Name: Clavibacter nebraskensis II 296
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7290

Type strain:

Species: Clavibacter nebraskensis

Strain Designation: II 296

Culture col. no.: DSM 7483, ATCC 27794, CIP 105362, ICMP 3298, NCPPB 2581, CCUG 38894, LMG 3700, LMG 5627, LMG 7223

Strain history: <- NCPPB <- M.L. Schuster, II296

NCBI tax ID(s): 31963 (subspecies)

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

Other strains from Clavibacter nebraskensis

C. nebraskensis Fur-1, DSM 20400, ATCC 27822, CCM ...
C. nebraskensis phil, DSM 20401
C. nebraskensis CCUG 23907, LMG 7173, CIP 104847

Section

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

mesophilic
plant pathogen
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Clavibacter*
	Species	**Clavibacter nebraskensis**
	Full Scientific Name (LPSN)	Clavibacter nebraskensis (Vidaver and Mandel 1974) Li et al. 2018

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3182]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #3182]

Culture medium growth

[Ref.: #3182]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3182]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3182]			growth	28 °C

[Ref.: #3182]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3182]	Murein short key	B07
[Ref.: #3182]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #3182]	Sample type/isolated from	Zea mays
[Ref.: #3182]	Host species	Zea mays

[Ref.: #54535]	Sample type/isolated from	Leaf frecle,Zea mays
[Ref.: #54535]	Sampling date	1971
[Ref.: #54535]	Country	USA
[Ref.: #54535]	Country ISO 3 Code	USA
[Ref.: #54535]	Continent	North America
* 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 X77434 (>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.: #3182]	Pathogenicity (plant)	yes
[Ref.: #3182]	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:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #3182]	Clavibacter michiganensis subsp. nebraskensis partial 16S rRNA gene, type strain DSM 7483	AM410697	1478	ENA	31963 tax ID
[Ref.: #20218]	Clavibacter michiganensis subsp. nebraskensis strain ATCC 27794 16S-23S ribosomal RNA intergenic spacer, partial sequence	JX216836	460	ENA	31963 tax ID	*
[Ref.: #20218]	C.michiganense (DSM 7483) 16S rRNA gene	X77434	1471	ENA	28447 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clavibacter nebraskensis NCPPB 2581 type strain: NCPPB 2581	GCA_000355695	complete	GenBank	1097677 tax ID	*
[Ref.: #66792]	Clavibacter michiganensis subsp. nebraskensis NCPPB 2581	1097677.3	complete	PATRIC	1097677 tax ID	*
[Ref.: #66792]	Clavibacter michiganensis nebraskensis NCPPB 2581	2540341046	complete	JGI IMG/M	1097677 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 type strain: NCPPB 2581 NCBI: GCA_000355695.1
[Ref.: #69480]	motile	no	92.072	no
[Ref.: #69480]	flagellated	no	97.84	no
[Ref.: #69480]	gram-positive	yes	94.037	no
[Ref.: #69480]	anaerobic	no	99.332	no
[Ref.: #69480]	aerobic	yes	92.885	no
[Ref.: #69480]	halophile	no	84.773	no
[Ref.: #69480]	spore-forming	no	92.499	no
[Ref.: #69480]	glucose-util	yes	87.906	no
[Ref.: #69480]	thermophile	no	98.932	no
[Ref.: #69480]	glucose-ferment	no	91.733	no

Availability in culture collections External links

[Ref.: #3182]

Culture collection no.

DSM 7483, ATCC 27794, CIP 105362, ICMP 3298, NCPPB 2581, CCUG 38894, LMG 3700, LMG 5627, LMG 7223

[Ref.: #76740]

SI-ID 1817

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*
	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	*
	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	*

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 .

#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) .

#76740

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-ID1817.1 )

* These data were automatically processed and therefore are not curated

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Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 type strain: NCPPB 2581

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