Strain identifier
BacDive ID: 7290
Type strain:
Species: Clavibacter nebraskensis
Strain Designation: II 296
Strain history: <- NCPPB <- M.L. Schuster, II296
NCBI tax ID(s): 31963 (subspecies)
General
@ref: 3182
BacDive-ID: 7290
DSM-Number: 7483
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, plant pathogen
description: Clavibacter nebraskensis II 296 is a mesophilic plant pathogen that was isolated from Zea mays.
NCBI tax id
- NCBI tax id: 31963
- Matching level: subspecies
strain history
- @ref: 3182
- history: <- NCPPB <- M.L. Schuster, II296
doi: 10.13145/bacdive7290.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- 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
@ref synonym 20215 Clavibacter michiganense subsp. nebraskense 20215 Clavibacter michiganensis subsp. nebraskensis 20215 Corynebacterium michiganense subsp. nebraskense 20215 Clavibacter nebraskensis 20215 Corynebacterium nebraskense 20215 Clavibacter michiganensis subsp. nebraskense
@ref: 3182
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Clavibacter
species: Clavibacter nebraskensis
full scientific name: Clavibacter nebraskensis (Vidaver and Mandel 1974) Li et al. 2018
strain designation: II 296
type strain: yes
Culture and growth conditions
culture medium
- @ref: 3182
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: 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: 3182
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
murein
- @ref: 3182
- murein short key: B07
- type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 54535 C16:0 3.2 16 54535 C14:0 ISO 0.4 13.618 54535 C15:0 ANTEISO 51.4 14.711 54535 C15:0 ISO 1.3 14.621 54535 C15:1 ANTEISO A 1.5 14.526 54535 C16:0 iso 10.8 15.626 54535 C17:0 anteiso 26.5 16.722 54535 C17:0 iso 0.8 16.629 54535 C18:1 ω9c 0.7 17.769 54535 C18:2 ω6,9c/C18:0 ANTE 0.8 17.724 54535 Unidentified 1.7 15.013 54535 Unidentified 1.1 17.023 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | sampling date | country | origin.country | continent |
---|---|---|---|---|---|---|
3182 | Zea mays | Zea mays | ||||
54535 | Leaf frecle,Zea mays | 1971 | USA | USA | North America |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
taxonmaps
- @ref: 69479
- File name: preview.99_730.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_446;97_510;98_586;99_730&stattab=map
- Last taxonomy: Clavibacter michiganensis
- 16S sequence: X77434
- Sequence Identity:
- Total samples: 54773
- soil counts: 15732
- aquatic counts: 10493
- animal counts: 18473
- plant counts: 10075
Safety information
risk assessment
- @ref: 3182
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clavibacter michiganensis subsp. nebraskensis strain ATCC 27794 16S-23S ribosomal RNA intergenic spacer, partial sequence | JX216836 | 460 | ena | 31963 |
20218 | C.michiganense (DSM 7483) 16S rRNA gene | X77434 | 1471 | ena | 28447 |
3182 | Clavibacter michiganensis subsp. nebraskensis partial 16S rRNA gene, type strain DSM 7483 | AM410697 | 1478 | ena | 31963 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clavibacter nebraskensis NCPPB 2581 type strain: NCPPB 2581 | GCA_000355695 | complete | ncbi | 1097677 |
66792 | Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 | 1097677.3 | complete | patric | 1097677 |
66792 | Clavibacter michiganensis nebraskensis NCPPB 2581 | 2540341046 | complete | img | 1097677 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.072 | no |
flagellated | no | 97.84 | no |
gram-positive | yes | 94.037 | no |
anaerobic | no | 99.332 | no |
aerobic | yes | 92.885 | no |
halophile | no | 84.773 | no |
spore-forming | no | 92.499 | no |
glucose-util | yes | 87.906 | no |
thermophile | no | 98.932 | no |
glucose-ferment | no | 91.733 | no |
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
straininfo link
- @ref: 76740
- straininfo: 1817
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27452898 | 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 | DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genome, Bacterial/*genetics, Micrococcaceae/*genetics/isolation & purification, Multiplex Polymerase Chain Reaction/methods, Phylogeny, Plant Diseases/*microbiology, Real-Time Polymerase Chain Reaction/*methods, Sensitivity and Specificity, Sequence Analysis, DNA, Zea mays/*microbiology | Genetics |
30703902 | 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 | 33481876 | 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 | Bacterial Proteins/genetics, Clavibacter/*genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, High-Throughput Nucleotide Sequencing, Nanopore Sequencing/*methods, Nucleobase Transport Proteins/genetics, Plant Diseases/*microbiology, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Zea mays/*microbiology | Enzymology |
36116105 | 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 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3182 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7483) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7483 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
54535 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 38894) | https://www.ccug.se/strain?id=38894 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
76740 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1817.1 | StrainInfo: A central database for resolving microbial strain identifiers |