Name: Microbacterium ginsengiterrae DSM 24823
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7455

Type strain:

Species: Microbacterium ginsengiterrae

Culture col. no.: DSM 24823, JCM 15516, KCTC 19526, DCY 37, NBRC 110802

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 546115 (species)

SI-ID 374135

JCM15516, KCTC 19526, DSM 24823

Section

Microbacterium ginsengiterrae DSM 24823 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of ginseng field.

Gram-positive
rod-shaped
spore-forming
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	*Microbacterium*
	Species	**Microbacterium ginsengiterrae**
	Full Scientific Name (LPSN)	Microbacterium ginsengiterrae Kim et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29554]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29554]	Cell length	1.5-2 µm

[Ref.: #29554]	Cell width	0.5-0.7 µm

[Ref.: #29554]	Cell shape	rod-shaped

[Ref.: #29554]	Motility	no

[Ref.: #29554]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17780]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17780]

Culture medium growth

[Ref.: #17780]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17780]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17780]	growth	28 °C
[Ref.: #29554]	growth	15-45 °C
[Ref.: #29554]	optimum	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #17780]	Temperature range	mesophilic
[Ref.: #29554]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29554]			optimum	7
[Ref.: #29554]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29554]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29554]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.828

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29554]		NaCl		growth	01-08	%
[Ref.: #29554]		NaCl		optimum	01-08	%

[Ref.: #29554]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-12, MK-13
[Ref.: #67771]	Observation	quinones: MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29554]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #29554]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #29554]	rhamnose ChEBI	+	carbon source
[Ref.: #29554]	ribose ChEBI	+	carbon source
[Ref.: #29554]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29554]	catalase	+	1.11.1.6
[Ref.: #29554]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29554]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	degradation of sugar acids	88	22 of 25
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	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]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #17780]	Sample type/isolated from	soil of ginseng field
[Ref.: #17780]	Country	Republic of Korea
[Ref.: #17780]	Country ISO 3 Code	KOR
[Ref.: #17780]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil, ginseng field
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

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

[Ref.: #17780]

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.: #17780]	Microbacterium ginsengiterrae strain DCY37 16S ribosomal RNA gene, partial sequence	EU873314	1427	ENA	546115 tax ID
[Ref.: #29554]	Microbacterium ginsengiterrae strain DCY37 16S ribosomal RNA gene, partial sequence	EU873314.1	1427	GenBank	546115 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microbacterium ginsengiterrae DSM 24823	GCA_014205075	contig	GenBank	546115 tax ID	*
[Ref.: #66792]	Microbacterium ginsengiterrae JCM 15516	GCA_015278215	contig	GenBank	546115 tax ID	*
[Ref.: #66792]	Microbacterium ginsengiterrae strain DSM 24823	546115.4	wgs	PATRIC	546115 tax ID	*
[Ref.: #66792]	Microbacterium ginsengiterrae strain JCM 15516	546115.5	wgs	PATRIC	546115 tax ID	*
[Ref.: #66792]	Microbacterium ginsengiterrae DSM 24823	2870791180	draft	JGI IMG/M	546115 tax ID	*

[Ref.: #17780]	GC-content	64.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29554]	GC-content	64.5 mol%
[Ref.: #67771]	GC-content	64.54 mol%

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: Microbacterium ginsengiterrae strain DSM 24823 PATRIC: 546115.3
[Ref.: #69481]	spore-forming	yes	89	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium ginsengiterrae strain DSM 24823 PATRIC: 546115.4
[Ref.: #69480]	gram-positive	yes	96.322	no
[Ref.: #69480]	anaerobic	no	99.555	yes
[Ref.: #69480]	halophile	no	80.699	no
[Ref.: #69480]	spore-forming	no	85.544	yes
[Ref.: #69480]	glucose-util	yes	84.881	no
[Ref.: #69480]	thermophile	no	99.461	yes
[Ref.: #69480]	aerobic	yes	94.405	no
[Ref.: #69480]	motile	no	88.303	no
[Ref.: #69480]	flagellated	no	97.6	yes
[Ref.: #69480]	glucose-ferment	no	89.182	no

Availability in culture collections External links

[Ref.: #17780]

Culture collection no.

DSM 24823, JCM 15516, KCTC 19526, DCY 37, NBRC 110802

[Ref.: #76902]

SI-ID 374135

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean.	Peng S, Dongying L, Bingxin Y, Mingjun L, Gehong W	Int J Syst Evol Microbiol	10.1099/ijs.0.000116	2015	*
Phylogeny	Microbacterium ginsengiterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim YJ, Kim MK, Bui TPN, Kim HB, Srinivasan S, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.015784-0	2010	*

References

#17780

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24823

#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 )

#29554

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 #25949 (see below)

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#76902

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-ID374135.1 )

#25949

IJSEM 2808 2010 ( DOI 10.1099/ijs.0.015784-0 , PubMed 20081025 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Microbacterium ginsengiterrae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Microbacterium ginsengiterrae strain DSM 24823

Microbacterium ginsengiterrae strain DSM 24823

Change proposal

Change proposal