Catenulispora rubra (DSM 44948, JCM 16000, NBRC 101179)

Name: Catenulispora rubra (DSM 44948, JCM 16000, NBRC 101179)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17637

Type strain

Strain Designation Aac-30

Culture col. no. DSM 44948 JCM 16000 NBRC 101179 Aac-30

NCBI tax ID(s) 280293

Special Collections DSMZ JCM Wink compendium Literature strains

History DSMZ <- NBRC <- T. Sakane; Aac-30 JCM <-- DSM 44948 <-- T. Tamura Aac-30 <-- T. Sakane.

Links

Catenulispora rubra Aac-30 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

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

Name and taxonomic classification

SI-ID 297462

DSM 44948,NBRC 101179,JCM 16000

@ref 20215

Last LPSN update 2026-05-29 08:29:03

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Catenulisporales

Family Catenulisporaceae

Genus Catenulispora

Species Catenulispora rubra

Full scientific name Catenulispora rubra Tamura et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
32161	positive	1.1 µm	rod-shaped
125439	positive			99.307
125439				95.235

Colony morphology

@ref	Colony color	Incubation period	Medium used
19893	Yellow orange	10-14 days	ISP 2
19893	Sun yellow	10-14 days	ISP 3
19893	Cream	10-14 days	ISP 4
19893	Yellow orange	10-14 days	ISP 5
19893	Yellow orange	10-14 days	ISP 6
19893	Yellow orange	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19893			ISP 2
19893			ISP 3
19893			ISP 4
19893			ISP 5
19893	Aerial Mycelium	Cream	ISP 6
19893			ISP 7

Pigmentation

32161

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12112	YEAST STARCH AGAR (A) (DSMZ Medium 1027)	Medium recipe at MediaDive	Name: YEAST STARCH AGAR (A) (DSMZ Medium 1027) Composition: Agar 15.0 g/l Starch 10.0 g/l Yeast extract 2.0 g/l Distilled water
19893	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
19893	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:
19893	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
19893	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
19893	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
19893	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)
12112	positive	growth	28
32161	positive	growth	20-30
32161	positive	optimum	25
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32161	positive	optimum	5
32161	positive	growth	04-06	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32161	aerobe
125439	obligate aerobe	97.637

Spore formation

32161

Spore formationyes

Observation

@ref	Observation
32161	aggregates in chains
67770	quinones: MK-9(H₆), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19893	22599 ChEBI	arabinose	-
32161	22599 ChEBI	arabinose	+	carbon source
19893	62968 ChEBI	cellulose	+
32161	4853 ChEBI	esculin	+	hydrolysis
19893	28757 ChEBI	fructose	+
32161	28757 ChEBI	fructose	+	carbon source
19893	17234 ChEBI	glucose	+
32161	17234 ChEBI	glucose	+	carbon source
19893	29864 ChEBI	mannitol	+
19893	17268 ChEBI	myo-inositol	-
19893	16634 ChEBI	raffinose	-
32161	16634 ChEBI	raffinose	+	carbon source
19893	26546 ChEBI	rhamnose	-
19893	17992 ChEBI	sucrose	+
32161	17992 ChEBI	sucrose	+	carbon source
19893	18222 ChEBI	xylose	-
32161	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32161	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
32161	alkaline phosphatase	+	3.1.3.1
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
19893	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
12112	soil	Oodate, Akita	Japan	JPN	Asia
67770	Forest soil	Oodate, Akita Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB180773 (>99% sequence identity) for Catenulispora from Microbeatlas

Aquatic Samples	870
Soil Samples	16042
Animal Samples	1233
Plant Samples	2953
Total Samples	21098

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12112	1	Risk group (German classification) According to TRBA 466
19893	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1535682v1 assembly for Catenulispora rubra DSM 44948	contig	GCA_015356825	280293.3	280293	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12112	Catenulispora rubra gene for 16S rRNA, partial sequence	AB180773	1472		280293

GC content

@ref	GC-content (mol%)	Method
12112	69.1
67770	69.1	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: ASM1535682v1 assembly for Catenulispora rubra DSM 44948
BV-BRC: 280293.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.64	no
125439	motility	BacteriaNetⓘ	no	95.24	no
125439	gram_stain	BacteriaNetⓘ	positive	99.31	no
125439	spore_formation	BacteriaNetⓘ	yes	71.37	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Catenulispora rubra strain DSM 44948
PATRIC: 280293.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.39	no
125438	anaerobic	anaerobicⓘ	no	97.82	yes
125438	spore-forming	spore-formingⓘ	yes	89.65	yes
125438	aerobic	aerobicⓘ	yes	89.58	yes
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	88.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genomic-based classification of Catenulispora pinisilvae sp. nov., novel actinobacteria isolated from a pine forest soil in Poland and emended description of Catenulispora rubra.	Swiecimska M, Golinska P, Wypij M, Goodfellow M	Syst Appl Microbiol	10.1016/j.syapm.2020.126164	2020
Phylogeny	Catenulispora fulva sp. nov., isolated from forest soil.	Lee HJ, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.000711	2015
Phylogeny	Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil.	Lee HJ, Han SI, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.035501-0	2011
Phylogeny	Catenulispora rubra sp. nov., an acidophilic actinomycete isolated from forest soil.	Tamura T, Ishida Y, Sakane T, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijs.0.65056-0	2007

References

#12112	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44948
#19893	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 )
#28404	IJSEM 2272 2007 ( DOI 10.1099/ijs.0.65056-0 , PubMed 17911295 )
#32161	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 #28404
#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 .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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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Catenulispora rubra (DSM 44948, JCM 16000, NBRC 101179)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_015356825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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