Strain identifier

BacDive ID: 7286

Type strain: Yes

Species: Clavibacter insidiosus

Strain history: ICMP 2621 <-- D. W. Dye CK12 <-- ICPB CI142 <-- W. H. Burkholder PB.

NCBI tax ID(s): 33014 (subspecies)

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General

@ref: 8581

BacDive-ID: 7286

DSM-Number: 20157

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, plant pathogen

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

NCBI tax id

  • NCBI tax id: 33014
  • Matching level: subspecies

strain history

@refhistory
8581<- ATCC <- W.H. Burkholder <- E.D. Hansing
67770K. Suzuki CNF 101 <-- AJ 1409 <-- ATCC 10253 <-- W. H. Burkholder <-- E. D. Hansing.
67770ICMP 2621 <-- D. W. Dye CK12 <-- ICPB CI142 <-- W. H. Burkholder PB.

doi: 10.13145/bacdive7286.20230509.8.1

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 insidiosus
  • full scientific name: Clavibacter insidiosus (McCulloch 1925) Li et al. 2018

  • synonyms

    @refsynonym
    20215Aplanobacter insidiosum
    20215Corynebacterium insidiosum
    20215Clavibacter michiganensis subsp. insidiosus
    20215Clavibacter michiganense subsp. insidiosum
    20215Corynebacterium michiganense subsp. insidiosum
    20215Clavibacter michiganensis subsp. insidiosum

@ref: 8581

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Clavibacter

species: Clavibacter insidiosus

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

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.432
69480100positive

Culture and growth conditions

culture medium

  • @ref: 8581
  • name: CORYNEBACTERIUM AGAR (DSMZ Medium 53)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/53
  • composition: 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

@refgrowthtypetemperaturerange
8581positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no93
69480no99.996

murein

  • @ref: 8581
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
54536Lucerne,alfafa,Medicago sativa
67770Alfalfa (Medicago sativa)Medicago sativaKings Ferry, NYUSAUSANorth America

isolation source categories

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

Safety information

risk assessment

  • @ref: 8581
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clavibacter michiganensis subsp. insidiosus clone K0091 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceHM181751505ena33014
20218Clavibacter michiganensis subsp. insidiosus partial 16S rRNA gene, type strain DSM 20157AM4106951471ena33014
20218Clavibacter michiganensis gene for 16S ribosomal RNA, strain: JCM1369D450511462ena28447
20218Clavibacter michiganensis subsp. insidiosus partial 16S rRNA gene, strain LMG3663TFR728294453ena33014
20218Clavibacter michiganensis insidiosum LMG 3663 16S-23S rRNA spacer regionU09378487ena28447
20218Clavibacter michiganensis insidiosum LMG 3663 16S rRNAU097611471ena28447

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clavibacter michiganensis subsp. insidiosus ATCC 10253GCA_003076355completencbi33014
66792Clavibacter michiganensis subsp. insidiosus CFBP 2404GCA_003693415scaffoldncbi33014
66792Clavibacter insidiosus strain ATCC 1025333014.13completepatric33014
66792Clavibacter michiganensis subsp. insidiosus33014.8wgspatric33014
66792Clavibacter michiganensis subsp. insidiosus strain CFBP 240433014.25wgspatric33014
66792Clavibacter michiganensis CFBP 24042837076217draftimg28447
66792Clavibacter michiganensis ATCC 102532841240826completeimg28447
67770Clavibacter michiganensis subsp. insidiosus LMG 3663GCA_002240565contigncbi33014

GC content

@refGC-contentmethod
858178.1
6777078.1thermal denaturation, midpoint method (Tm)
6777076.1thermal denaturation, midpoint method (Tm)
6777072.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
flagellatedno97.577no
gram-positiveyes93.895no
anaerobicno99.285no
halophileno84.071no
spore-formingno93.291no
glucose-utilyes88.43no
aerobicyes93.252no
thermophileno99.199no
motileno91.914no
glucose-fermentno91.158no

External links

@ref: 8581

culture collection no.: DSM 20157, ATCC 10253, CIP 105363, NCPPB 1109, CCUG 38895, LMG 3663, JCM 1369, CGMCC 1.1908, ICMP 2616, KCCM 41086, LMG 3661, NCPPB 852, JCM 9664, CECT 5042, CFBP 2404, CIP 105048, ICMP 2621, VKM Ac-1402

straininfo link

  • @ref: 76736
  • straininfo: 1756

literature

  • topic: Phylogeny
  • Pubmed-ID: 6183393
  • title: Nucleic acid hybridization studies on Microbacterium, Curtobacterium, Agromyces and related taxa.
  • authors: Dopfer H, Stackebrandt E, Fiedler F
  • journal: J Gen Microbiol
  • DOI: 10.1099/00221287-128-8-1697
  • year: 1982
  • mesh: Actinomycetales/*classification/metabolism, DNA, Bacterial, *Nucleic Acid Hybridization, RNA, Bacterial, RNA, Ribosomal
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20157)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20157
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
54536Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38895)https://www.ccug.se/strain?id=38895
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76736Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1756.1StrainInfo: A central database for resolving microbial strain identifiers