Kitasatospora viridis (DSM 44826, AS 4.1878, 52108a)

Name: Kitasatospora viridis (DSM 44826, AS 4.1878, 52108a)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14867

Type strain

Strain Designation 52108a

Culture col. no. DSM 44826 AS 4.1878 52108a CGMCC 4.1878 JCM 14111

NCBI tax ID(s) 281105

Special Collections DSMZ JCM Literature strains

Links

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

spore-forming Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138010

AS 4.1878,DSM 44826,JCM 14111,CGMCC 4.1878

@ref 20215

Last LPSN update 2025-12-16 09:50:27

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Kitasatospora

Species Kitasatospora viridis

Full scientific name Kitasatospora viridis Liu et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Confidence
31330	positive
125439	positive	100
125439		90.5

Pigmentation

31330

Productionno

Multimedia

@ref:	12008
multimedia content:	DSM_44826.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44826.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12008	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12008	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12008	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	Medium recipe at MediaDive	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12008	positive	growth	28	mesophilic
31330	positive	growth	10-37
31330	positive	optimum	23.5	psychrophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31330	positive	optimum	5.5
31330	positive	growth	04-07	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31330	aerobe
125439	obligate aerobe	99.5

Spore formation

@ref	Spore formation	Confidence
31330
125439		94.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31330	NaCl	positive	growth	<10 %
31330	NaCl	positive	optimum	5 %

Observation

@ref	Observation
31330	aggregates in chains
67770	quinones: MK-9(H₆), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31330	16449 ChEBI	alanine	+	carbon source
31330	29016 ChEBI	arginine	+	carbon source
31330	17057 ChEBI	cellobiose	+	carbon source
31330	28757 ChEBI	fructose	+	carbon source
31330	28260 ChEBI	galactose	+	carbon source
31330	24265 ChEBI	gluconate	+	carbon source
31330	17234 ChEBI	glucose	+	carbon source
31330	29987 ChEBI	glutamate	+	carbon source
31330	27570 ChEBI	histidine	+	carbon source
31330	17716 ChEBI	lactose	+	carbon source
31330	17306 ChEBI	maltose	+	carbon source
31330	29864 ChEBI	mannitol	+	carbon source
31330	37684 ChEBI	mannose	+	carbon source
31330	28053 ChEBI	melibiose	+	carbon source
31330	28044 ChEBI	phenylalanine	+	carbon source
31330	16634 ChEBI	raffinose	+	carbon source
31330	26546 ChEBI	rhamnose	+	carbon source
31330	15963 ChEBI	ribitol	+	carbon source
31330	17814 ChEBI	salicin	+	carbon source
31330	30911 ChEBI	sorbitol	+	carbon source
31330	17992 ChEBI	sucrose	+	carbon source
31330	26986 ChEBI	threonine	+	carbon source
31330	27082 ChEBI	trehalose	+	carbon source
31330	17151 ChEBI	xylitol	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	taurine degradation	100	1 of 1
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	aerobactin biosynthesis	100	1 of 1
66794	starch degradation	100	10 of 10
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	enterobactin biosynthesis	100	3 of 3
66794	aspartate and asparagine metabolism	100	9 of 9
66794	4-hydroxymandelate degradation	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	mannosylglycerate biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	gluconeogenesis	100	8 of 8
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	proline metabolism	90.91	10 of 11
66794	metabolism of disaccharids	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	allantoin degradation	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	tryptophan metabolism	84.21	32 of 38
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	histidine metabolism	82.76	24 of 29
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	80.85	76 of 94
66794	methionine metabolism	80.77	21 of 26
66794	factor 420 biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	degradation of sugar acids	80	20 of 25
66794	myo-inositol biosynthesis	80	8 of 10
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	propionate fermentation	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	tyrosine metabolism	78.57	11 of 14
66794	degradation of hexoses	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	citric acid cycle	71.43	10 of 14
66794	aclacinomycin biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	phenol degradation	70	14 of 20
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	urea cycle	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	degradation of pentoses	67.86	19 of 28
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	oxidative phosphorylation	64.84	59 of 91
66794	d-xylose degradation	63.64	7 of 11
66794	cholesterol biosynthesis	63.64	7 of 11
66794	carotenoid biosynthesis	63.64	14 of 22
66794	arginine metabolism	62.5	15 of 24
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	carnitine metabolism	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	cysteine metabolism	61.11	11 of 18
66794	polyamine pathway	60.87	14 of 23
66794	coenzyme M biosynthesis	60	6 of 10
66794	bacilysin biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	glutathione metabolism	57.14	8 of 14
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	alginate biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	hydrogen production	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	chlorophyll metabolism	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
12008	soil rhizosphere of wild tea plant (Camellia oleifera)	Camellia oleifera	Jiangxi	China	CHN	Asia
67770	Rhizosphere soil of wild tea plants (Camellia oleifera) growing on Jiangxi Agric. Univ.	Camellia oleifera	Jiangxi Province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12008	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM782981v1 assembly for Kitasatospora viridis DSM 44826	contig	GCA_007829815	281105.3	2818991472	281105	72.74
124043	ASM3952953v1 assembly for Kitasatospora viridis JCM 14111	scaffold	GCA_039529535			281105	55.98

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31330	Kitasatospora viridis 16S ribosomal RNA gene, partial sequence	AY613990	1422		281105

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Kitasatospora viridis DSM 44826
NCBI: GCA_007829815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.40	no
125439	motility	BacteriaNetⓘ	no	90.50	no
125439	gram_stain	BacteriaNetⓘ	positive	100.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Kitasatospora viridis strain DSM 44826
PATRIC: 281105.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.89	yes
125438	anaerobic	anaerobicⓘ	no	97.41	no
125438	spore-forming	spore-formingⓘ	yes	89.27	yes
125438	thermophilic	thermophileⓘ	no	97.49	yes
125438	aerobic	aerobicⓘ	yes	88.55	yes
125438	flagellated	motile2+ⓘ	no	87.10	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kitasatospora cathayae sp. nov., a novel endophytic actinomycete isolated from the leaves of Cathaya argyrophylla.	Zheng Y, Mo P, Li J, Zhou Z, Huang K, Luo Y, Xie P, Wang Y.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006406	2024
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 )
#27644	IJSEM 707 2005 ( DOI 10.1099/ijs.0.63329-0 , PubMed 15774648 )
#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
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Kitasatospora viridis (DSM 44826, AS 4.1878, 52108a)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_007829815

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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