Actinocorallia glomerata (DSM 44360, IFO 15960, JCM 9376)

Name: Actinocorallia glomerata (DSM 44360, IFO 15960, JCM 9376)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16912

Type strain

Strain Designation I-226

Culture col. no. DSM 44360 IFO 15960 JCM 9376 NBRC 15960 I-226 1 more

NCBI tax ID(s) 46203

Special Collections DSMZ JCM Wink compendium

History DSMZ <- JCM <- T. Itoh, Kitasato Inst., Tokyo, I-226 JCM <-- T. Itoh I-226.

Links

Actinocorallia glomerata I-226 is a bacterium that builds an aerial mycelium and was isolated from decayed leaf of a deciduous tree from a pond.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 50589

DSM 44360,IFO 15960,JCM 9376,NBRC 15960

@ref 20215

Last LPSN update 2026-05-29 08:28:53

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Actinocorallia

Species Actinocorallia glomerata

Full scientific name Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001

Synonyms (1)

Actinomadura glomerata

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	95.245

Colony morphology

@ref	Incubation period	Medium used
19653	10-14 days	ISP 2
19653	10-14 days	ISP 3
19653	10-14 days	ISP 4
19653	10-14 days	ISP 5
19653	10-14 days	ISP 6
19653	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19653	Aerial Mycelium	Oyster white	ISP 2
19653	Aerial Mycelium	Oyster white	ISP 3
19653			ISP 4
19653			ISP 5
19653			ISP 6
19653			ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11703	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
11703	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
19653	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
19653	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:
19653	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
19653	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
19653	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
19653	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)
11703	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94.638

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19653	NaCl	positive	growth	0 %

Observation

67770

Observationquinones: MK-9(H₆), MK-9(H₄), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19653	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
19653	62968 ChEBI	cellulose	+
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
19653	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19653	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
19653	29864 ChEBI	mannitol	+
19653	17268 ChEBI	myo-inositol	+
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
19653	16634 ChEBI	raffinose	+
19653	26546 ChEBI	rhamnose	+
19653	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
19653	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

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
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	-	3.2.1.23	from API 20E
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
68368	gelatinase	+		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68382	trypsin	+	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	+	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
19653	-	-	-	-	+	-	+	-	-	-	+	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

@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
19653	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Host	#Plants	#Decomposing plant
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11703	decayed leaf of a deciduous tree from a pond	Saitamo	Japan	JPN	Asia
67770	Decayed leaf of deciduous tree	Saitama Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AF134068 (>99% sequence identity) for Actinocorallia glomerata from Microbeatlas

Aquatic Samples	3
Soil Samples	132
Animal Samples	3
Plant Samples	83
Total Samples	221

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11703	1	Risk group (German classification) According to TRBA 466
19653	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953410v1 assembly for Actinocorallia glomerata JCM 9376	scaffold	GCA_039534105	46203	18.52

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinomadura glomerata partial 16S rRNA gene, strain IMSNU 22179T	AJ293704	1509	46203
20218	Actinomadura glomerata 16S ribosomal RNA gene, partial sequence	AF134068	1454	46203
20218	Actinomadura glomerata 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF134098	381	46203
20218	Actinocorallia glomerata gene for 16S rRNA, partial sequence	D50660	1350	46203
20218	Actinocorallia glomerata gene for 16S rRNA, partial sequence, strain: NBRC 15960	AB364591	1464	46203

GC content

@ref	GC-content (mol%)	Method
11703	71.7
67770	70.9	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: ASM3953410v1 assembly for Actinocorallia glomerata JCM 9376
NCBI: GCA_039534105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	95.25	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.64	no
125439	motility	BacteriaNetⓘ	no	80.75	no
125439	spore_formation	BacteriaNetⓘ	no	89.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinocorallia lasiicapitis sp. nov., an actinomycete isolated from the head of an ant (Lasius fuliginosus L.).	Liu C, Li Y, Ye L, Zhao J, Piao C, Li Z, Li J, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.001005	2016

References

#11703	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44360
#19653	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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#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 .
#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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Actinocorallia glomerata (DSM 44360, IFO 15960, JCM 9376)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039534105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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