Strain identifier

BacDive ID: 7485

Type strain: Yes

Species: Rathayibacter tritici

Strain Designation: CT102

Strain history: CIP <- 1994, VKM <- ICMP

NCBI tax ID(s): 1328864 (strain), 33888 (species)

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General

@ref: 3185

BacDive-ID: 7485

DSM-Number: 7486

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped, plant pathogen

description: Rathayibacter tritici CT102 is an obligate aerobe, mesophilic, Gram-positive plant pathogen that was isolated from Triticum aestivum.

NCBI tax id

NCBI tax idMatching level
33888species
1328864strain

strain history

@refhistory
3185<- NCPPB <- M.P. Starr, CT102 <- R. Vasudeva, B
67770ICMP 2626 <-- ICPB CT102 <-- R. S. Vasudeva B.
123585CIP <- 1994, VKM <- ICMP

doi: 10.13145/bacdive7485.20230509.8.1

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 tritici
  • full scientific name: Rathayibacter tritici (Carlson and Vidaver 1982 ex Hutchinson 1917) Zgurskaya et al. 1993

  • synonyms

    @refsynonym
    20215Clavibacter tritici
    20215Corynebacterium tritici

@ref: 3185

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Rathayibacter

species: Rathayibacter tritici

full scientific name: Rathayibacter tritici (Carlson and Vidaver 1982) Zgurskaya et al. 1993

strain designation: CT102

type strain: yes

Morphology

cell morphology

  • @ref: 123585
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19727Golden yellow10-14 days5006
19727Golden yellow10-14 days5425
19727Golden yellow10-14 days5428
19727Golden yellow10-14 days5530
19727Golden yellow10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
19727noISP 2
19727no5006
19727no5425
19727no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3185TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
19727ISP 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
197275006yesMedium: 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
197275425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
197275428yes
197275530yes
38161MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
123585CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
3185positivegrowth28mesophilic
38161positivegrowth30mesophilic
67770positivegrowth30mesophilic
123585positivegrowth22-30
123585nogrowth10psychrophilic
123585nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123585
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 19727
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 3185
  • 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
123585nitrate-reduction17632
123585nitrite-reduction16301
123585tributyrin-hydrolysis35020
123585nitrate-respiration17632
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
12358535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12358515688acetoin-
12358517234glucose-

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
123585oxidase-
123585alcohol dehydrogenase-1.1.1.1
123585gelatinase-
123585amylase-
123585DNase-
123585caseinase-3.4.21.50
123585catalase+1.11.1.6
123585lipase-
123585lysine decarboxylase-4.1.1.18
123585ornithine decarboxylase-4.1.1.17
123585urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19727------+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19727--+-++---++---++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19727----+-+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123585+--+-+----+++----++-----------+------+-+-+-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123585+++++----------+----+++-----+--+-+-+------------------------+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3185Triticum aestivumTriticum aestivumEgyptEGYAfrica
47888Triticum aestivum (Aestivum Group)
67770Wheat (Triticum aestivum)Triticum aestivumEgyptEGYAfrica
123585Food, Wheat, Triticum aestivumEgyptEGYAfrica

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7179.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_461;97_795;98_920;99_7179&stattab=map
  • Last taxonomy: Rathayibacter
  • 16S sequence: X77438
  • Sequence Identity:
  • Total samples: 8091
  • soil counts: 2646
  • aquatic counts: 712
  • animal counts: 2197
  • plant counts: 2536

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3185yes1Risk group (German classification)
197271Risk group (German classification)
1235851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rathayibacter tritici partial 16S rRNA gene, isolate OS-16.aAM2373431470ena33888
20218Rathayibacter tritici partial 16S rRNA gene, type strain DSM 7486AM4106851471ena33888
20218Rathayibacter tritici 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAY191505606ena33888
3185R.tritici (DSM 7486) 16S rRNA geneX774381471ena33888

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rathayibacter tritici strain DSM 748633888.11wgspatric33888
66792Rathayibacter tritici DSM 74862868629091draftimg33888
67770Rathayibacter tritici DSM 7486GCA_002932875scaffoldncbi33888

GC content

  • @ref: 67770
  • GC-content: 69
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes93.756no
anaerobicno99.49no
halophileno87.334no
spore-formingno94.316no
glucose-utilyes86.476no
flagellatedno98.262no
aerobicyes91.483no
motileno94.821no
thermophileno99.262yes
glucose-fermentno88.871yes

External links

@ref: 3185

culture collection no.: CCUG 23914, LMG 3728, CIP 104038, DSM 7486, ATCC 11403, ICMP 2626, NCPPB 1857, VKM Ac-1603, JCM 9309, CFBP 1385, ICPB CT102, PDDCC 2626

straininfo link

  • @ref: 76931
  • straininfo: 1931

literature

  • topic: Metabolism
  • Pubmed-ID: 32564741
  • title: Rhamnomannans and Teichuronic Acid from the Cell Wall of Rathayibacter tritici VKM Ac-1603(T).
  • authors: Shashkov AS, Tul'skaya EM, Streshinskaya GM, Dmitrenok AS, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LI
  • journal: Biochemistry (Mosc)
  • DOI: 10.1134/S0006297920030128
  • year: 2020
  • mesh: Actinobacteria/*metabolism, Cell Wall/*metabolism, Glycoproteins/chemistry, Magnetic Resonance Spectroscopy, Mannans/*metabolism, Mannose/chemistry, Phosphates/chemistry, Polymers/chemistry, Rhamnose/*metabolism, Species Specificity, Uronic Acids/*metabolism
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3185Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7486)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7486
19727Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7486.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
38161Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15902
47888Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23914)https://www.ccug.se/strain?id=23914
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
76931Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1931.1StrainInfo: A central database for resolving microbial strain identifiers
123585Curators of the CIPCollection of Institut Pasteur (CIP 104038)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104038