Clavibacter insidiosus (DSM 20157, ATCC 10253, CIP 105363)

Name: Clavibacter insidiosus (DSM 20157, ATCC 10253, CIP 105363)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7286

Type strain

Culture col. no. DSM 20157 ATCC 10253 CIP 105363 NCPPB 1109 CCUG 38895 13 more

NCBI tax ID(s) 33014

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- ATCC <- W.H. Burkholder <- E.D. Hansing JCM <-- K. Suzuki CNF 101 <-- AJ 1409 <-- ATCC 10253 <-- W. H. Burkholder <-- E. D. Hansing. JCM <-- ICMP 2621 <-- D. W. Dye CK12 <-- ICPB CI142 <-- W. H. Burkholder PB.

Links

Clavibacter insidiosus DSM 20157 is a plant pathogen that was isolated from Lucerne,alfafa,Medicago sativa.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1756

LMG 3661,ATCC 10253,DSM 20157,ICMP 2616,JCM 1369,NCPPB 852,PDDCC 2616,LMG 3663,ICMP 2621,NCIB 9026,NCPPB 1109,PDDCC 2621,CCUG 38895,CIP 105363,CIP 105048,JCM 9664,VKM Ac-1402,CECT 5042,CFBP 2404,NCIMB 9026,BCRC 15903,CCRC 15903,CGMCC 1.1908

@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 insidiosus

Full scientific name Clavibacter insidiosus (McCulloch 1925) Li et al. 2018

Synonyms (6)

Corynebacterium michiganense subsp. insidiosum
"Aplanobacter insidiosum"
Clavibacter michiganensis subsp. insidiosus
Clavibacter michiganensis subsp. insidiosum
Corynebacterium insidiosum
Clavibacter michiganense subsp. insidiosum

BacDive ID	Other strains from **Clavibacter insidiosus** (6)	Type strain
7285	C. insidiosus DSM 340
144241	C. insidiosus CCUG 23899, CIP 104861, LMG 3675
144242	C. insidiosus CCUG 23901, LMG 7326
157321	C. insidiosus IMI 347331
157322	C. insidiosus IMI 347334
157323	C. insidiosus IMI 347336

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	92.5
125438	90.958	positive
125439	94.274	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8581	CORYNEBACTERIUM AGAR (DSMZ Medium 53)		Medium recipe at MediaDive	Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8581	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.315

Murein

@ref	Murein short key	Type
8581	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
54536	Lucerne,alfafa,Medicago sativa
67770	Alfalfa (Medicago sativa)	Medicago sativa	Kings Ferry, NY	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
8581		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	ASM307635v1 assembly for Clavibacter michiganensis subsp. insidiosus ATCC 10253	complete	GCA_003076355	33014.13	2841240826	33014	95.12
67770	ASM224056v1 assembly for Clavibacter michiganensis subsp. insidiosus LMG 3663	contig	GCA_002240565	33014.8	8118239796	33014	74.59
66792	ASM369341v1 assembly for Clavibacter michiganensis subsp. insidiosus CFBP 2404	scaffold	GCA_003693415	33014.25	2837076217	33014	59.77
124043	ASM4264668v1 assembly for Clavibacter michiganensis subsp. insidiosus ICMP 2621	contig	GCA_042646685			33014	56.67

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clavibacter michiganensis subsp. insidiosus partial 16S rRNA gene, type strain DSM 20157	AM410695	1471	33014
20218	Clavibacter michiganensis gene for 16S ribosomal RNA, strain: JCM1369	D45051	1462	28447
20218	Clavibacter michiganensis subsp. insidiosus partial 16S rRNA gene, strain LMG3663T	FR728294	453	33014
20218	Clavibacter michiganensis insidiosum LMG 3663 16S-23S rRNA spacer region	U09378	487	28447
20218	Clavibacter michiganensis subsp. insidiosus 16S ribosomal RNA, complete sequence	U09761	1471	28447
124043	Clavibacter michiganensis subsp. insidiosus strain ICMP 2621 16S ribosomal RNA gene, partial sequence.	MT758032	1356	33014
124043	Clavibacter michiganensis subsp. insidiosus strain ICMP 2621 16S ribosomal RNA gene, partial sequence.	MT760000	1356	33014

GC content

@ref	GC-content (mol%)	Method
8581	78.1
67770	78.1	thermal denaturation, midpoint method (Tm)
67770	76.1	thermal denaturation, midpoint method (Tm)
67770	72.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM307635v1 assembly for Clavibacter michiganensis subsp. insidiosus ATCC 10253
BV-BRC: 33014.13

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.32	no
125439	gram_stain	BacteriaNetⓘ	positive	94.27	no
125439	motility	BacteriaNetⓘ	no	73.96	no
125439	spore_formation	BacteriaNetⓘ	no	86.96	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clavibacter michiganensis subsp. insidiosus ATCC 10253
NCBI: GCA_003076355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.96	no
125438	anaerobic	anaerobicⓘ	no	95.22	no
125438	aerobic	aerobicⓘ	yes	81.70	no
125438	spore-forming	spore-formingⓘ	no	80.40	no
125438	thermophilic	thermophileⓘ	no	94.38	no
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Re-classification of Clavibacter michiganensis subspecies on the basis of whole-genome and multi-locus sequence analyses.	Li X, Tambong J, Yuan KX, Chen W, Xu H, Levesque CA, De Boer SH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002492	2018
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
	Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues.	Dupas E, Briand M, Jacques MA, Cesbron S.	Front Plant Sci	10.3389/fpls.2019.01732	2019
Phylogeny	Nucleic acid hybridization studies on Microbacterium, Curtobacterium, Agromyces and related taxa.	Dopfer H, Stackebrandt E, Fiedler F	J Gen Microbiol	10.1099/00221287-128-8-1697	1982

References

#8581	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20157
#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 )
#54536	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38895
#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;
#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 insidiosus (DSM 20157, ATCC 10253, CIP 105363)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003076355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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