Actinorugispora endophytica (DSM 46770, JCM 30099, KCTC 29480)

Name: Actinorugispora endophytica (DSM 46770, JCM 30099, KCTC 29480)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131391

Type strain

Culture col. no. DSM 46770 JCM 30099 KCTC 29480 YIM 690008

NCBI tax ID(s) 1605990

Special Collections DSMZ JCM KCTC

History <- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM 690008 <- J. Li W.-J. Li YIM 690008. <- Wen-jun Li, YIM 690008

Links

Actinorugispora endophytica DSM 46770 is an aerobe bacterium that was isolated from surface-sterilized roots of Daucus carota.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403184

KCTC 29480,JCM 30099,DSM 46770

@ref 20215

Last LPSN update 2026-02-09 11:31:27

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Nocardiopsidaceae

Genus Actinorugispora

Species Actinorugispora endophytica

Full scientific name Actinorugispora endophytica Liu et al. 2015

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	91.5
125438	90.626	positive
125439	98.3	positive

Multimedia

@ref:	22618
multimedia content:	DSM_46770.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_46770.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22618	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
22618	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22618	positive	growth	28
67770	positive	growth	28
67771	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	aerobe	96.5

Observation

67770

Observationquinones: MK-10(H₄), MK-10(H₆), MK-10(H₈), MK-10(H₂)

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	denitrification	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	glycogen biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	myo-inositol biosynthesis	100	10 of 10
66794	heme metabolism	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	flavin biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	vitamin B12 metabolism	85.29	29 of 34
66794	purine metabolism	84.04	79 of 94
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	metabolism of disaccharids	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	D-cycloserine biosynthesis	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	degradation of hexoses	77.78	14 of 18
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	tryptophan metabolism	76.32	29 of 38
66794	pyrimidine metabolism	75.56	34 of 45
66794	sulfopterin metabolism	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	gluconeogenesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	histidine metabolism	72.41	21 of 29
66794	tyrosine metabolism	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	degradation of sugar acids	68	17 of 25
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	alanine metabolism	65.52	19 of 29
66794	degradation of pentoses	64.29	18 of 28
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	methionine metabolism	61.54	16 of 26
66794	lipoate biosynthesis	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	carotenoid biosynthesis	54.55	12 of 22
66794	sulfate reduction	53.85	7 of 13
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	kanosamine biosynthesis II	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	chlorophyll metabolism	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	carnitine metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	catecholamine biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
22618	surface-sterilized roots of Daucus carota	Daucus carota	Republic of Korea	KOR	Asia
67770	Daucus carota (wild carrot) from South Korea	Daucus carota
67771	From Daucus carota(plant) collected from South Korea.		China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22618	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM436307v1 assembly for Actinorugispora endophytica DSM 46770	scaffold	GCA_004363075	1605990.4	2795385473	1605990	67.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22618	Actinorugispora endophytica strain YIM 690008 16S ribosomal RNA gene, partial sequence	KM925046	1542		1605990

GC content

@ref	GC-content (mol%)	Method
22618	63.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Actinorugispora endophytica DSM 46770
NCBI: GCA_004363075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	84.20	no
125439	motility	BacteriaNetⓘ	no	84.40	no
125439	gram_stain	BacteriaNetⓘ	positive	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinorugispora endophytica strain DSM 46770
PATRIC: 1605990.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.63	no
125438	anaerobic	anaerobicⓘ	no	94.84	yes
125438	spore-forming	spore-formingⓘ	yes	81.68	no
125438	thermophilic	thermophileⓘ	no	92.96	yes
125438	aerobic	aerobicⓘ	yes	80.42	no
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus.	Karmakar B, Saha B, Jana K, Gupta Bhattacharya S.	J Biol Chem	10.1074/jbc.ra120.015801	2020
Phylogeny	Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota.	Liu MJ, Zhu WY, Li J, Zhao GZ, Xiong Z, Park DJ, Hozzein WN, Kim CJ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.000304	2015

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 )
#22618	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46770
#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;
#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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Actinorugispora endophytica (DSM 46770, JCM 30099, KCTC 29480)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004363075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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