Name: Agromyces binzhouensis OAct-353
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132534

Type strain:

Species: Agromyces binzhouensis

Strain Designation: OAct-353, OAct353

Culture col. no.: DSM 28305, CGMCC 4.7180, NRRL B-59115, JCM 32487

Strain history: CGMCC 4.7180 <-- J. Li; Ocean Univ. of China, China; OAct353.

NCBI tax ID(s): 1817495 (species)

SI-ID 404915

DSM 28305

Special Collections

Section

Agromyces binzhouensis OAct-353 is an aerobe, heterotroph, Gram-positive bacterium that forms circular colonies and was isolated from soil from a coastal wetland river delta.

colony-forming
Gram-positive
rod-shaped
aerobe
heterotroph
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 binzhouensis**
	Full Scientific Name (LPSN)	Agromyces binzhouensis Chen et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43631]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.724

[Ref.: #43631]	Cell length	0.4-2 µm

[Ref.: #43631]	Cell width	0.2-0.7 µm

[Ref.: #43631]	Cell shape	rod-shaped

[Ref.: #69480]	Motility	no Confidence in %92.5

[Ref.: #43631]	Colony size	0.5-1 mm
[Ref.: #43631]	Colony color	Yellow
[Ref.: #43631]	Colony shape	circular
[Ref.: #43631]	Incubation period	4 days
[Ref.: #43631]	Cultivation medium used	Yeast extract-malt extract agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43631]

Culture medium

Yeast extract-malt extract agar

[Ref.: #43631]

Culture medium growth

[Ref.: #24323]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #24323]

Culture medium growth

[Ref.: #24323]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24323]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24323]	growth	28 °C
[Ref.: #43631]	growth	12-36 °C
[Ref.: #43631]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43631]			optimum	7
[Ref.: #43631]			growth	5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43631]	Oxygen tolerance	aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %93.643

[Ref.: #43631]

Nutrition type

heterotroph

[Ref.: #43631]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43631]		NaCl		growth	0-10	%(w/v)
[Ref.: #43631]		NaCl		optimum	2-3	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-12, MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43631]	arbutin ChEBI	+	oxidation
[Ref.: #43631]	casein	-	hydrolysis
[Ref.: #43631]	D-mannitol ChEBI	+	oxidation
[Ref.: #43631]	D-psicose ChEBI	+	oxidation
[Ref.: #43631]	D-ribose ChEBI	+	oxidation
[Ref.: #43631]	D-xylose ChEBI	+	oxidation
[Ref.: #43631]	esculin ChEBI	-	hydrolysis
[Ref.: #43631]	gelatin ChEBI	-	hydrolysis
[Ref.: #43631]	glycerol ChEBI	+	oxidation
[Ref.: #43631]	L-alaninamide ChEBI	+	oxidation
[Ref.: #43631]	L-arabinose ChEBI	+	oxidation
[Ref.: #43631]	methyl beta-D-galactoside ChEBI	+	oxidation
[Ref.: #43631]	nitrate ChEBI	-	reduction
[Ref.: #43631]	pyruvate ChEBI	+	oxidation
[Ref.: #43631]	raffinose ChEBI	+	oxidation
[Ref.: #43631]	salicin ChEBI	+	oxidation
[Ref.: #43631]	starch ChEBI	-	hydrolysis
[Ref.: #43631]	sucrose ChEBI	+	oxidation
[Ref.: #43631]	thymidine ChEBI	+	oxidation
[Ref.: #43631]	thymidine 5'-monophosphate ChEBI	+	oxidation
[Ref.: #43631]	tween 40 ChEBI	+	oxidation
[Ref.: #43631]	tween 80 ChEBI	+	oxidation
[Ref.: #43631]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43631]		hydrogen sulfide ChEBI	no
[Ref.: #43631]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43631]	acid phosphatase	+	3.1.3.2
[Ref.: #43631]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43631]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43631]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43631]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43631]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43631]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43631]	beta-galactosidase	+	3.2.1.23
[Ref.: #43631]	beta-glucosidase	-	3.2.1.21
[Ref.: #43631]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43631]	catalase	-	1.11.1.6
[Ref.: #43631]	cystine arylamidase	+	3.4.11.3
[Ref.: #43631]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43631]	esterase (C 4)	+
[Ref.: #43631]	esterase Lipase (C 8)	+
[Ref.: #43631]	leucine arylamidase	+	3.4.11.1
[Ref.: #43631]	lipase (C 14)	-
[Ref.: #43631]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43631]	phosphohydrolase	-
[Ref.: #43631]	pyrazinamidase	+	3.5.1.B15
[Ref.: #43631]	pyrrolidonyl arylamidase	-	3.4.19.3
[Ref.: #43631]	trypsin	-	3.4.21.4
[Ref.: #43631]	urease	-	3.5.1.5
[Ref.: #43631]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24323]	Sample type/isolated from	soil from a coastal wetland river delta
[Ref.: #24323]	Geographic location (country and/or sea, region)	Shandong, Binzhou, Yellow River delta
[Ref.: #24323]	Country	China
[Ref.: #24323]	Country ISO 3 Code	CHN
[Ref.: #24323]	Continent	Asia

[Ref.: #43631]	Sample type/isolated from	a soil sample collected from a coastal wetland of the Yellow River delta
[Ref.: #43631]	Geographic location (country and/or sea, region)	Binzhou, Shandong
[Ref.: #43631]	Country	China
[Ref.: #43631]	Country ISO 3 Code	CHN
[Ref.: #43631]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from a coastal wetland of the Yellow River delta in Binzhou
[Ref.: #67770]	Geographic location (country and/or sea, region)	Shandong
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#River (Creek)
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Wetland (Swamp)

What are isolation sources categories?

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

[Ref.: #24323]

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.: #24323]	Agromyces binzhouensis strain OAct353 16S ribosomal RNA gene, partial sequence	KC493987	1451	GenBank ENA	1817495 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces binzhouensis CGMCC 4.7180	GCA_004135055	contig	GenBank ENA	1817495 tax ID
[Ref.: #66792]	Agromyces binzhouensis strain CGMCC 4.7180	1817495.5	wgs	PATRIC	1817495 tax ID	*
[Ref.: #66792]	Agromyces binzhouensis CGMCC 4.7180	2866589525	draft	JGI IMG/M	1817495 tax ID	*

[Ref.: #24323]

GC-content

69.6 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces binzhouensis strain CGMCC 4.7180 PATRIC: 1817495.5
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.724	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.87	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	73.148	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	93.643	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92.5	no

Availability in culture collections External links

[Ref.: #24323]

Culture collection no.

DSM 28305, CGMCC 4.7180, NRRL B-59115, JCM 32487

[Ref.: #90860]

SI-ID 404915

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov., isolated from the gut of larvae of Protaetia brevitarsis seulensis, reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and emended description of the genus Pseudolysinimonas.	Lee SA, Heo J, Kim MA, Tamura T, Saitou S, Kwon SW, Weon HY	Int J Syst Evol Microbiol	10.1099/ijsem.0.004669	2021	*
Phylogeny	Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta.	Chen Z, Guan Y, Wang J, Li J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001022	2016	*

References

#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 )

#24323

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28305

#43631

Zhirong Chen, Yingying Guan, Jingjing Wang and Jing Li: Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta. IJSEM 66: 2278 - 2283 2016 ( DOI 10.1099/ijsem.0.001022 , PubMed 26977901 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#90860

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-ID404915.1 )

* These data were automatically processed and therefore are not curated

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Agromyces binzhouensis strain CGMCC 4.7180

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