Polymorphospora rubra (DSM 44947, NBRC 101157, TT97-42)

Name: Polymorphospora rubra (DSM 44947, NBRC 101157, TT97-42)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8025

Type strain

Strain Designation TT97-42

Culture col. no. DSM 44947 NBRC 101157 TT97-42 CGMCC 4.5572 JCM 14904

NCBI tax ID(s) 338584

Special Collections DSMZ JCM Wink compendium Literature strains

Links

Polymorphospora rubra TT97-42 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from soil around roots of Buruguiera gymnorrhiza.

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

Name and taxonomic classification

SI-ID 297299

DSM 44947,NBRC 101157,BCRC 16832,CCRC 16832,JCM 14904

@ref 20215

Last LPSN update 2025-12-16 09:48:44

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Polymorphospora

Species Polymorphospora rubra

Full scientific name Polymorphospora rubra Tamura et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31682	positive	0.8-1.5 µm	0.6-0.9 µm	rod-shaped
125439	positive				99.9
125439					93
125438	positive				90.825

Colony morphology

@ref	Colony color	Incubation period	Medium used
19892	Beige	10-14 days	ISP 2
19892	Beige	10-14 days	ISP 3
19892	Beige	10-14 days	ISP 4
19892	Beige	10-14 days	ISP 5
19892	Beige	10-14 days	ISP 6
19892	Beige	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19892		ISP 2
19892		ISP 3
19892		ISP 4
19892		ISP 5
19892		ISP 6
19892		ISP 7

Pigmentation

31682

Productionyes

Multimedia

@ref:	12111
multimedia content:	DSM_44947.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44947.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12111	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
12111	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
12111	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
19892	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
19892	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:
19892	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
19892	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
19892	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
19892	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)	Range
12111	positive	growth	28	mesophilic
19892	positive	optimum	28	mesophilic
31682	positive	growth	20-30
31682	positive	optimum	20-30
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
31682	positive	optimum	7
31682	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
12111	aerobe
31682	aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
31682
125439		95.4

Observation

@ref	Observation
31682	aggregates in chains
67770	quinones: MK-10(H₆), MK-10(H₄), MK-9(H₆), MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19892	22599 ChEBI	arabinose	+
19892	62968 ChEBI	cellulose	+
19892	28757 ChEBI	fructose	+
31682	28260 ChEBI	galactose	+	carbon source
19892	17234 ChEBI	glucose	+
31682	17234 ChEBI	glucose	+	carbon source
31682	17306 ChEBI	maltose	+	carbon source
19892	29864 ChEBI	mannitol	+
31682	29864 ChEBI	mannitol	+	carbon source
31682	37684 ChEBI	mannose	+	carbon source
31682	28053 ChEBI	melibiose	+	carbon source
19892	17268 ChEBI	myo-inositol	+
19892	16634 ChEBI	raffinose	+
19892	26546 ChEBI	rhamnose	-
31682	26546 ChEBI	rhamnose	+	carbon source
19892	17992 ChEBI	sucrose	+
19892	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
19892	not determinedn.d.	+	+	+	-	-	-	-	-	+	+	+	-	-	-	-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12111	soil around roots of Buruguiera gymnorrhiza	Okinawa, Iriomote	Japan	JPN	Asia
67770	Soil surrounding mangrove roots at the mouth of the River Shiira	Iriomote Island, Okinawa Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12111	1	Risk group (German classification) According to TRBA 466
19892	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	ASM1832425v1 assembly for Polymorphospora rubra NBRC 101157	complete	GCA_018324255	338584.4	2993890609	338584	92.03
124043	ASM3953026v1 assembly for Polymorphospora rubra JCM 14904	scaffold	GCA_039530265			338584	30.05

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12111	Polymorphospora rubra gene for 16S rRNA, partial sequence, strain: TT 97-42	AB223089	1471		338584

GC content

@ref	GC-content (mol%)	Method
31682	70
67770	70.2	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: Polymorphospora rubra strain NBRC 101157
PATRIC: 338584.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.40	no
125439	motility	BacteriaNetⓘ	no	93.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Polymorphospora rubra NBRC 101157
NCBI: GCA_018324255.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.83	yes
125438	anaerobic	anaerobicⓘ	no	93.10	no
125438	aerobic	aerobicⓘ	yes	88.97	no
125438	spore-forming	spore-formingⓘ	yes	87.12	no
125438	thermophilic	thermophileⓘ	no	94.00	yes
125438	flagellated	motile2+ⓘ	no	86.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polymorphospora lycopeni sp. nov., a lycopene-producing actinomycetes isolated from lakeside soil sample of Baiyangdian.	Liu J, Li S, Duan X, Li H, Zhang X.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006543	2024
Phylogeny	A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov.	Tamura T, Hatano K, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijs.0.64046-0	2006

References

#12111	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44947
#19892	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 )
#31682	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 #27959 (see below)
#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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Polymorphospora rubra (DSM 44947, NBRC 101157, TT97-42)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

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_018324255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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