Strain identifier
BacDive ID: 7299
Type strain:
Species: Clavibacter tessellarius
Strain Designation: 78181
Strain history: ICMP 7221 <-- A. K. Vidaver 78181.
NCBI tax ID(s): 31965 (subspecies)
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
@ref | history |
---|---|
9050 | <- ATCC <- A.K. Vidaver, 78181 <- R.R. Carlson |
67770 | ICMP 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
@ref synonym 20215 Corynebacterium michiganense subsp. tessellarius 20215 Clavibacter michiganense subsp. tessellarius 20215 Clavibacter 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
@ref | colony color | incubation period | medium used |
---|---|---|---|
18771 | Pastel orange | 10-14 days | ISP 2 |
18771 | Pastel orange | 10-14 days | ISP 3 |
18771 | Pastel orange | 10-14 days | ISP 4 |
18771 | Pastel orange | 10-14 days | ISP 5 |
18771 | Pastel orange | 10-14 days | ISP 6 |
18771 | Pastel orange | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18771 | no | ISP 2 |
18771 | no | ISP 3 |
18771 | no | ISP 4 |
18771 | no | ISP 5 |
18771 | no | ISP 6 |
18771 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
18771 | ISP 2 | yes | Name: 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 | |
18771 | ISP 3 | yes | Name: 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: | |
18771 | ISP 4 | yes | Name: 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 | |
18771 | ISP 5 | yes | Name: 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 | |
18771 | ISP 6 | yes | Name: 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 | |
18771 | ISP 7 | yes | Name: 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 | |
9050 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | 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 | https://mediadive.dsmz.de/medium/92 |
culture temp
@ref | growth | type | temperature |
---|---|---|---|
18771 | positive | optimum | 28 |
9050 | positive | growth | 30 |
67770 | positive | growth | 30 |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18771 | - | - | + | + | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18771 | + | - | + | - | + | - | - | - | - | + | - | + | + | - | + | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18771 | + | - | - | - | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | host species |
---|---|---|---|
9050 | winter wheat | ||
54537 | Winter wheat,Triticum aestivum | 1978 | |
67770 | Wheat (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
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
9050 | yes | 1 | Risk group (German classification) |
18771 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clavibacter michiganensis subsp. tessellarius strain ATCC 33566 16S ribosomal RNA gene, partial sequence | U30254 | 1490 | nuccore | 31965 |
20218 | Clavibacter michiganensis subsp. tessellarius 16S ribosomal RNA gene, partial sequence | U96181 | 1266 | nuccore | 31965 |
20218 | Clavibacter michiganensis subsp. tessellarius partial 16S rRNA gene, type strain DSM 20741 | AM410693 | 1490 | nuccore | 31965 |
20218 | Clavibacter michiganensis subsp. tessellarius partial 16S rRNA gene, strain LMG7294T | FR728303 | 441 | nuccore | 31965 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clavibacter michiganensis subsp. tessellarius | 31965.5 | wgs | patric | 31965 |
66792 | Clavibacter michiganensis tessellarius ATCC 33566 | 2866971023 | draft | img | 31965 |
67770 | Clavibacter michiganensis subsp. tessellarius ATCC 33566 | GCA_002240635 | contig | ncbi | 31965 |
66792 | Clavibacter michiganensis subsp. tessellarius ATCC 33566 | GCA_021922985 | complete | ncbi | 31965 |
GC content
- @ref: 9050
- GC-content: 74.0
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.349 | no |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.696 | no |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.12 | no |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 78.967 | no |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.333 | yes |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 93.5 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9050 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20741) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20741 | |||
18771 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM20741.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 | |
54537 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 38896) | https://www.ccug.se/strain?id=38896 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76749 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1914.1 | StrainInfo: A central database for resolving microbial strain identifiers |