Name: Clavibacter michiganensis S 05
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7289

Type strain:

Species: Clavibacter michiganensis

Strain Designation: S 05, SO5

Culture col. no.: CCUG 23363, CIP 104846, DSM 46364, ICPB CM 177, IMET 11518, LMG 7333, NCPPB 2979, PDDCC 2550, JCM 9665, CFBP 2352, CFBP 4999, ICMP 2550, IMSNU 21316, KACC 20122, KCCM 41108, VKM Ac-1403, VTT E-97058

Strain history: ICMP 2550 <-- D. W. Dye CC31 <-- ICPB CM177 <-- Z. Klement SO5.

NCBI tax ID(s): 28447 (species), 33013 (subspecies)

SI-ID 386953

LMG 7333, ICMP 2550, NCPPB 2979, PDDCC 2550, CCUG 23363, CIP 104846, DSM 46364, IMET 11518, JCM 9665, VKM Ac-1403, CFBP 2352, KACC 20122, CFBP 4999, VTT E-97058

Special Collections

Other strains from Clavibacter michiganensis

Section

Clavibacter michiganensis S 05 is a mesophilic, Gram-positive plant pathogen that was isolated from Lycopersicon lycopersicum.

Gram-positive
mesophilic
plant pathogen
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Clavibacter*
	Species	**Clavibacter michiganensis**
	Full Scientific Name (LPSN)	Clavibacter michiganensis corrig. (Smith 1910) Davis et al. 1984

	Synonym	"Bacterium* michiganense"*
	Synonym	Clavibacter michiganense
	Synonym	Corynebacterium michiganense

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %90.437

[Ref.: #69480]	Motility	no Confidence in %92.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12537]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #12537]

Culture medium growth

[Ref.: #12537]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12537]

Culture medium composition

expand / minimize

[Ref.: #12537]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #12537]

Culture medium growth

[Ref.: #12537]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12537]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #12537]			growth	25 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #12537]	Murein short key	B07
[Ref.: #12537]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #67770]

Observation

quinones: MK-9

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #47797]	Sample type/isolated from	Lycopersicon lycopersicum
[Ref.: #47797]	Sampling date	1957
[Ref.: #47797]	Country	Hungary
[Ref.: #47797]	Country ISO 3 Code	HUN
[Ref.: #47797]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Tomato (Lycopercicon esculentum)
[Ref.: #67770]	Host species	Lycopercicon esculentum
[Ref.: #67770]	Country	Hungary
[Ref.: #67770]	Country ISO 3 Code	HUN
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X77435 (>99% sequence identity) for Clavibacter michiganensis from Microbeatlas

Aquatic Samples	10493
Soil Samples	15732
Animal Samples	18473
Plant Samples	10075
Total Samples	54773

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

[Ref.: #12537]	Pathogenicity (plant)	yes
[Ref.: #12537]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #12537]	Clavibacter michiganensis strain DSM 46364 16S ribosomal RNA, partial sequence	NR_115040	1471	GenBank ENA	28447 tax ID
[Ref.: #67770]	C.michiganense (DSM 46364) 16S rRNA gene	X77435	1471	GenBank ENA	28447 tax ID
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603278	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603279	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603280	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603281	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603282	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603283	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603284	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603285	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603286	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603287	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene, partial sequence.	JN603288	1359	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603290	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603291	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603292	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603293	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603294	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603295	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603296	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603297	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603298	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603299	773	GenBank ENA	33013 tax ID	*
[Ref.: #124043]	Clavibacter michiganensis subsp. michiganensis strain PF008 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JN603300	773	GenBank ENA	33013 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis subsp. michiganensis partial 16S rRNA gene, type strain DSM 46364	AM410696	1471	GenBank ENA	33013 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis subsp. michiganensis strain ICMP 2550 16S-23S ribosomal RNA intergenic spacer, partial sequence	FJ205139	516	GenBank ENA	33013 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis subsp. michiganensis partial 16S rRNA gene, strain LMG7333T	FR728336	452	GenBank ENA	33013 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis subsp. michiganensis strain LMG 7333 16S ribosomal RNA gene, partial sequence	JN603277	1359	GenBank ENA	33013 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis subsp. michiganensis strain LMG 7333 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	JN603289	773	GenBank ENA	33013 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis michiganensis LGM 7333 16S-23S rRNA spacer region	U09380	481	GenBank ENA	28447 tax ID	*
[Ref.: #20218]	Clavibacter michiganensis michiganensis LMG 7333 16S rRNA	U09762	1491	GenBank ENA	28447 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Clavibacter michiganensis VKM Ac-1403	GCA_900168345	scaffold	GenBank ENA	28447 tax ID
[Ref.: #67770]	Clavibacter michiganensis subsp. michiganensis LMG 7333	GCA_002240575	contig	GenBank ENA	33013 tax ID
[Ref.: #67770]	Clavibacter michiganensis subsp. michiganensis CFBP 4999	GCA_003697295	scaffold	GenBank ENA	33013 tax ID
[Ref.: #66792]	Clavibacter michiganensis strain LMG7333	28447.208	complete	PATRIC	28447 tax ID	*
[Ref.: #66792]	Clavibacter michiganensis subsp. michiganensis strain CFBP 4999	33013.190	wgs	PATRIC	33013 tax ID	*
[Ref.: #66792]	Clavibacter michiganensis CFBP 4999	2846599232	draft	JGI IMG/M	28447 tax ID	*

[Ref.: #67770]

GC-content

72.7 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Clavibacter michiganensis subsp. michiganensis strain CFBP 4999 PATRIC: 33013.190
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clavibacter michiganensis LMG7333 NCBI: GCA_021216655.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.437	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.594	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.581	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	78.07	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.379	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92.5	no

Availability in culture collections External links

[Ref.: #12537]

Culture collection no.

CCUG 23363, CIP 104846, DSM 46364, ICPB CM 177, IMET 11518, LMG 7333, NCPPB 2979, PDDCC 2550, JCM 9665, CFBP 2352, CFBP 4999, ICMP 2550, IMSNU 21316, KACC 20122, KCCM 41108, VKM Ac-1403, VTT E-97058

[Ref.: #76739]

SI-ID 386953

Literature:

	Title	Authors	Journal	DOI	Year
Enzymology	Functional Characterization of Two Cellulase Genes in the Gram-Positive Pathogenic Bacterium Clavibacter michiganensis for Wilting in Tomato.	Hwang IS, Oh EJ, Lee HB, Oh CS	Mol Plant Microbe Interact	10.1094/MPMI-08-18-0227-R	2019	*
Genetics	Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.	Li XS, Yuan XK	Genome Announc	10.1128/genomeA.00721-17	2017	*
	Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333(T) Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species.	Oh EJ, Hwang IS, Park IW, Oh CS	Front Microbiol	10.3389/fmicb.2021.793345	2022	*
	Novel galactofuranan and pyruvylated galactomannan in the cell wall of Clavibacter michiganensis subsp. michiganensis VKM Ac-1403(T).	Kim D, Shashkov AS, Dmitrenok AS, Potekhina NV, Senchenkova SN, Dorofeeva LV, Evtushenko LI, Tul'skaya EM	Carbohydr Res	10.1016/j.carres.2021.108247	2021	*
	First Report of Bacterial Canker of Tomato Caused by Clavibacter michiganensis subsp. michiganensis in Korea.	Myung IS, Kim DG, An SH, Lee YK, Kim WG	Plant Dis	10.1094/PDIS-92-10-1472A	2008	*

References

#12537

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46364

#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 )

#47797 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 23363

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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 )

#76739

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-ID386953.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Clavibacter michiganensis subsp. michiganensis strain CFBP 4999

Clavibacter michiganensis LMG7333

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