Strain identifier

BacDive ID: 7290

Type strain: Yes

Species: Clavibacter nebraskensis

Strain Designation: II 296

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

NCBI tax ID(s): 31963 (subspecies)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

    @refsynonym
    20215Clavibacter michiganense subsp. nebraskense
    20215Clavibacter michiganensis subsp. nebraskensis
    20215Corynebacterium michiganense subsp. nebraskense
    20215Clavibacter nebraskensis
    20215Corynebacterium nebraskense
    20215Clavibacter 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

    @reffatty acidpercentageECL
    54535C16:03.216
    54535C14:0 ISO0.413.618
    54535C15:0 ANTEISO51.414.711
    54535C15:0 ISO1.314.621
    54535C15:1 ANTEISO A1.514.526
    54535C16:0 iso10.815.626
    54535C17:0 anteiso26.516.722
    54535C17:0 iso0.816.629
    54535C18:1 ω9c0.717.769
    54535C18:2 ω6,9c/C18:0 ANTE0.817.724
    54535Unidentified1.715.013
    54535Unidentified1.117.023
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typehost speciessampling datecountryorigin.countrycontinent
3182Zea maysZea mays
54535Leaf frecle,Zea mays1971USAUSANorth 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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clavibacter michiganensis subsp. nebraskensis strain ATCC 27794 16S-23S ribosomal RNA intergenic spacer, partial sequenceJX216836460ena31963
20218C.michiganense (DSM 7483) 16S rRNA geneX774341471ena28447
3182Clavibacter michiganensis subsp. nebraskensis partial 16S rRNA gene, type strain DSM 7483AM4106971478ena31963

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clavibacter nebraskensis NCPPB 2581 type strain: NCPPB 2581GCA_000355695completencbi1097677
66792Clavibacter michiganensis subsp. nebraskensis NCPPB 25811097677.3completepatric1097677
66792Clavibacter michiganensis nebraskensis NCPPB 25812540341046completeimg1097677

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.072no
flagellatedno97.84no
gram-positiveyes94.037no
anaerobicno99.332no
aerobicyes92.885no
halophileno84.773no
spore-formingno92.499no
glucose-utilyes87.906no
thermophileno98.932no
glucose-fermentno91.733no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27452898Genome 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 IPhytopathology10.1094/PHYTO-05-16-0188-R2016DNA, 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/*microbiologyGenetics
30703902First 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 TPlant Dis10.1094/PDIS-04-14-0397-PDN2014
Phylogeny33481876MinION 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 JTPLoS One10.1371/journal.pone.02453332021Bacterial 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/*microbiologyEnzymology
36116105Clavibacter 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 RMMol Plant Pathol10.1111/mpp.132682022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3182Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7483)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7483
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
54535Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38894)https://www.ccug.se/strain?id=38894
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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
76740Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1817.1StrainInfo: A central database for resolving microbial strain identifiers