Strain identifier

BacDive ID: 7482

Type strain: Yes

Species: Rathayibacter rathayi

Strain Designation: CE4

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

NCBI tax ID(s): 1328865 (strain), 33887 (species)

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General

@ref: 3184

BacDive-ID: 7482

DSM-Number: 7485

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

description: Rathayibacter rathayi CE4 is a facultative anaerobe, mesophilic plant pathogen that was isolated from Dactylis glomerata.

NCBI tax id

NCBI tax idMatching level
33887species
1328865strain

strain history

@refhistory
3184<- NCPPB <- ICMP <- D.W. Dye, CE4 <- W.J. Kemp
67770ICMP 2574 <-- D. W. Dye CE4.
122141CIP <- 1994, VKM <- ICMP

doi: 10.13145/bacdive7482.20230509.8.1

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 rathayi
  • full scientific name: Rathayibacter rathayi (Smith 1913) Zgurskaya et al. 1993

  • synonyms

    @refsynonym
    20215Aplanobacter rathayi
    20215Corynebacterium rathayi
    20215Clavibacter rathayi

@ref: 3184

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Rathayibacter

species: Rathayibacter rathayi

full scientific name: Rathayibacter rathayi (Smith 1913) Zgurskaya et al. 1993

strain designation: CE4

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.933
69480100positive
122141nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19726Ivory10-14 days5006
19726Ivory10-14 days5425
19726Ivory10-14 days5428
19726Ivory10-14 days5530
19726Ivory10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
19726
19726noISP 2
19726no5006
19726no5425
19726no5530

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19726ISP 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
197265006yesMedium: 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
197265425yesName: 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
197265428yes
197265530yes
3184TRYPTICASE 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
35609MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122141CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122141CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111

culture temp

@refgrowthtypetemperaturerange
3184positivegrowth28mesophilic
35609positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122141
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

halophily

  • @ref: 19726
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 3184
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12214117632nitrate+reduction
12214116301nitrite-reduction
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
12214135581indoleno

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-
68382lipase (C 14)-
68382esterase (C 4)-
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
122141oxidase-
122141catalase+1.11.1.6
122141urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19726+--+-----+-+---+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19726+-+------++---+----
122141----+----++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19726-++++-+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3184Dactylis glomerataDactylis glomerataNew ZealandNZLAustralia and Oceania
67770Cooksfoot (Dactylis glomerata)Dactylis glomerataNew ZealandNZLAustralia and Oceania
122141Dactylis glomerataNew ZealandNZLAustralia and Oceania

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: X77439
  • 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
3184yes1Risk group (German classification)
197261Risk group (German classification)
1221411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3184
  • description: R.rathayi (DSM 7485) 16S rRNA gene
  • accession: X77439
  • length: 1474
  • database: ena
  • NCBI tax ID: 33887

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rathayibacter rathayi DSM 7485GCA_004011095completencbi33887
66792Rathayibacter rathayi NCPPB 2980 = VKM Ac-1601GCA_009806975contigncbi1328865
66792Rathayibacter rathayi NCPPB 2980 = VKM Ac-16011328865.4wgspatric1328865
66792Rathayibacter rathayi strain DSM 748533887.27completepatric33887
66792Rathayibacter rathayi strain DSM 748533887.29wgspatric33887
66792Rathayibacter rathayi DSM 74852840627797completeimg33887
66792Rathayibacter rathayi DSM 74852814123447draftimg33887
67770Rathayibacter rathayi NCPPB 2980 = VKM Ac-1601GCA_900215645scaffoldncbi1328865
67770Rathayibacter rathayi DSM 7485GCA_007828845contigncbi33887

GC content

  • @ref: 67770
  • GC-content: 67
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno55no
motileno93.42no
flagellatedno98.126no
gram-positiveyes91.951no
anaerobicno99.425no
aerobicyes90.132no
halophileno85.422no
spore-formingno94.173no
thermophileno98.862yes
glucose-utilyes86.71no
glucose-fermentno89.995yes

External links

@ref: 3184

culture collection no.: DSM 7485, ICMP 2574, NCPPB 2980, VKM Ac-1601, JCM 9307, CECT 4210, CFBP 2406, CIP 104036, LMG 7288

straininfo link

  • @ref: 76927
  • straininfo: 13617

Reference

@idauthorscataloguedoi/urltitle
3184Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7485)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7485
19726Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7485.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
35609Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15899
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)
76927Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13617.1StrainInfo: A central database for resolving microbial strain identifiers
122141Curators of the CIPCollection of Institut Pasteur (CIP 104036)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104036