Rhodococcus kyotonensis (DSM 45159, CCTCC AB 206088, CIP 109729)

Name: Rhodococcus kyotonensis (DSM 45159, CCTCC AB 206088, CIP 109729)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11045

Type strain

Strain Designation DS472

Culture col. no. DSM 45159 CCTCC AB 206088 CIP 109729 IAM 15415 JCM 23211 1 more

NCBI tax ID(s) 398843

Special Collections DSMZ JCM CIP Literature strains

History DSMZ <- JCM/RIKEN <- IAM <- A. Yokota; DS472 JCM <-- IAM 15415 <-- A. Yokota DS472. CIP <- 2007, JCM <- 2007, IAM <- A. Yokota, Tokyo Univ., Tokyo, Japan: strain DS472

Links

Rhodococcus kyotonensis DS472 is an obligate aerobe, Gram-positive bacterium that was isolated from soil.

Gram-positive obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 309554

DSM 45159,IAM 15415,JCM 23211,CIP 109729

@ref 20215

Last LPSN update 2026-05-29 08:27:28

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Species Rhodococcus kyotonensis

Full scientific name Rhodococcus kyotonensis Li et al. 2007

Synonyms (1)

Rhodococcoides kyotonense

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31989	positive
120521	positive	rod-shaped
125438	positive		90.503

Pigmentation

31989

Productionyes

Multimedia

@ref:	15471
multimedia content:	DSM_45159.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45159.jpg
caption:	Medium 215 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15471	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
15471	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
37827	MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
120521	CIP Medium 116	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15471	positive	growth	28
31989	positive	growth	10-37
31989	positive	optimum	28.5
37827	positive	growth	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
31989	positive	optimum	7
31989	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120521	obligate aerobe
125438	aerobe	90.073
125439	obligate aerobe	98.787

Spore formation

@ref	Spore formation	Confidence
31989
125439		92.306

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31989	NaCl	positive	growth	0-9 %
31989	NaCl	positive	optimum	4.5 %

Observation

67770

Observationquinones: MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31989	4853 ChEBI	esculin	+	hydrolysis
31989	28757 ChEBI	fructose	+	carbon source
31989	28260 ChEBI	galactose	+	carbon source
31989	24265 ChEBI	gluconate	+	carbon source
31989	17234 ChEBI	glucose	+	carbon source
31989	17754 ChEBI	glycerol	+	carbon source
31989	18403 ChEBI	L-arabitol	+	carbon source
31989	29864 ChEBI	mannitol	+	carbon source
31989	17268 ChEBI	myo-inositol	+	carbon source
120521	17632 ChEBI	nitrate	-	reduction
120521	16301 ChEBI	nitrite	-	reduction
31989	26546 ChEBI	rhamnose	+	carbon source
31989	33942 ChEBI	ribose	+	carbon source
31989	30911 ChEBI	sorbitol	+	carbon source
31989	17992 ChEBI	sucrose	+	carbon source
31989	17151 ChEBI	xylitol	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120521	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
31989	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31989	catalase	+	1.11.1.6
120521	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120521	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
31989	urease	+	3.5.1.5
120521	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	acetate fermentation	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	octane oxidation	100	3 of 3
66794	enterobactin biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	3-chlorocatechol degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	starch degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	propanol degradation	100	7 of 7
66794	valine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	glycolysis	88.24	15 of 17
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycine betaine biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	purine metabolism	78.72	74 of 94
66794	serine metabolism	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	glycogen biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	carotenoid biosynthesis	72.73	16 of 22
66794	metabolism of disaccharids	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	non-pathway related	71.05	27 of 38
66794	myo-inositol biosynthesis	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	cysteine metabolism	66.67	12 of 18
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	phenol degradation	65	13 of 20
66794	glutathione metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	ascorbate metabolism	63.64	14 of 22
66794	arginine metabolism	62.5	15 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	methionine metabolism	61.54	16 of 26
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tyrosine metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	cholesterol biosynthesis	54.55	6 of 11
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	creatinine degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	chlorophyll metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	polyamine pathway	34.78	8 of 23
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120521	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15471	soil	Kyoto city	Japan	JPN	Asia
67770	Soil	Kyoto City	Japan	JPN	Asia
120521	Environment, Soil	Kyoto	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15471	1	Risk group (German classification) According to TRBA 466
120521	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2675903021 annotated assembly for Rhodococcoides kyotonense JCM 23211	scaffold	GCA_900188125	398843.7	2675903021	398843	68.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15471	Rhodococcus kyotonensis gene for 16S rRNA, partial sequence	AB269261	1420		398843
124043	Rhodococcus kyotonensis strain DSM 45159 16S ribosomal RNA gene, partial sequence.	KF410355	1357		398843

GC content

@ref	GC-content (mol%)	Method
15471	64.5
67770	64.5	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: IMG-taxon 2675903021 annotated assembly for Rhodococcoides kyotonense JCM 23211
BV-BRC: 398843.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.79	no
125439	gram_stain	BacteriaNetⓘ	positive	72.41	no
125439	motility	BacteriaNetⓘ	no	67.68	no
125439	spore_formation	BacteriaNetⓘ	no	92.31	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus kyotonensis strain JCM 23211
PATRIC: 398843.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.50	no
125438	anaerobic	anaerobicⓘ	no	97.86	yes
125438	spore-forming	spore-formingⓘ	no	54.49	yes
125438	aerobic	aerobicⓘ	yes	90.07	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006229	2024
Phylogeny	Rhodococcus sovatensis sp. nov., an actinomycete isolated from the hypersaline and heliothermal Lake Ursu.	Tancsics A, Mathe I, Benedek T, Toth EM, Atasayar E, Sproer C, Marialigeti K, Felfoldi T, Kriszt B	Int J Syst Evol Microbiol	10.1099/ijsem.0.001514	2017
Phylogeny	Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil.	Li B, Furihata K, Ding LX, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64770-0	2007

References

#15471	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45159
#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 )
#28243	IJSEM 1956 2007 ( DOI 10.1099/ijs.0.64770-0 , PubMed 17766854 )
#31989	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 #28243
#37827	; Curators of the CIP;
#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;
#68382	Automatically annotated from API zym .
#120521	Collection of Institut Pasteur ; Curators of the CIP; CIP 109729
#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 )

Content

About us

Rhodococcus kyotonensis (DSM 45159, CCTCC AB 206088, CIP 109729)

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

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900188125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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