09 11:19:37

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Spirilliplanes

Species Spirilliplanes yamanashiensis

Full scientific name Spirilliplanes yamanashiensis Tamura et al. 1997

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.9

Colony morphology

@ref	Colony color	Incubation period	Medium used
20045	Yellow orange (2000)	10-14 days	ISP 2
20045	Yellow orange (2000)	10-14 days	ISP 3
20045	Yellow orange (2000)	10-14 days	ISP 4
20045	Yellow orange (2000)	10-14 days	ISP 5
20045	Yellow orange (2000)	10-14 days	ISP 6
20045	Yellow orange (2000)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20045		ISP 2
20045		ISP 3
20045		ISP 4
20045		ISP 5
20045		ISP 6
20045		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11671	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
11671	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
20045	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20045	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20045	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20045	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20045	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20045	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
11671	positive	growth	28
20045	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.7

Spore formation

@ref	Spore formation	Confidence
125439		95.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
20045	NaCl	positive	growth	0 %

Observation

67770

Observationquinones: MK-10(H₄), MK-10(H₆), MK-10(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
20045	22599 ChEBI	arabinose	+/-
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
20045	62968 ChEBI	cellulose	+
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
20045	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
20045	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
20045	29864 ChEBI	mannitol	+
20045	17268 ChEBI	myo-inositol	-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
20045	16634 ChEBI	raffinose	+
20045	26546 ChEBI	rhamnose	+
20045	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
20045	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
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68382	trypsin	+	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

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
20045	-	-	-	-	-	-	-	-	-	+	-	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.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
20045	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
11671	soil sample	Yamanashi Prefecture, Kofu	Japan	JPN	Asia
67770	Soil	Kofu, Yamanashi Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11671	1	Risk group (German classification) According to TRBA 466
20045	1	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
124043	ASM3081137v1 assembly for Spirilliplanes yamanashiensis DSM 44325	contig	GCA_030811375	42233.4	2923602881	42233	75.72
124043	ASM3952419v1 assembly for Spirilliplanes yamanashiensis JCM 10032	scaffold	GCA_039524195			42233	66.79
66792	ASM1686347v1 assembly for Spirilliplanes yamanashiensis NBRC 15828	contig	GCA_016863475	42233.3	8062113892	42233	64.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Spirilliplanes yamanashiensis gene for 16S ribosomal RNA, partial sequence	D63912	1470		42233
67770	Spirilliplanes yamanashiensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 10032	LC068779	1465		42233

GC content

@ref	GC-content (mol%)	Method
11671	69
67770	69	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Spirilliplanes yamanashiensis NBRC 15828
NCBI: GCA_016863475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.20	no
125439	motility	BacteriaNetⓘ	no	86.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Spirilliplanes yamanashiensis strain NBRC 15828
PATRIC: 42233.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.16	no
125438	anaerobic	anaerobicⓘ	no	94.84	no
125438	spore-forming	spore-formingⓘ	yes	88.13	no
125438	aerobic	aerobicⓘ	yes	85.13	no
125438	thermophilic	thermophileⓘ	no	90.88	no
125438	flagellated	motile2+ⓘ	no	57.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Involvement of an orphan response regulator of the two-component regulatory system in the formation of physiologically mature sporangia in Actinoplanes missouriensis.	Akutsu T, Tan Z, Hirata A, Tezuka T, Ohnishi Y.	Microbiol Spectr	10.1128/spectrum.03272-24	2025
	Molecular mechanism of flagellar motor rotation arrest in bacterial zoospores of Actinoplanes missouriensis before germination.	Kato H, Tanemura H, Kimura T, Katsuyama Y, Tezuka T, Ohnishi Y.	Commun Biol	10.1038/s42003-024-07104-6	2024
	[Cell wall teichoic acids from Streptomyces daghestanicus VKM Ac-1722T and Streptomyces murinus INA-00524T].	Streshinskaia GM, Koslova IuI, Alferova IV, Shashkov AS, Evtushenko LI.	Mikrobiologiia	10.1007/s11021-005-0026-7	2005
	NMR-based identification of cell wall anionic polymers of Spirilliplanes yamanashiensis VKM Ac-1993(T).	Shashkov AS, Streshinskaya GM, Evtushenko LI, Naumova IB	Carbohydr Res	10.1016/s0008-6215(01)00224-5	2001
Phylogeny	Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae.	Rheims H, Schumann P, Rohde M, Stackebrandt E.	Int J Syst Bacteriol	10.1099/00207713-48-4-1119	1998
Phylogeny	A new genus of the order Actinomycetales, Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov.	Tamura T, Hayakawa M, Hatano K	Int J Syst Bacteriol	10.1099/00207713-47-1-97	1997

References

#11671	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44325
#20045	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 .
#68382	Automatically annotated from API zym .
#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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Spirilliplanes yamanashiensis (DSM 44325, IFO 15828, NBRC 15828)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030811375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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