Planotetraspora silvatica (DSM 44746, NBRC 100141, TT 00-51)

Name: Planotetraspora silvatica (DSM 44746, NBRC 100141, TT 00-51)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16582

Type strain

Strain Designation TT 00-51

Culture col. no. DSM 44746 NBRC 100141 TT 00-51 CGMCC 4.5632 BCRC 16800 1 more

NCBI tax ID(s) 234614

Special Collections DSMZ JCM Wink compendium Literature strains

History <- T. Tamura; TT 00-51 NBRC 100141 <-- T. Tamura TT 00-51.

Links

Planotetraspora silvatica TT 00-51 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from forest soil.

spore-forming Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 134454

DSM 44746,NBRC 100141,JCM 12867,BCRC 16800,CCRC 16800

@ref 20215

Last LPSN update 2025-12-16 09:50:53

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Streptosporangiaceae

Genus Planotetraspora

Species Planotetraspora silvatica

Full scientific name Planotetraspora silvatica Tamura and Sakane 2004

Morphology

Cell morphology

@ref	Gram stain	Confidence
30134	positive
125439	positive	98.7

Colony morphology

@ref	Colony color	Incubation period	Medium used
20110	Grey brown (8019)	10-14 days	ISP 2
20110	Grey brown (8019)	10-14 days	ISP 3
20110	Beige (1001)	10-14 days	ISP 4
20110	Beige (1001)	10-14 days	ISP 5
20110	Golden yellow (1004)	10-14 days	ISP 6
20110	Beige (1001)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20110		ISP 2
20110		ISP 3
20110		ISP 4
20110		ISP 5
20110		ISP 6
20110		ISP 7

Pigmentation

30134

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
20110	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
20110	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:
20110	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
20110	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
20110	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
20110	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
12055	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
12055	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
12055	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12055	positive	growth	28	mesophilic
20110	positive	optimum	28	mesophilic
30134	positive	growth	25-30	mesophilic
30134	positive	optimum	27.5	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30134	aerobe
125438	aerobe	91.264
125439	obligate aerobe	96.9

Spore formation

30134

Spore formationyes

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₂), MK-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
20110	22599 ChEBI	arabinose	+
20110	62968 ChEBI	cellulose	+
20110	28757 ChEBI	fructose	+
30134	28260 ChEBI	galactose	+	carbon source
20110	17234 ChEBI	glucose	+
30134	17234 ChEBI	glucose	+	carbon source
30134	17716 ChEBI	lactose	+	carbon source
30134	17306 ChEBI	maltose	+	carbon source
20110	29864 ChEBI	mannitol	+
30134	29864 ChEBI	mannitol	+	carbon source
30134	28053 ChEBI	melibiose	+	carbon source
20110	17268 ChEBI	myo-inositol	+
20110	16634 ChEBI	raffinose	+
30134	16634 ChEBI	raffinose	+	carbon source
20110	26546 ChEBI	rhamnose	+
30134	26546 ChEBI	rhamnose	+	carbon source
20110	17992 ChEBI	sucrose	+
20110	18222 ChEBI	xylose	-

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
68382	beta-galactosidase	+	3.2.1.23	from API zym
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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	+	3.4.21.4	from API zym
68382	valine arylamidase	+		from API zym

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
20110	not determinedn.d.	+	+	+	-	+	+	+	+	-	+	+	+	+	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12055	forest soil	Amami-island, Kagoshima pref.	Japan	JPN	Asia
67770	Forest soil	Amami Island, Kagoshima Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12055	1	Risk group (German classification) According to TRBA 466
20110	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
66792	ASM1686331v1 assembly for Planotetraspora silvatica NBRC 100141	contig	GCA_016863315	234614.3	2994630621	234614	46.18
124043	ASM3952799v1 assembly for Planotetraspora silvatica JCM 12867	contig	GCA_039527995			234614	35.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12055	Planotetraspora silvatica gene for 16S ribosomal RNA, partial sequence	AB112082	1472		234614

GC content

@ref	GC-content (mol%)	Method
30134	71
67770	70-71	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: Planotetraspora silvatica NBRC 100141
NCBI: GCA_016863315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	53.30	no
125439	motility	BacteriaNetⓘ	no	80.60	no
125439	gram_stain	BacteriaNetⓘ	positive	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planotetraspora silvatica strain NBRC 100141
PATRIC: 234614.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.78	yes
125438	anaerobic	anaerobicⓘ	no	94.84	no
125438	spore-forming	spore-formingⓘ	yes	88.08	yes
125438	aerobic	aerobicⓘ	yes	91.26	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora.	Tamura T, Sakane T	Int J Syst Evol Microbiol	10.1099/ijs.0.02981-0	2004

References

#12055	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44746
#20110	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 )
#26485	IJSEM 2053 2004 ( DOI 10.1099/ijs.0.02981-0 , PubMed 15545433 )
#30134	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26485
#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;
#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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Planotetraspora silvatica (DSM 44746, NBRC 100141, TT 00-51)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016863315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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