Actinocatenispora rupis (DSM 45178, JCM 16894, NBRC 107355)

Name: Actinocatenispora rupis (DSM 45178, JCM 16894, NBRC 107355)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7797

Type strain

Strain Designation CS5-AC17

Culture col. no. DSM 45178 JCM 16894 NBRC 107355 NRRL B-24660 CS5-AC17

NCBI tax ID(s) 519421

Special Collections DSMZ JCM Wink compendium Literature strains

Links

Actinocatenispora rupis CS5-AC17 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from soil of cliff.

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

Name and taxonomic classification

SI-ID 403338

NBRC 107355,JCM 16894,DSM 45178

@ref 20215

Last LPSN update 2025-12-16 09:48:40

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Actinocatenispora

Species Actinocatenispora rupis

Full scientific name Actinocatenispora rupis Seo and Lee 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width
29428	positive	1.25 µm	0.45 µm
125438
125438	positive
125439	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
20175	Light ivory (1015)	10-14 days	ISP 2
20175	Cream (9001)	10-14 days	ISP 3
20175	Light ivory (1015)	10-14 days	ISP 4
20175	Light ivory (1015)	10-14 days	ISP 5
20175	Ivory (1014)	10-14 days	ISP 6
20175	Cream (9001)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20175		ISP 2
20175		ISP 3
20175		ISP 4
20175		ISP 5
20175		ISP 6
20175		ISP 7

Pigmentation

29428

Productionno

Multimedia

@ref:	15642
multimedia content:	DSM_45178.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45178.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
15642	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
15642	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
20175	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
20175	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:
20175	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
20175	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
20175	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
20175	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
15642	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
15642	ISP2 MEDIUM (DSMZ Medium 987)	Medium recipe at MediaDive	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15642	positive	growth	28	mesophilic
20175	positive	optimum	28	mesophilic
29428	positive	growth	25-42
29428	positive	optimum	37	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
29428	positive	optimum	7.1
29428	positive	growth	5.1-12.1

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29428	aerobe
125438	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
29428
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29428	NaCl	positive	growth	0-4 %
29428	NaCl	positive	optimum	7.1 %

Observation

@ref	Observation
29428	aggregates in clumps
67770	quinones: MK-9(H₄), MK-9(H₆), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity
20175	22599 ChEBI	arabinose	+/-
29428	22599 ChEBI	arabinose	+
29428	17057 ChEBI	cellobiose	+
20175	62968 ChEBI	cellulose	-
29428	16947 ChEBI	citrate	+
29428	4853 ChEBI	esculin	+
20175	28757 ChEBI	fructose	+
29428	28260 ChEBI	galactose	+
20175	17234 ChEBI	glucose	+
29428	17754 ChEBI	glycerol	+
29428	17716 ChEBI	lactose	+
29428	17306 ChEBI	maltose	+
20175	29864 ChEBI	mannitol	+
29428	29864 ChEBI	mannitol	+
29428	37684 ChEBI	mannose	+
20175	17268 ChEBI	myo-inositol	+/-
20175	16634 ChEBI	raffinose	-
20175	26546 ChEBI	rhamnose	+/-
29428	26546 ChEBI	rhamnose	+
29428	15963 ChEBI	ribitol	+
29428	30911 ChEBI	sorbitol	+
20175	17992 ChEBI	sucrose	+
29428	17992 ChEBI	sucrose	+
29428	27082 ChEBI	trehalose	+
29428	53426 ChEBI	tween 80	+
20175	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
20175	not determinedn.d.	+	+	+	-	+	+	-	+	-	+	+	+	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15642	soil of cliff	Jeju, Mara Island	Republic of Korea	KOR	Asia
67770	Soil from a cliff on Mara Island	Jeju	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AM980986 (>99% sequence identity) for Actinocatenispora rupis subclade from Microbeatlas

Aquatic Samples	83
Soil Samples	2086
Animal Samples	242
Plant Samples	454
Total Samples	2865

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15642	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	ASM1686197v1 assembly for Actinocatenispora rupis NBRC 107355	contig	GCA_016861975	519421.3	3000609119	519421	52.65
124043	ASM3953690v1 assembly for Actinocatenispora rupis JCM 16894	scaffold	GCA_039536905			519421	51.07

Genome browser: GCA_016861975

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15642	Actinocatenispora rupis partial 16S rRNA gene, type strain CS5-AC17T	AM980986	1408		519421

GC content

@ref	GC-content (mol%)	Method
15642	74.3	high performance liquid chromatography (HPLC)
29428	74.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinocatenispora rupis NBRC 107355
NCBI: GCA_016861975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.90	no
125439	motility	BacteriaNetⓘ	no	88.50	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinocatenispora rupis strain NBRC 107355
PATRIC: 519421.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.96	yes
125438	anaerobic	anaerobicⓘ	no	94.42	yes
125438	spore-forming	spore-formingⓘ	yes	83.91	no
125438	aerobic	aerobicⓘ	yes	90.93	no
125438	thermophilic	thermophileⓘ	no	94.92	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum.	Oyunbileg N, Iizaka Y, Hamada M, Davaapurev BO, Fukumoto A, Tsetseg B, Kato F, Tamura T, Batkhuu J, Anzai Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.004861	2021
Phylogeny	Actinocatenispora rupis sp. nov., isolated from cliff soil, and emended description of the genus Actinocatenispora.	Seo SH, Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.012922-0	2009

References

#15642	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45178
#20175	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 )
#29428	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 #25834 (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 .
#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 .
#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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Actinocatenispora rupis (DSM 45178, JCM 16894, NBRC 107355)

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

Halophily

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_016861975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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