Agromyces allii (DSM 21551, JCM 13584, KCTC 19181)

Name: Agromyces allii (DSM 21551, JCM 13584, KCTC 19181)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7279

Type strain

Strain Designation UMS-62

Culture col. no. DSM 21551 JCM 13584 KCTC 19181 UMS-62 CIP 109546

NCBI tax ID(s) 393607

Special Collections DSMZ JCM KCTC CIP Literature strains

History <- JCM <- J.-H. Yoon; UMS-62 J.-H. Yoon UMS-62. <- JH Yoon, KRIBB CIP <- 2007, JCM <- 2006, J. H. Yoon, KRIBB, Teajon, South Korea: strain UMS-62

Links

Agromyces allii UMS-62 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from rhizosphere of Allium victorialis var. platyphyllum.

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

Name and taxonomic classification

SI-ID 297114

JCM 13584,KCTC 19181,CIP 109546,DSM 21551

@ref 20215

Last LPSN update 2026-02-09 11:19:26

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Agromyces

Species Agromyces allii

Full scientific name Agromyces allii Jung et al. 2007

BacDive ID	Other strains from **Agromyces allii** (1)	Type strain
156260	A. allii CCUG 60897

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31970	positive	1 µm	0.3 µm	rod-shaped
67771	positive
116257	positive			rod-shaped
125438					93
125438	positive				91.684
125439	positive				96.8

Pigmentation

31970

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15790	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
37761	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116257	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15790	positive	growth	28
31970	positive	growth	04-33
31970	positive	optimum	30
37761	positive	growth	30
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
31970	positive	optimum	7
31970	positive	growth	5.5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31970	aerobe
67771	aerobe
116257	obligate aerobe
125438	aerobe	91.803
125439	obligate aerobe	99.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31970	NaCl	positive	growth	<3 %

Observation

67770

Observationquinones: MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31970	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
31970	17057 ChEBI	cellobiose	+	carbon source
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
31970	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
31970	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31970	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
31970	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
31970	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
31970	25115 ChEBI	malate	+	carbon source
31970	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
31970	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
31970	28053 ChEBI	melibiose	+	carbon source
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
31970	17632 ChEBI	nitrate	+	reduction
116257	17632 ChEBI	nitrate	+	reduction
116257	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
31970	26546 ChEBI	rhamnose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
31970	33942 ChEBI	ribose	+	carbon source
31970	17814 ChEBI	salicin	+	carbon source
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
31970	30031 ChEBI	succinate	+	carbon source
31970	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
31970	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
31970	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116257	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
31970	acid phosphatase	+	3.1.3.2
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
31970	catalase	+	1.11.1.6
116257	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31970	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
31970	gelatinase	+
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
116257	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
116257	urease	-	3.5.1.5
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
116257	-	-	-	+	-	+	+	+	-	-	+	+	-	+	-	+	+	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
116257	not determinedn.d.	-	-	+/-	-	-	+/-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+/-	+	+	+	+	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	+/-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
15790	rhizosphere of Allium victorialis var. platyphyllum	Allium victorialis var. platyphyllum	Ulleung island	Republic of Korea	KOR	Asia
67770	Rhizosphere of Allium victorialis var. platyphyllum (a type of wild edible greens)	Allium victorialis var. platyphyllum	Ulleung Island	Republic of Korea	KOR	Asia
67771	From rhizospheric soil of `Allium victorialis` var. `platyphyllum`			Republic of Korea	KOR	Asia
116257	Environment, Rhizosphere of Allium victorialis var. Platyphyllum		Ulleung island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ673873 (>99% sequence identity) for Agromyces from Microbeatlas

Aquatic Samples	38
Soil Samples	271
Animal Samples	92
Plant Samples	12
Total Samples	413

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15790	1	Risk group (German classification) According to TRBA 466
116257	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	ASM974938v1 assembly for Agromyces allii JCM 13584	contig	GCA_009749385	393607.3	2995708883	393607	65.05
124043	ASM3952923v1 assembly for Agromyces allii JCM 13584	scaffold	GCA_039529235			393607	47.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15790	Agromyces allii strain UMS-62 16S ribosomal RNA gene, partial sequence	DQ673873	1483		393607

GC content

@ref	GC-content (mol%)	Method
15790	71.1
31970	71.2
67770	71.1	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: Agromyces allii JCM 13584
NCBI: GCA_009749385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.90	no
125439	motility	BacteriaNetⓘ	no	52.40	no
125439	gram_stain	BacteriaNetⓘ	positive	96.80	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: Agromyces allii strain JCM 13584
PATRIC: 393607.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.68	no
125438	anaerobic	anaerobicⓘ	no	98.91	yes
125438	spore-forming	spore-formingⓘ	no	71.15	no
125438	aerobic	aerobicⓘ	yes	91.80	yes
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	no	93.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces laixinhei sp. nov. isolated from bat feces in China.	Cheng Y, Bai Y, Huang Y, Yang J, Lu S, Jin D, Pu J, Zheng H, Li J, Huang Y, Wang S, Xu J	J Microbiol	10.1007/s12275-021-0546-5	2021
Phylogeny	Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum.	Jung SY, Lee SY, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.64733-0	2007

References

#15790	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21551
#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 )
#28225	IJSEM 588 2007 ( DOI 10.1099/ijs.0.64733-0 , PubMed 17329790 )
#31970	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 #28225
#37761	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68371	Automatically annotated from API 50CH acid .
#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 .
#116257	Collection of Institut Pasteur ; Curators of the CIP; CIP 109546
#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 allii (DSM 21551, JCM 13584, KCTC 19181)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009749385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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