Clavibacter michiganensis subsp. sepedonicus (DSM 20744, ATCC 33113, ICPB CS101)

Name: Clavibacter michiganensis subsp. sepedonicus (DSM 20744, ATCC 33113, ICPB CS101)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7294

Type strain

Strain Designation C-1

Culture col. no. DSM 20744 ATCC 33113 ICPB CS101 NCPPB 2137 CCUG 23908 10 more

NCBI tax ID(s) 31964

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- ATCC <- NCPPB <- ICPB <- H.N. Racicot, C-1 JCM <-- ICMP 2535 <-- D. W. Dye CB5 <-- ICPB CS101 <-- H. N. Racicot C1.

Links

Clavibacter michiganensis subsp. sepedonicus C-1 is a plant pathogen that was isolated from Solanum tuberosum.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1833

LMG 2889,ATCC 33113,ICMP 2535,NCPPB 2137,PDDCC 2535,CCUG 23908,CIP 104844,JCM 9667,VKM Ac-1405,CECT 4886,CFBP 2049,KACC 20123,DSM 20744

@ref 20215

Last LPSN update 2026-05-29 08:26:36

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Clavibacter

Species Clavibacter michiganensis subsp. sepedonicus

Full scientific name Clavibacter michiganensis subsp. sepedonicus corrig. (Spieckermann and Kotthoff 1914) Davis et al. 1984

Synonyms (7)

Clavibacter michiganense subsp. sepedonicus
Clavibacter sepedonicus
Clavibacter michiganensis subsp. sepedonicum
Clavibacter michiganense subsp. sepedonicum
"Bacterium sepedonicum"
Corynebacterium sepedonicum
Corynebacterium michiganense subsp. sepedonicum

BacDive ID	Other strains from Clavibacter michiganensis subsp. sepedonicus (1)	Type strain
179143	C. michiganensis subsp. sepedonicus IMET 11009, STI11009

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	97.245
125438		93.5
125438	positive	90.001

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9053	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
9053	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9053	positive	growth	25
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.14

Observation

67770

Observationquinones: MK-9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	ribulose monophosphate pathway	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	aerobactin biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	metabolism of disaccharids	90.91	10 of 11
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolysis	82.35	14 of 17
66794	lipoate biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	pyrimidine metabolism	77.78	35 of 45
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	palmitate biosynthesis	77.27	17 of 22
66794	butanoate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	leucine metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	tryptophan metabolism	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	alanine metabolism	62.07	18 of 29
66794	methionine metabolism	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	oxidative phosphorylation	60.44	55 of 91
66794	Entner Doudoroff pathway	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	degradation of pentoses	53.57	15 of 28
66794	histidine metabolism	51.72	15 of 29
66794	phenylmercury acetate degradation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	ascorbate metabolism	50	11 of 22
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	lysine metabolism	47.62	20 of 42
66794	carotenoid biosynthesis	45.45	10 of 22
66794	arachidonic acid metabolism	44.44	8 of 18
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	glycine metabolism	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sphingosine metabolism	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	heme metabolism	28.57	4 of 14
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	CMP-KDO biosynthesis	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	sulfate reduction	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
9053	Solanum tuberosum	Solanum tuberosum
47885	Solanum tuberosum,ringrot	Solanum tuberosum
67770	Potato (Solanum tuberosum)	Solanum tuberosum	Canada	CAN	North America

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
9053		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	ASM6922v1 assembly for Clavibacter sepedonicus ATCC33113	complete	GCA_000069225	31964.6	642555124	31964	98.11
124043	ASM5106851v1 assembly for Clavibacter sepedonicus LMG 2889	contig	GCA_051068515			31964	55.74

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clavibacter michiganensis subsp. sepedonicus partial 16S rRNA gene, type strain DSM 20744	AM410694	1492	31964
20218	Clavibacter michiganensis subsp. sepedonicus partial 16S rRNA gene, strain LMG2889T	FR728289	445	31964
20218	Clavibacter michiganensis sepedonicus LMG 2889 16S-23S rRNA spacer region	U09382	470	28447
20218	Clavibacter michiganensis strain LMG 2889 16S ribosomal RNA, partial sequence	U09764	1492	28447
20218	Clavibacter michiganensis subsp. sepedonicus strain Ac-1405 16S-23S ribosomal RNA intergenic spacer, partial sequence	HQ394204	445	31964

GC content

67770

GC-content (mol%)72.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM6922v1 assembly for Clavibacter sepedonicus ATCC33113
BV-BRC: 31964.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.14	no
125439	gram_stain	BacteriaNetⓘ	positive	97.25	no
125439	motility	BacteriaNetⓘ	no	75.95	no
125439	spore_formation	BacteriaNetⓘ	no	85.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clavibacter michiganensis subsp. sepedonicus ATCC33113
NCBI: GCA_000069225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.00	no
125438	anaerobic	anaerobicⓘ	no	95.69	no
125438	aerobic	aerobicⓘ	yes	84.07	no
125438	spore-forming	spore-formingⓘ	no	77.49	no
125438	thermophilic	thermophileⓘ	no	94.88	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
	Pest categorisation of Clavibacter sepedonicus.	EFSA Panel on Plant Health (EFSA PLH Panel), Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappala L, Van der Wolf J, Kaluski T, Pautasso M, Jacques MA.	EFSA J	10.2903/j.efsa.2019.5670	2019
Phylogeny	Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains.	Osdaghi E, Rahimi T, Taghavi SM, Ansari M, Zarei S, Portier P, Briand M, Jacques MA.	Appl Environ Microbiol	10.1128/aem.02873-19	2020
	Detection of Potato Pathogen Clavibacter sepedonicus by CRISPR/Cas13a Analysis of NASBA Amplicons.	Khmeleva SA, Kurbatov LK, Ptitsyn KG, Timoshenko OS, Morozova DD, Suprun EV, Radko SP, Lisitsa AV.	Int J Mol Sci	10.3390/ijms252212218	2024
	Synthesis, toxicity evaluation and determination of possible mechanisms of antimicrobial effect of arabinogalactane-capped selenium nanoparticles.	Lesnichaya M, Perfileva A, Nozhkina O, Gazizova A, Graskova I.	J Trace Elem Med Biol	10.1016/j.jtemb.2021.126904	2022
	Bacterial ring rot of potato caused by Clavibacter sepedonicus: A successful example of defeating the enemy under international regulations.	Osdaghi E, van der Wolf JM, Abachi H, Li X, De Boer SH, Ishimaru CA.	Mol Plant Pathol	10.1111/mpp.13191	2022
	Starch-capped sulphur nanoparticles synthesised from bulk powder sulphur and their anti-phytopathogenic activity against Clavibacter sepedonicus.	Lesnichaya M, Gazizova A, Perfileva A, Nozhkina O, Graskova I, Sukhov B.	IET Nanobiotechnol	10.1049/nbt2.12044	2021

References

#9053	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20744
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#47885	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 23908
#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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Clavibacter michiganensis subsp. sepedonicus (DSM 20744, ATCC 33113, ICPB CS101)

Name and taxonomic classification

Morphology

Cell morphology

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_000069225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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