Agromyces bracchium (DSM 14596, IFO 16238, NBRC 16238)

Name: Agromyces bracchium (DSM 14596, IFO 16238, NBRC 16238)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7267

Type strain

Strain Designation 65

Culture col. no. DSM 14596 IFO 16238 NBRC 16238 VKM Ac-2088 65 5 more

NCBI tax ID(s) 88376

Special Collections DSMZ JCM KCTC CIP Wink compendium

History <- K. Hatano; no. 65 IFO 16238 <-- M. Takeuchi 65. CIP <- 2005, JCM <- M. Takeuchi, IFO

Links

Agromyces bracchium 65 is a Gram-positive, rod-shaped bacterium that was isolated from soil, rhizosphere of Bruguera gymnorrhiza.

Gram-positive rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49557

DSM 14596,IFO 16238,VKM Ac-2088,JCM 11433,KCTC 13909,NBRC 16238,ATCC BAA-403,NCIMB 13881,CIP 108985,IAM 15146

@ref 20215

Last LPSN update 2026-02-09 11:19:25

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Agromyces

Species Agromyces bracchium

Full scientific name Agromyces bracchium Takeuchi and Hatano 2001

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
116987	positive	rod-shaped
125438			93.5
125438	positive		92.329
125439	positive		96.4

Colony morphology

@ref	Colony color	Incubation period	Medium used
18386	Beige (1001)	10-14 days	ISP 2
18386	Beige (1001)	10-14 days	ISP 3
18386	Beige (1001)	10-14 days	ISP 4
18386	Beige (1001)	10-14 days	ISP 5
18386	Beige (1001)	10-14 days	ISP 6
18386	Beige (1001)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18386		ISP 2
18386		ISP 3
18386		ISP 4
18386		ISP 5
18386		ISP 6
18386		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5399	PP-MEDIUM (DSMZ Medium 513)	Medium recipe at MediaDive	Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water
18386	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
18386	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:
18386	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
18386	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
18386	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
18386	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
39704	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116987	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5399	positive	growth	28
18386	positive	optimum	28
39704	positive	growth	30
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.681
125439	obligate aerobe	96.9

Murein

@ref	Murein short key	Type
5399	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Observation

67770

Observationquinones: MK-12, MK-13, NK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

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
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	+	3.2.1.31	from API zym
68379	beta-glucuronidase	+	3.2.1.31	from API Coryne
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
68379	gelatinase	-		from API Coryne
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
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18386	+	-	-	+	+	+	+	-	+	-	-	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
18386	not determinedn.d.	+	+	+	-	+	+	+	-	-	+	+	-	+	+	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
5399	soil, rhizosphere of Bruguera gymnorrhiza	Bruguiera gymnorhiza	Japan, Okinawa, Iriomote Island	Japan	JPN	Asia
67770	Soil of the rhizosphere of Bruguera gymnorrhiza, mangrove in the estuary of the Shiira River	Bruguera gymnorrhiza	Iriomote Island	Japan	JPN	Asia
116987	Environment, Soil, rhizosphere of Bruguera gymmorrhiza		Shiira river, Iriomote Island	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5399	1	Risk group (German classification) According to TRBA 466
18386	1	German classification According to TRBA 466
116987	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM970967v1 assembly for Agromyces bracchium JCM 11433	contig	GCA_009709675	88376.3	2995701289	88376	60.94
124043	ASM4242930v1 assembly for Agromyces bracchium JCM 11433	contig	GCA_042429305			88376	53.01
124043	ASM3952584v1 assembly for Agromyces bracchium JCM 11433	scaffold	GCA_039525845			88376	35.7

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5399	Agromyces sp. IFO16238 gene for 16S rRNA	AB023359	1511		88376

GC content

@ref	GC-content (mol%)	Method
5399	70
67770	70	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: Agromyces bracchium JCM 11433
NCBI: GCA_009709675

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	82.30	no
125439	motility	BacteriaNetⓘ	no	51.40	no
125439	gram_stain	BacteriaNetⓘ	positive	96.40	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: Agromyces bracchium strain JCM 11433
PATRIC: 88376.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.33	no
125438	anaerobic	anaerobicⓘ	no	97.78	no
125438	aerobic	aerobicⓘ	yes	91.68	no
125438	spore-forming	spore-formingⓘ	no	72.52	no
125438	thermophilic	thermophileⓘ	no	96.33	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces aurantiacus sp. nov., isolated from a Chinese primeval forest.	Li WJ, Zhang LP, Xu P, Cui XL, Xu LH, Zhang Z, Schumann P, Stackebrandt E, Jiang CL.	Int J Syst Evol Microbiol	10.1099/ijs.0.02350-0	2003
Phylogeny	Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere.	Takeuchi M, Hatano K	Int J Syst Evol Microbiol	10.1099/00207713-51-4-1529	2001

References

#5399	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14596
#18386	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 )
#39704	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#116987	Collection of Institut Pasteur ; Curators of the CIP; CIP 108985
#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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Agromyces bracchium (DSM 14596, IFO 16238, NBRC 16238)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009709675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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