Name: Agromyces flavus DSM 22059
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7283

Type strain:

Species: Agromyces flavus

Culture col. no.: DSM 22059, CCM 7623, KCTC 19578, CPCC 202695, JCM 30488, NBRC 109064

Strain history: <- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

NCBI tax ID(s): 589382 (species)

SI-ID 398772

DSM 22059

Section

Agromyces flavus DSM 22059 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil sample.

Gram-positive
aerobe
mesophilic
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 flavus**
	Full Scientific Name (LPSN)	Agromyces flavus Chen et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69223]	Colony color	Ivory (1014)
[Ref.: #69223]	Cultivation medium used	suter without tyrosine

[Ref.: #69223]	Colony color	Lemon yellow (1012)
[Ref.: #69223]	Cultivation medium used	ISP 2

[Ref.: #69223]	Colony color	Lemon yellow (1012)
[Ref.: #69223]	Cultivation medium used	ISP 6

[Ref.: #69223]	Colony color	Light ivory (1015)
[Ref.: #69223]	Cultivation medium used	ISP 3

[Ref.: #69223]	Colony color	Zinc yellow (1018)
[Ref.: #69223]	Cultivation medium used	ISP 4

[Ref.: #69223]	Colony color	Zinc yellow (1018)
[Ref.: #69223]	Cultivation medium used	ISP 5

[Ref.: #69223]	Colony color	Zinc yellow (1018)
[Ref.: #69223]	Cultivation medium used	ISP 7

[Ref.: #69223]	Colony color	Zinc yellow (1018)
[Ref.: #69223]	Cultivation medium used	suter with tyrosine

[Ref.: #69223]	Pigment production	no
[Ref.: #69223]	Pigment name	Melanin
[Ref.: #69223]	Pigment production	no
[Ref.: #69223]	Pigment name	soluble pigment

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	ISP 2

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	ISP 3

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	ISP 4

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	ISP 5

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	ISP 6

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	ISP 7

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69223]	Multicellular complex forming ability	no
[Ref.: #69223]	Multicellular complex name	Aerial mycelium
[Ref.: #69223]	Medium Name (multicellularity)	suter without tyrosine

Multimedia content

[Ref.: #69223]

Caption:

Plates (92, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69223]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69223]

Caption:

Plates (92, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69223]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16113]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #16113]

Culture medium growth

[Ref.: #16113]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16113]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16113]	growth	28 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #16113]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %94
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.987

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69223]		NaCl		growth	0-10	%

[Ref.: #67770]

Observation

quinones: MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69223]	arabinose ChEBI	+	growth
[Ref.: #69223]	cellulose ChEBI	+/-	growth
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #69223]	fructose ChEBI	+	growth
[Ref.: #69223]	glucose ChEBI	+	growth
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69223]	inositol ChEBI	+/-	growth
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69223]	mannose ChEBI	+	growth
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #69223]	raffinose ChEBI	+/-	growth
[Ref.: #69223]	rhamnose ChEBI	+	growth
[Ref.: #69223]	sucrose ChEBI	+	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69223]	xylose ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym, API Coryne
[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, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[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, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69223]	3717	-	-	-	-	-	-	+	-	-	+	+/-	not determinedn.d.	-	-	-	-	-	-	-	-	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.: #69223]	5901	not determinedn.d.	-	+/-	+	-	+	+	+	+/-	-	+/-	-	+	-	-	+	+	-	-	-

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

[Ref.: #16113]	Sample type/isolated from	soil sample
[Ref.: #16113]	Geographic location (country and/or sea, region)	Qinghai Province, Tibet plateau
[Ref.: #16113]	Country	China
[Ref.: #16113]	Country ISO 3 Code	CHN
[Ref.: #16113]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Qinghai Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from the Qinghai-Tibet plateau
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #16113]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #16113]	Agromyces flavus strain CPCC 202695 16S ribosomal RNA gene, partial sequence	FJ529717	1466	ENA	589382 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces flavus CPCC 202695	GCA_004366335	contig	GenBank	589382 tax ID
[Ref.: #66792]	Agromyces flavus CPCC 202695	GCA_900104685	chromosome	GenBank	589382 tax ID	*
[Ref.: #66792]	Agromyces flavus strain CCM 7623	589382.12	wgs	PATRIC	589382 tax ID	*
[Ref.: #66792]	Agromyces flavus strain CPCC 202695	589382.3	complete	PATRIC	589382 tax ID	*
[Ref.: #66792]	Agromyces flavus strain CPCC 202695	589382.7	wgs	PATRIC	589382 tax ID	*
[Ref.: #66792]	Agromyces flavus CPCC 202695	2681812891	draft	JGI IMG/M	589382 tax ID	*

[Ref.: #16113]

GC-content

70.9 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Agromyces flavus strain CPCC 202695 PATRIC: 589382.3
[Ref.: #69481]	spore-forming	no	94	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces flavus strain CPCC 202695 PATRIC: 589382.3
[Ref.: #69480]	gram-positive	yes	93.815	yes
[Ref.: #69480]	anaerobic	no	99.696	yes
[Ref.: #69480]	halophile	no	88.936	no
[Ref.: #69480]	spore-forming	no	92.054	no
[Ref.: #69480]	glucose-util	yes	85.706	no
[Ref.: #69480]	thermophile	no	98.815	yes
[Ref.: #69480]	flagellated	no	98.08	no
[Ref.: #69480]	aerobic	yes	95.982	yes
[Ref.: #69480]	motile	no	88.991	no
[Ref.: #69480]	glucose-ferment	no	89.299	yes

Availability in culture collections External links

[Ref.: #16113]

Culture collection no.

DSM 22059, CCM 7623, KCTC 19578, CPCC 202695, JCM 30488, NBRC 109064

[Ref.: #76734]

SI-ID 398772

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces flavus sp. nov., an actinomycete isolated from soil.	Chen J, Chen HM, Zhang YQ, Wei YZ, Li QP, Liu HY, Su J, Zhang YQ, Yu LY	Int J Syst Evol Microbiol	10.1099/ijs.0.023242-0	2010	*

References

#16113

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22059

#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 )

#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;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69223

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#76734

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-ID398772.1 )

* These data were automatically processed and therefore are not curated

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Search for species Agromyces flavus in external resources:
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Agromyces flavus strain CPCC 202695

Agromyces flavus strain CPCC 202695

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