Strain identifier

BacDive ID: 7299

Type strain: Yes

Species: Clavibacter tessellarius

Strain Designation: 78181

Strain history: ICMP 7221 <-- A. K. Vidaver 78181.

NCBI tax ID(s): 31965 (subspecies)

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

@ref: 9050

BacDive-ID: 7299

DSM-Number: 20741

keywords: genome sequence, 16S sequence, Bacteria, Gram-positive, plant pathogen

description: Clavibacter tessellarius 78181 is a Gram-positive plant pathogen that was isolated from winter wheat.

NCBI tax id

  • NCBI tax id: 31965
  • Matching level: subspecies

strain history

@refhistory
9050<- ATCC <- A.K. Vidaver, 78181 <- R.R. Carlson
67770ICMP 7221 <-- A. K. Vidaver 78181.

doi: 10.13145/bacdive7299.20240916.9.1

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 tessellarius
  • full scientific name: Clavibacter tessellarius (Carlson and Vidaver 1982) Li et al. 2018
  • synonyms

    @refsynonym
    20215Corynebacterium michiganense subsp. tessellarius
    20215Clavibacter michiganense subsp. tessellarius
    20215Clavibacter michiganensis subsp. tessellarius

@ref: 9050

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Clavibacter

species: Clavibacter tessellarius

full scientific name: Clavibacter tessellarius (Carlson and Vidaver 1982) Li et al. 2018

strain designation: 78181

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • motility: no
  • confidence: 93.5

colony morphology

@refcolony colorincubation periodmedium used
18771Pastel orange10-14 daysISP 2
18771Pastel orange10-14 daysISP 3
18771Pastel orange10-14 daysISP 4
18771Pastel orange10-14 daysISP 5
18771Pastel orange10-14 daysISP 6
18771Pastel orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18771noISP 2
18771noISP 3
18771noISP 4
18771noISP 5
18771noISP 6
18771noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18771ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18771ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18771ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18771ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18771ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18771ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
9050TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: 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 waterhttps://mediadive.dsmz.de/medium/92

culture temp

@refgrowthtypetemperature
18771positiveoptimum28
9050positivegrowth30
67770positivegrowth30

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

murein

  • @ref: 9050
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18771--++-++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18771+-+-+----+-++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18771+---+------

Isolation, sampling and environmental information

isolation

@refsample typesampling datehost species
9050winter wheat
54537Winter wheat,Triticum aestivum1978
67770Wheat (Triticum aestivum)Triticum aestivum

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: AM410693
  • Sequence Identity:
  • Total samples: 54773
  • soil counts: 15732
  • aquatic counts: 10493
  • animal counts: 18473
  • plant counts: 10075

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
9050yes1Risk group (German classification)
187711Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clavibacter michiganensis subsp. tessellarius strain ATCC 33566 16S ribosomal RNA gene, partial sequenceU302541490nuccore31965
20218Clavibacter michiganensis subsp. tessellarius 16S ribosomal RNA gene, partial sequenceU961811266nuccore31965
20218Clavibacter michiganensis subsp. tessellarius partial 16S rRNA gene, type strain DSM 20741AM4106931490nuccore31965
20218Clavibacter michiganensis subsp. tessellarius partial 16S rRNA gene, strain LMG7294TFR728303441nuccore31965

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clavibacter michiganensis subsp. tessellarius31965.5wgspatric31965
66792Clavibacter michiganensis tessellarius ATCC 335662866971023draftimg31965
67770Clavibacter michiganensis subsp. tessellarius ATCC 33566GCA_002240635contigncbi31965
66792Clavibacter michiganensis subsp. tessellarius ATCC 33566GCA_021922985completencbi31965

GC content

  • @ref: 9050
  • GC-content: 74.0

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.349no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.696no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.12no
69480spore-formingspore-formingAbility to form endo- or exosporesno78.967no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.333yes
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 9050

culture collection no.: DSM 20741, ATCC 33566, CIP 105364, CCUG 38896, JCM 9668, CFBP 3496, ICMP 7221, KCCM 41105, LMG 7294, NCPPB 3664, VKM Ac-1406

straininfo link

  • @ref: 76749
  • straininfo: 1914

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9050Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20741)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20741
18771Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20741.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
54537Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38896)https://www.ccug.se/strain?id=38896
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
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
76749Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1914.1StrainInfo: A central database for resolving microbial strain identifiers