Strain identifier

BacDive ID: 7483

Type strain: Yes

Species: Rathayibacter toxicus

Strain Designation: CS14

Strain history: CIP <- 1995, ATCC <- I.T. Riley

NCBI tax ID(s): 1123052 (strain), 145458 (species)

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General

@ref: 3187

BacDive-ID: 7483

DSM-Number: 7488

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, rod-shaped

description: Rathayibacter toxicus CS14 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from annual ryegrass.

NCBI tax id

NCBI tax idMatching level
145458species
1123052strain

strain history

@refhistory
3187<- NCPPB <- I.T. Riley, CS14
67770ICMP 9525 <-- I. T. Riley CS14.
123568CIP <- 1995, ATCC <- I.T. Riley

doi: 10.13145/bacdive7483.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Rathayibacter
  • species: Rathayibacter toxicus
  • full scientific name: Rathayibacter toxicus (Riley and Ophel 1992) Sasaki et al. 1998

  • synonyms

    • @ref: 20215
    • synonym: Clavibacter toxicus

@ref: 3187

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Rathayibacter

species: Rathayibacter toxicus

full scientific name: Rathayibacter toxicus (Riley and Ophel 1992) Sasaki et al. 1998 emend. Nouioui et al. 2018

strain designation: CS14

type strain: yes

Morphology

cell morphology

  • @ref: 123568
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20201Golden yellow (1004)10-14 days5006
20201Golden yellow (1004)10-14 daysISP 2
20201Golden yellow (1004)10-14 daysISP 4
20201Golden yellow (1004)10-14 daysISP 5
20201Golden yellow (1004)10-14 daysISP 6
20201Golden yellow (1004)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20201no5006
20201noISP 2
20201noISP 4
20201noISP 5
20201noISP 6
20201noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3187DOEPEL MEDIUM (DSMZ Medium 698)yeshttps://mediadive.dsmz.de/medium/698Name: DOEPEL MEDIUM (DSMZ Medium 698) Composition: Yeast extract 8.0 g/l Casein hydrolysate 8.0 g/l Glucose 5.0 g/l K2HPO4 2.0 g/l MgSO4 0.3 g/l Distilled water
202015006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
20201ISP 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
20201ISP 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
20201ISP 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
20201ISP 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
20201ISP 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
39068MEDIUM 111 - for ClavibacteryesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
123568CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111

culture temp

@refgrowthtypetemperaturerange
20201positiveoptimum28mesophilic
3187positivegrowth28mesophilic
39068positivegrowth30mesophilic
67770positivegrowth30mesophilic
123568positivegrowth30mesophilic
123568nogrowth10psychrophilic
123568nogrowth37mesophilic
123568nogrowth45thermophilic

Physiology and metabolism

murein

  • @ref: 3187
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
123568esculin-hydrolysis4853
123568nitrate-reduction17632
123568nitrite-reduction16301
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12356835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12356815688acetoin-
12356817234glucose-

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
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-
68382lipase (C 14)-
68382esterase lipase (C 8)+
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
123568oxidase-
123568beta-galactosidase-3.2.1.23
123568alcohol dehydrogenase-1.1.1.1
123568gelatinase-
123568DNase-
123568caseinase-3.4.21.50
123568catalase+1.11.1.6
123568tween esterase-
123568lecithinase-
123568lysine decarboxylase-4.1.1.18
123568ornithine decarboxylase-4.1.1.17
123568urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20201------+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20201--+------++---+----
123568-++-+----+----+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20201---------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123568-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123568---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost speciesgeographic location
3187annual ryegrassAustraliaAUSAustralia and Oceania
67770Seed gall of Lolium rigidumAustraliaAUSAustralia and OceaniaLolium rigidumMurray Bridge, South Australia
123568Animal, Nematode, galls on rye grassAustraliaAUSAustralia and OceaniaMurray bridge

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_762.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_461;97_528;98_608;99_762&stattab=map
  • Last taxonomy: Rathayibacter toxicus subclade
  • 16S sequence: LC066140
  • Sequence Identity:
  • Total samples: 1344
  • soil counts: 951
  • aquatic counts: 82
  • animal counts: 127
  • plant counts: 184

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31871Risk group (German classification)
202011German classification
1235681Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rathayibacter toxicus gene for 16S rRNA, partial sequenceD841271477ena145458
67770Rathayibacter toxicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 9669LC0661401463ena145458

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rathayibacter toxicus DSM 74881123052.5wgspatric1123052
66792Rathayibacter toxicus DSM 74882524023208draftimg1123052
67770Rathayibacter toxicus DSM 7488GCA_000425325scaffoldncbi1123052

GC content

@refGC-contentmethod
318767.0thermal denaturation, midpoint method (Tm)
6777067thermal denaturation, midpoint method (Tm)
6777060high performance liquid chromatography (HPLC)
6777061.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.02no
flagellatedno97.067no
gram-positiveyes91.093no
anaerobicno99.144no
aerobicyes82.723no
halophileno73.873no
spore-formingno94.444no
thermophileno92.237yes
glucose-utilyes87.546no
glucose-fermentno89.822yes

External links

@ref: 3187

culture collection no.: DSM 7488, ATCC 49908, ICMP 9525, NCPPB 3552, JCM 9669, CIP 104617, VKM Ac-1600

straininfo link

@refstraininfo
769282091
76929360102

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Metabolism30195328Rhamnose-Containing Cell Wall Glycopolymers from Rathayibacter toxicus VKM Ac-1600 and "Rathayibacter tanaceti" VKM Ac-2596.Shashkov AS, Tul'skaya EM, Dmitrenok AS, Streshinskaya GM, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LIBiochemistry (Mosc)10.1134/S00062979180600932018Actinomycetales/*metabolism, Carbohydrate Sequence, Cell Wall/*metabolism, Magnetic Resonance Spectroscopy, Polysaccharides/*chemistry, Rhamnose/*metabolism
30200871Erratum to: "Rhamnose-Containing Cell Wall Glycopolymers from Rathayibacter toxicus VKM Ac-1600 and "Rathayibacter tanaceti" VKM Ac-2596" [Biochemistry (Moscow), 83, 717 (2018)].Shashkov AS, Tul'skaya EM, Dmitrenok AS, Streshinskaya GM, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LIBiochemistry (Mosc)10.1134/S00062979180701062018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3187Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7488)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7488
20201Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7488.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
39068Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16546
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
76928Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2091.1StrainInfo: A central database for resolving microbial strain identifiers
76929Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360102.1StrainInfo: A central database for resolving microbial strain identifiers
123568Curators of the CIPCollection of Institut Pasteur (CIP 104617)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104617