Strain identifier
BacDive ID: 7484
Type strain:
Species: Rathayibacter iranicus
Strain Designation: 66-807, NCCPB 2253
Strain history: CIP <- 1994, VKM <- ICMP
NCBI tax ID(s): 1328868 (strain), 59737 (species)
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 id | Matching level |
---|---|
1328868 | strain |
59737 | species |
strain history
@ref | history |
---|---|
3183 | <- NCPPB <- M. Ride, 66-807 <- F. Eskandari |
67770 | ICMP 3496 <-- C. N. Hale CL2 <-- NCPPB 2253 <-- M. Ride 66-807. |
120281 | CIP <- 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
@ref synonym 20215 Clavibacter iranicus 20215 Clavibacter iranicum 20215 Corynebacterium 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
@ref | colony color | incubation period | medium used |
---|---|---|---|
19725 | Cream | 10-14 days | 5006 |
19725 | Cream | 10-14 days | 5425 |
19725 | Cream | 10-14 days | 5428 |
19725 | Cream | 10-14 days | 5530 |
19725 | Cream | 10-14 days | ISP 2 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19725 | no | ISP 2 |
19725 | no | 5006 |
19725 | no | 5425 |
19725 | no | 5530 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3183 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | 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 |
19725 | 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 | |
19725 | 5006 | yes | Medium: 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 | |
19725 | 5425 | yes | Name: 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 | |
19725 | 5428 | yes | ||
19725 | 5530 | yes | ||
34459 | MEDIUM 29- Brain heart agar | yes | Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g) | |
120281 | CIP Medium 29 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3183 | positive | growth | 28 | mesophilic |
34459 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
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
@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 |
120281 | 17632 | nitrate | + | reduction |
120281 | 16301 | nitrite | - | reduction |
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 |
120281 | 35581 | indole | yes |
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 | esterase lipase (C 8) | + | |
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 |
120281 | oxidase | - | |
120281 | catalase | + | 1.11.1.6 |
120281 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19725 | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19725 | - | - | + | + | - | - | - | - | - | + | + | - | - | - | + | - | - | - | - | |
120281 | - | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19725 | - | + | + | + | + | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
3183 | Triticum aestivum | Triticum aestivum | Iran | IRN | Asia | ||
47876 | Triticum aestivum (Aestivum group) | Iran | IRN | Asia | 1966 | ||
67770 | Wheat (Triticum aestivum) | Triticum aestivum | Iran | IRN | Asia | ||
120281 | Food, Wheat, Triticum aesticum | Iran | IRN | Asia | 1966 |
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
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
3183 | yes | 1 | Risk group (German classification) |
19725 | 1 | Risk group (German classification) | |
120281 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rathayibacter iranicus partial 16S rRNA gene, type strain DSM 7484 | AM410684 | 1270 | ena | 59737 |
20218 | Rathayibacter iranicus 16S ribosomal RNA gene, partial sequence | U96184 | 1270 | ena | 59737 |
20218 | Rathayibacter iranicus partial 16S rRNA gene, strain LMG3677T | FR728296 | 442 | ena | 59737 |
20218 | Rathayibacter iranicus strain VKM Ac-1602 16S ribosomal RNA gene, partial sequence | KC188341 | 1489 | ena | 59737 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602 | GCA_009806955 | contig | ncbi | 1328868 |
66792 | Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602 | 1328868.4 | wgs | patric | 1328868 |
66792 | Rathayibacter iranicus strain DSM 7484 | 59737.5 | wgs | patric | 59737 |
66792 | Rathayibacter iranicus DSM 7484 | 2846098012 | draft | img | 59737 |
67770 | Rathayibacter iranicus NCCPB 2253 | GCA_004011115 | complete | ncbi | 59737 |
67770 | Rathayibacter iranicus DSM 7484 | GCA_002933035 | scaffold | ncbi | 59737 |
67770 | Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602 | GCA_003149025 | scaffold | ncbi | 1328868 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 63 | thermal denaturation, midpoint method (Tm) |
67770 | 66 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 93.31 | no |
gram-positive | yes | 94.005 | no |
anaerobic | no | 99.36 | no |
halophile | no | 86.897 | no |
spore-forming | no | 93.835 | no |
glucose-util | yes | 86.58 | no |
aerobic | yes | 90.154 | no |
flagellated | no | 97.84 | no |
thermophile | no | 98.824 | no |
glucose-ferment | no | 89.745 | yes |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3183 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7484) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7484 | |||
19725 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM7484.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 | |
34459 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15901 | ||||
47876 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 23897) | https://www.ccug.se/strain?id=23897 | |||
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 | |||
76930 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1754.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120281 | Curators of the CIP | Collection of Institut Pasteur (CIP 104037) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104037 |