Clavibacter nebraskensis (DSM 7483, ATCC 27794, CIP 105362)

Name: Clavibacter nebraskensis (DSM 7483, ATCC 27794, CIP 105362)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7290

Type strain

Strain Designation II 296

Culture col. no. DSM 7483 ATCC 27794 CIP 105362 ICMP 3298 NCPPB 2581 5 more

NCBI tax ID(s) 1097677 31963

Special Collections DSMZ CCUG CIP

History DSMZ <- NCPPB <- M.L. Schuster, II296

Links

Clavibacter nebraskensis II 296 is a plant pathogen that was isolated from Zea mays.

plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1817

LMG 3700,ATCC 27794,ICMP 3298,LMG 5627,LMG 7223,NCPPB 2581,PDDCC 3298,CCUG 38894,CIP 105362,JCM 9666,VKM Ac-1404,CECT 4209,CECT 5040,CFBP 2405,ICMP 5700,DSM 7483

@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 nebraskensis

Full scientific name Clavibacter nebraskensis (Vidaver and Mandel 1974) Li et al. 2018

Synonyms (6)

Clavibacter nebraskensis
Clavibacter michiganense subsp. nebraskense
Corynebacterium nebraskense
Clavibacter michiganensis subsp. nebraskensis
Corynebacterium michiganense subsp. nebraskense
Clavibacter michiganensis subsp. nebraskense

BacDive ID	Other strains from **Clavibacter nebraskensis** (3)	Type strain
7291	C. nebraskensis Fur-1, DSM 20400, ATCC 27822, CCM 2749, NCPPB ...
7292	C. nebraskensis phil, DSM 20401
144248	C. nebraskensis CCUG 23907, LMG 7173, CIP 104847

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	92
125438	90.394	positive
125439	93.125	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3182	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)
3182	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94.801

Murein

@ref	Murein short key	Type
3182	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Fatty acid profile

Metadata FA analysis

@ref

54535

Fatty acid	Percentage	ECL
C15:0 ANTEISO	51.4	14.711
C17:0 anteiso	26.5	16.722
C16:0 iso	10.8	15.626
C16:0	3.2	16
Unidentified	1.7	15.013
C15:1 ANTEISO A	1.5	14.526
C15:0 ISO	1.3	14.621
Unidentified	1.1	17.023
C17:0 iso	0.8	16.629
C18:2 ω6,9c/C18:0 ANTE	0.8	17.724
C18:1 ω9c	0.7	17.769
C14:0 ISO	0.4	13.618

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent	Host species
3182	Zea mays					Zea mays
54535	Leaf frecle,Zea mays	1971	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence X77434 (>99% sequence identity) for Clavibacter michiganensis from Microbeatlas

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

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
3182		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	ASM35569v1 assembly for Clavibacter nebraskensis NCPPB 2581 type strain: NCPPB 2581	complete	GCA_000355695	1097677.3	2540341046	1097677	76.74

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clavibacter michiganensis subsp. nebraskensis strain ATCC 27794 16S-23S ribosomal RNA intergenic spacer, partial sequence	JX216836	460	31963
20218	C.michiganense (DSM 7483) 16S rRNA gene	X77434	1471	28447
3182	Clavibacter michiganensis subsp. nebraskensis partial 16S rRNA gene, type strain DSM 7483	AM410697	1478	31963
124043	Clavibacter michiganensis subsp. nebraskensis partial 16S rRNA gene, strain LMG3700	FR728275	448	31963
124043	Clavibacter michiganensis nebraskensis LMG 5627 16S-23S rRNA spacer region.	U09381	485	31963
124043	Clavibacter michiganensis nebraskensis LMG 5627 16S rRNA.	U09763	1478	31963

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM35569v1 assembly for Clavibacter nebraskensis NCPPB 2581 type strain: NCPPB 2581
BV-BRC: 1097677.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.80	no
125439	gram_stain	BacteriaNetⓘ	positive	93.13	no
125439	motility	BacteriaNetⓘ	no	68.86	no
125439	spore_formation	BacteriaNetⓘ	no	88.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 type strain: NCPPB 2581
NCBI: GCA_000355695.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.39	no
125438	anaerobic	anaerobicⓘ	no	95.74	no
125438	aerobic	aerobicⓘ	yes	85.87	no
125438	spore-forming	spore-formingⓘ	no	77.14	no
125438	thermophilic	thermophileⓘ	no	94.88	no
125438	flagellated	motile2+ⓘ	no	92.00	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
	Virulence is not directly related to strain success in planta in Clavibacter nebraskensis.	Veregge M, Hirsch CD, Moscou MJ, Burghardt L, Tiffin P, Khokhani D.	mSystems	10.1128/msystems.01355-24	2025
Phylogeny	Genome Analysis and Development of a Multiplex TaqMan Real-Time PCR for Specific Identification and Detection of Clavibacter michiganensis subsp. nebraskensis.	Tambong JT, Xu R, Daayf F, Briere S, Bilodeau GJ, Tropiano R, Hartke A, Reid LM, Cott M, Cote T, Agarkova I	Phytopathology	10.1094/PHYTO-05-16-0188-R	2016
	First Report of Goss's Bacterial Leaf Blight and Wilt of Corn Caused by Clavibacter michiganensis subsp. nebraskensis in North Dakota.	Friskop A, Kinzer K, McConnell M, Liu Z, Korus K, Timmerman A, Jackson T	Plant Dis	10.1094/PDIS-04-14-0397-PDN	2014
Phylogeny	MinION Nanopore-based detection of Clavibacter nebraskensis, the corn Goss's wilt pathogen, and bacteriomic profiling of necrotic lesions of naturally-infected leaf samples.	Xu R, Adam L, Chapados J, Soliman A, Daayf F, Tambong JT	PLoS One	10.1371/journal.pone.0245333	2021
	Clavibacter nebraskensis causing Goss's wilt of maize: Five decades of detaining the enemy in the New World.	Osdaghi E, Robertson AE, Jackson-Ziems TA, Abachi H, Li X, Harveson RM	Mol Plant Pathol	10.1111/mpp.13268	2022
	Corrigendum to "Comparative genomics and pan-genomics of the Myxococcaceae, including a description of five novel species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov. and Pyxidicoccus trucidator sp. nov." [Genome Biol. Evol. 12(12) (2020) 2289-2302].	Chambers J, Sparks N, Sydney N, Livingstone PG, Cookson AR, Whitworth DE.	Genome Biol Evol	10.1093/gbe/evab040	2021
Genetics	Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov.	Chambers J, Sparks N, Sydney N, Livingstone PG, Cookson AR, Whitworth DE.	Genome Biol Evol	10.1093/gbe/evaa212	2020

References

#3182	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7483
#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 )
#54535	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38894
#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) .
#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 .
#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 nebraskensis (DSM 7483, ATCC 27794, CIP 105362)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000355695

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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