Name: Spirilliplanes yamanashiensis YU 127-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8028

Type strain:

Species: Spirilliplanes yamanashiensis

Strain Designation: YU 127-1

Culture col. no.: DSM 44325, IFO 15828, NBRC 15828, JCM 10032, CGMCC 4.5503, VKM Ac-1993

Strain history: IFO 15828 <-- M. Hayakawa YU127-1.

NCBI tax ID(s): 42233 (species)

SI-ID 50567

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

Section

Spirilliplanes yamanashiensis YU 127-1 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil sample.

Gram-positive
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	*Micromonosporales*
	Family	*Micromonosporaceae*
	Genus	*Spirilliplanes*
	Species	**Spirilliplanes yamanashiensis**
	Full Scientific Name (LPSN)	Spirilliplanes yamanashiensis Tamura et al. 1997

Information on morphological and physiological properties Morphology

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

[Ref.: #20045]	Colony color	Yellow orange (2000)
[Ref.: #20045]	Incubation period	10-14 days
[Ref.: #20045]	Cultivation medium used	ISP 2

[Ref.: #20045]	Colony color	Yellow orange (2000)
[Ref.: #20045]	Incubation period	10-14 days
[Ref.: #20045]	Cultivation medium used	ISP 3

[Ref.: #20045]	Colony color	Yellow orange (2000)
[Ref.: #20045]	Incubation period	10-14 days
[Ref.: #20045]	Cultivation medium used	ISP 4

[Ref.: #20045]	Colony color	Yellow orange (2000)
[Ref.: #20045]	Incubation period	10-14 days
[Ref.: #20045]	Cultivation medium used	ISP 5

[Ref.: #20045]	Colony color	Yellow orange (2000)
[Ref.: #20045]	Incubation period	10-14 days
[Ref.: #20045]	Cultivation medium used	ISP 6

[Ref.: #20045]	Colony color	Yellow orange (2000)
[Ref.: #20045]	Incubation period	10-14 days
[Ref.: #20045]	Cultivation medium used	ISP 7

[Ref.: #20045]	Multicellular complex forming ability	no
[Ref.: #20045]	Medium Name (multicellularity)	ISP 2

[Ref.: #20045]	Multicellular complex forming ability	no
[Ref.: #20045]	Medium Name (multicellularity)	ISP 3

[Ref.: #20045]	Multicellular complex forming ability	no
[Ref.: #20045]	Medium Name (multicellularity)	ISP 4

[Ref.: #20045]	Multicellular complex forming ability	no
[Ref.: #20045]	Medium Name (multicellularity)	ISP 5

[Ref.: #20045]	Multicellular complex forming ability	no
[Ref.: #20045]	Medium Name (multicellularity)	ISP 6

[Ref.: #20045]	Multicellular complex forming ability	no
[Ref.: #20045]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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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

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Culture medium composition

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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

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 7

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Culture medium growth

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Culture medium composition

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		Temperature
[Ref.: #11671]	growth	28 °C
[Ref.: #20045]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #11671]	Temperature range	mesophilic
[Ref.: #20045]	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 %92
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.525

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #20045]		NaCl		growth	0	%

[Ref.: #67770]

Observation

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #20045]	arabinose ChEBI	+/-
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #20045]	cellulose ChEBI	+
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #20045]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #20045]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #20045]	mannitol ChEBI	+
[Ref.: #20045]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #20045]	raffinose ChEBI	+
[Ref.: #20045]	rhamnose ChEBI	+
[Ref.: #20045]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #20045]	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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E, API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #20045]	620	-	-	-	-	-	-	-	-	-	+	-	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:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #20045]	828	not determinedn.d.	+	-	-	-	+	-	-	+	-	+	-	-	-	-	+	+	+	-	-

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

[Ref.: #11671]	Sample type/isolated from	soil sample
[Ref.: #11671]	Geographic location (country and/or sea, region)	Yamanashi Prefecture, Kofu
[Ref.: #11671]	Country	Japan
[Ref.: #11671]	Country ISO 3 Code	JPN
[Ref.: #11671]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kofu, Yamanashi 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.: #11671]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #20045]	Biosafety level	1	German classification

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.: #67770]	Spirilliplanes yamanashiensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 10032	LC068779	1465	ENA	42233 tax ID
[Ref.: #20218]	Spirilliplanes yamanashiensis gene for 16S ribosomal RNA, partial sequence	D63912	1470	ENA	42233 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Spirilliplanes yamanashiensis NBRC 15828	GCA_016863475	contig	GenBank	42233 tax ID	*
[Ref.: #66792]	Spirilliplanes yamanashiensis strain NBRC 15828	42233.3	wgs	PATRIC	42233 tax ID	*
[Ref.: #66792]	Spirilliplanes yamanashiensis DSM 44325	2923602881	draft	JGI IMG/M	42233 tax ID	*

[Ref.: #11671]	GC-content	69 mol%
[Ref.: #67770]	GC-content	69 mol%	high performance liquid chromatography (HPLC)

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: Spirilliplanes yamanashiensis strain NBRC 15828 PATRIC: 42233.3
[Ref.: #69481]	spore-forming	yes	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Spirilliplanes yamanashiensis strain NBRC 15828 PATRIC: 42233.3
[Ref.: #69480]	gram-positive	yes	88.464	no
[Ref.: #69480]	anaerobic	no	98.845	no
[Ref.: #69480]	halophile	no	95.574	yes
[Ref.: #69480]	spore-forming	yes	84.385	no
[Ref.: #69480]	glucose-util	yes	88.971	yes
[Ref.: #69480]	aerobic	yes	92.144	no
[Ref.: #69480]	flagellated	no	87.66	no
[Ref.: #69480]	thermophile	no	98.179	yes
[Ref.: #69480]	motile	yes	62.15	no
[Ref.: #69480]	glucose-ferment	no	90.478	no

Availability in culture collections External links

[Ref.: #11671]

Culture collection no.

DSM 44325, IFO 15828, NBRC 15828, JCM 10032, CGMCC 4.5503, VKM Ac-1993

[Ref.: #77458]

SI-ID 50567

Literature:

	Title	Authors	Journal	DOI	Year
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	*
	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	*

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 .

#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 )

#77458

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-ID50567.1 )

* These data were automatically processed and therefore are not curated

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Spirilliplanes yamanashiensis strain NBRC 15828

Spirilliplanes yamanashiensis strain NBRC 15828

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