Strain identifier

BacDive ID: 7484

Type strain: Yes

Species: Rathayibacter iranicus

Strain Designation: 66-807, NCCPB 2253

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

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General

@ref: 3183

BacDive-ID: 7484

DSM-Number: 7484

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

description: Rathayibacter iranicus 66-807 is an obligate aerobe, mesophilic, Gram-positive plant pathogen that was isolated from Triticum aestivum.

NCBI tax id

NCBI tax idMatching level
1328868strain
59737species

strain history

@refhistory
3183<- NCPPB <- M. Ride, 66-807 <- F. Eskandari
67770ICMP 3496 <-- C. N. Hale CL2 <-- NCPPB 2253 <-- M. Ride 66-807.
120281CIP <- 1994, VKM <- ICMP

doi: 10.13145/bacdive7484.20230509.8.1

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 iranicus
  • full scientific name: Rathayibacter iranicus (Carlson and Vidaver 1982 ex Scharif 1961) Zgurskaya et al. 1993
  • synonyms

    @refsynonym
    20215Clavibacter iranicus
    20215Clavibacter iranicum
    20215Corynebacterium iranicum

@ref: 3183

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Rathayibacter

species: Rathayibacter iranicus

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

strain designation: 66-807, NCCPB 2253

type strain: yes

Morphology

cell morphology

  • @ref: 120281
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19725Cream10-14 days5006
19725Cream10-14 days5425
19725Cream10-14 days5428
19725Cream10-14 days5530
19725Cream10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
19725noISP 2
19725no5006
19725no5425
19725no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3183TRYPTICASE 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
19725ISP 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
197255006yesMedium: 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
197255425yesName: 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
197255428yes
197255530yes
34459MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
120281CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
3183positivegrowth28mesophilic
34459positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120281
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 19725
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 3183
  • 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
12028117632nitrate+reduction
12028116301nitrite-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
12028135581indoleyes

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-
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
120281oxidase-
120281catalase+1.11.1.6
120281urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19725--+------+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19725--++-----++---+----
120281-++-+----++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19725-++++-+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dateisolation date
3183Triticum aestivumTriticum aestivumIranIRNAsia
47876Triticum aestivum (Aestivum group)IranIRNAsia1966
67770Wheat (Triticum aestivum)Triticum aestivumIranIRNAsia
120281Food, Wheat, Triticum aesticumIranIRNAsia1966

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: KC188341
  • 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
3183yes1Risk group (German classification)
197251Risk group (German classification)
1202811Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rathayibacter iranicus partial 16S rRNA gene, type strain DSM 7484AM4106841270ena59737
20218Rathayibacter iranicus 16S ribosomal RNA gene, partial sequenceU961841270ena59737
20218Rathayibacter iranicus partial 16S rRNA gene, strain LMG3677TFR728296442ena59737
20218Rathayibacter iranicus strain VKM Ac-1602 16S ribosomal RNA gene, partial sequenceKC1883411489ena59737

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602GCA_009806955contigncbi1328868
66792Rathayibacter iranicus NCPPB 2253 = VKM Ac-16021328868.4wgspatric1328868
66792Rathayibacter iranicus strain DSM 748459737.5wgspatric59737
66792Rathayibacter iranicus DSM 74842846098012draftimg59737
67770Rathayibacter iranicus NCCPB 2253GCA_004011115completencbi59737
67770Rathayibacter iranicus DSM 7484GCA_002933035scaffoldncbi59737
67770Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602GCA_003149025scaffoldncbi1328868

GC content

@refGC-contentmethod
6777063thermal denaturation, midpoint method (Tm)
6777066high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.31no
gram-positiveyes94.005no
anaerobicno99.36no
halophileno86.897no
spore-formingno93.835no
glucose-utilyes86.58no
aerobicyes90.154no
flagellatedno97.84no
thermophileno98.824no
glucose-fermentno89.745yes

External links

@ref: 3183

culture collection no.: DSM 7484, ICMP 3496, NCPPB 2253, VKM Ac-1602, CCUG 23897, LMG 3677, JCM 9308, CECT 4208, CFBP 807, CIP 104037, ICPB CI148, PDDCC 3496

straininfo link

  • @ref: 76930
  • straininfo: 1754

literature

  • Pubmed-ID: 31306897
  • title: New glycopolymers containing both D- and L-rhamnopyranoses from Rathayibacter iranicus VKM Ac-1602(T) cell wall.
  • authors: Dmitrenok AS, Shashkov AS, Streshinskaya GM, Tul'skaya EM, Potekhina NV, Senchenkova SN, Dorofeeva LV, Evtushenko LI
  • journal: Carbohydr Res
  • DOI: 10.1016/j.carres.2019.06.007
  • year: 2019
  • mesh: Actinobacteria/*cytology, Carbohydrate Sequence, Cell Wall/*chemistry, Glycosylation, Monosaccharides/analysis, Pyrans/*chemistry, Rhamnose/*chemistry, Stereoisomerism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3183Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7484)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7484
19725Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7484.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
34459Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15901
47876Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23897)https://www.ccug.se/strain?id=23897
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
76930Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1754.1StrainInfo: A central database for resolving microbial strain identifiers
120281Curators of the CIPCollection of Institut Pasteur (CIP 104037)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104037