Name: Agromyces allii UMS-62
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7279

Type strain:

Species: Agromyces allii

Strain Designation: UMS-62

Culture col. no.: DSM 21551, JCM 13584, KCTC 19181, CIP 109546

Strain history: CIP <- 2007, JCM <- 2006, J. H. Yoon, KRIBB, Teajon, South Korea: strain UMS-62

NCBI tax ID(s): 393607 (species)

SI-ID 297114

JCM 13584, KCTC 19181, CIP 109546, DSM 21551

Special Collections

Other strains from Agromyces allii

Section

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
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Agromyces*
	Species	**Agromyces allii**
	Full Scientific Name (LPSN)	Agromyces allii Jung et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31970]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #116257]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.684

[Ref.: #31970]	Cell length	1 µm

[Ref.: #31970]	Cell width	0.3 µm

[Ref.: #31970]	Cell shape	rod-shaped
[Ref.: #116257]	Cell shape	rod-shaped

[Ref.: #31970]	Motility	no
[Ref.: #116257]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93

[Ref.: #31970]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15790]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #15790]

Culture medium growth

[Ref.: #15790]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15790]

Culture medium composition

expand / minimize

[Ref.: #37761]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37761]

Culture medium growth

[Ref.: #37761]

Culture medium composition

expand / minimize

[Ref.: #116257]

Culture medium

CIP Medium 72

[Ref.: #116257]

Culture medium growth

[Ref.: #116257]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15790]	growth	28 °C
[Ref.: #31970]	growth	04-33 °C
[Ref.: #31970]	optimum	30 °C
[Ref.: #37761]	growth	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31970]			optimum	7
[Ref.: #31970]			growth	5.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31970]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #116257]	Oxygen tolerance	obligate aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %91.803

[Ref.: #69481]

Ability of spore formation

no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31970]		NaCl		growth	<3	%

[Ref.: #67770]

Observation

quinones: MK-11, MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31970]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31970]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31970]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	lactose ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	malate ChEBI	+	carbon source
[Ref.: #31970]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31970]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	melibiose ChEBI	+	carbon source
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	nitrate ChEBI	+	reduction
[Ref.: #116257]	nitrate ChEBI	+	reduction
[Ref.: #116257]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	ribose ChEBI	+	carbon source
[Ref.: #31970]	salicin ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #31970]	succinate ChEBI	+	carbon source
[Ref.: #31970]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31970]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116257]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #31970]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31970]	catalase	+	1.11.1.6
[Ref.: #116257]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31970]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #31970]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116257]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116257]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #116257]	11588	not determinedn.d.	-	-	+/-	-	-	+/-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+/-	+	+	+	+	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	+/-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116257]	11944	-	-	-	+	-	+	+	+	-	-	+	+	-	+	-	+	+	+	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15790]	Sample type/isolated from	rhizosphere of Allium victorialis var. platyphyllum
[Ref.: #15790]	Host species	Allium victorialis var. platyphyllum
[Ref.: #15790]	Geographic location (country and/or sea, region)	Ulleung island
[Ref.: #15790]	Country	Republic of Korea
[Ref.: #15790]	Country ISO 3 Code	KOR
[Ref.: #15790]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Rhizosphere of Allium victorialis var. platyphyllum (a type of wild edible greens)
[Ref.: #67770]	Host species	Allium victorialis var. platyphyllum
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ulleung Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From rhizospheric soil of `Allium victorialis` var. `platyphyllum`
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #116257]	Sample type/isolated from	Environment, Rhizosphere of Allium victorialis var. Platyphyllum
[Ref.: #116257]	Geographic location (country and/or sea, region)	Ulleung island
[Ref.: #116257]	Country	Republic of Korea
[Ref.: #116257]	Country ISO 3 Code	KOR
[Ref.: #116257]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15790]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116257]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15790]	Agromyces allii strain UMS-62 16S ribosomal RNA gene, partial sequence	DQ673873	1483	GenBank ENA	393607 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces allii JCM 13584	GCA_009749385	contig	GenBank ENA	393607 tax ID
[Ref.: #66792]	Agromyces allii strain JCM 13584	393607.3	wgs	PATRIC	393607 tax ID	*

[Ref.: #15790]	GC-content	71.1 mol%
[Ref.: #31970]	GC-content	71.2 mol%
[Ref.: #67770]	GC-content	71.1 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Agromyces allii strain JCM 13584 PATRIC: 393607.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces allii strain JCM 13584 PATRIC: 393607.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.684	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.908	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	71.149	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	91.803	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	93	yes

Availability in culture collections External links

[Ref.: #15790]

Culture collection no.

DSM 21551, JCM 13584, KCTC 19181, CIP 109546

[Ref.: #76730]

SI-ID 297114

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 )

#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 (see below)

#37761 ; Curators of the CIP;

#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;
#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76730

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297114.1 )

#116257 Collection of Institut Pasteur ; Curators of the CIP; CIP 109546

#28225

IJSEM 588 2007 ( DOI 10.1099/ijs.0.64733-0 , PubMed 17329790 )

* These data were automatically processed and therefore are not curated

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Agromyces allii strain JCM 13584

Agromyces allii strain JCM 13584

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