Name: Kitasatospora viridis 52108a
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14867

Type strain:

Species: Kitasatospora viridis

Strain Designation: 52108a

Culture col. no.: DSM 44826, AS 4.1878, JCM 14111, CGMCC 4.1878

Strain history: CGMCC 4.1878 <-- Z. Liu 52108a.

NCBI tax ID(s): 281105 (species)

SI-ID 138010

AS 4.1878, DSM 44826, JCM 14111, CGMCC 4.1878

Section

Kitasatospora viridis 52108a is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil rhizosphere of wild tea plant .

Gram-positive
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	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Kitasatospora*
	Species	**Kitasatospora viridis**
	Full Scientific Name (LPSN)	Kitasatospora viridis Liu et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31330]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31330]	Motility	no

[Ref.: #31330]

Pigment production

Multimedia content

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Caption:

Medium 65 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12008]

Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #12008]	growth	28 °C
[Ref.: #31330]	growth	10-37 °C
[Ref.: #31330]	optimum	23.5 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #12008]	Temperature range	mesophilic
[Ref.: #31330]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31330]			optimum	5.5
[Ref.: #31330]			growth	04-07

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31330]

Oxygen tolerance

aerobe

[Ref.: #31330]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31330]		NaCl		growth	<10	%
[Ref.: #31330]		NaCl		optimum	5	%

[Ref.: #31330]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-9(H₆), MK-9(H₈)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31330]	alanine ChEBI	+	carbon source
[Ref.: #31330]	arginine ChEBI	+	carbon source
[Ref.: #31330]	cellobiose ChEBI	+	carbon source
[Ref.: #31330]	fructose ChEBI	+	carbon source
[Ref.: #31330]	galactose ChEBI	+	carbon source
[Ref.: #31330]	gluconate ChEBI	+	carbon source
[Ref.: #31330]	glucose ChEBI	+	carbon source
[Ref.: #31330]	glutamate ChEBI	+	carbon source
[Ref.: #31330]	histidine ChEBI	+	carbon source
[Ref.: #31330]	lactose ChEBI	+	carbon source
[Ref.: #31330]	maltose ChEBI	+	carbon source
[Ref.: #31330]	mannitol ChEBI	+	carbon source
[Ref.: #31330]	mannose ChEBI	+	carbon source
[Ref.: #31330]	melibiose ChEBI	+	carbon source
[Ref.: #31330]	phenylalanine ChEBI	+	carbon source
[Ref.: #31330]	raffinose ChEBI	+	carbon source
[Ref.: #31330]	rhamnose ChEBI	+	carbon source
[Ref.: #31330]	ribitol ChEBI	+	carbon source
[Ref.: #31330]	salicin ChEBI	+	carbon source
[Ref.: #31330]	sorbitol ChEBI	+	carbon source
[Ref.: #31330]	sucrose ChEBI	+	carbon source
[Ref.: #31330]	threonine ChEBI	+	carbon source
[Ref.: #31330]	trehalose ChEBI	+	carbon source
[Ref.: #31330]	xylitol ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	mannosylglycerate biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	metabolism of disaccharids	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	alanine metabolism	89.66	26 of 29
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	84.21	32 of 38
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	histidine metabolism	82.76	24 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	tyrosine 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]	glycolysis	76.47	13 of 17
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	aclacinomycin biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	cholesterol biosynthesis	63.64	7 of 11
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	bacilysin biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
		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.: #12008]	Sample type/isolated from	soil rhizosphere of wild tea plant (Camellia oleifera)
[Ref.: #12008]	Host species	Camellia oleifera
[Ref.: #12008]	Geographic location (country and/or sea, region)	Jiangxi
[Ref.: #12008]	Country	China
[Ref.: #12008]	Country ISO 3 Code	CHN
[Ref.: #12008]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Rhizosphere soil of wild tea plants (Camellia oleifera) growing on Jiangxi Agric. Univ.
[Ref.: #67770]	Host species	Camellia oleifera
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jiangxi Province
[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
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

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

[Ref.: #12008]

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.: #31330]	Kitasatospora viridis 16S ribosomal RNA gene, partial sequence	AY613990	1422	GenBank	281105 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Kitasatospora viridis DSM 44826	GCA_007829815	contig	GenBank	281105 tax ID	*
[Ref.: #66792]	Kitasatospora viridis strain DSM 44826	281105.3	wgs	PATRIC	281105 tax ID	*
[Ref.: #66792]	Kitasatospora viridis DSM 44826	2818991472	draft	JGI IMG/M	281105 tax ID	*

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: Kitasatospora viridis strain DSM 44826 PATRIC: 281105.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kitasatospora viridis strain DSM 44826 PATRIC: 281105.3
[Ref.: #69480]	motile	no	94.266	yes
[Ref.: #69480]	gram-positive	yes	91.715	yes
[Ref.: #69480]	anaerobic	no	99.366	yes
[Ref.: #69480]	halophile	no	88.883	yes
[Ref.: #69480]	spore-forming	yes	93.988	yes
[Ref.: #69480]	glucose-util	yes	91.751	yes
[Ref.: #69480]	flagellated	no	98.484	yes
[Ref.: #69480]	aerobic	yes	93.121	no
[Ref.: #69480]	thermophile	no	97.944	yes
[Ref.: #69480]	glucose-ferment	no	88.674	no

Availability in culture collections External links

[Ref.: #12008]

Culture collection no.

DSM 44826, AS 4.1878, JCM 14111, CGMCC 4.1878

[Ref.: #83980]

SI-ID 138010

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kitasatospora viridis sp. nov., a novel actinomycete from soil.	Liu Z, Rodriguez C, Wang L, Cui Q, Huang Y, Quintana ET, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.63329-0	2005	*

References

#12008

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44826

#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 )

#31330

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 #27644 (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;

#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 )

#83980

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-ID138010.1 )

#27644

IJSEM 707 2005 ( DOI 10.1099/ijs.0.63329-0 , PubMed 15774648 )

* These data were automatically processed and therefore are not curated

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Kitasatospora viridis strain DSM 44826

Kitasatospora viridis strain DSM 44826

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