Name: Rathayibacter iranicus 66-807
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7484

Type strain:

Species: Rathayibacter iranicus

Strain Designation: 66-807, NCCPB 2253

Culture col. 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

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

NCBI tax ID(s): 1328868 (strain), 59737 (species)

SI-ID 1754

LMG 3677, ICMP 3496, NCPPB 2253, PDDCC 3496, CCUG 23897, CIP 104037, VKM Ac-1602, DSM 7484, JCM 9308, CECT 4208, CFBP 807

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Rathayibacter*
	Species	**Rathayibacter iranicus**
	Full Scientific Name (LPSN)	Rathayibacter iranicus (Carlson and Vidaver 1982 ex Scharif 1961) Zgurskaya et al. 1993

	Synonym	Clavibacter iranicus
	Synonym	Clavibacter iranicum
	Synonym	Corynebacterium iranicum

Information on morphological and physiological properties Morphology

[Ref.: #120281]	Gram stain	positive

[Ref.: #120281]	Cell shape	rod-shaped

[Ref.: #120281]	Motility	no

[Ref.: #19725]	Colony color	Cream
[Ref.: #19725]	Incubation period	10-14 days
[Ref.: #19725]	Cultivation medium used	5006

[Ref.: #19725]	Colony color	Cream
[Ref.: #19725]	Incubation period	10-14 days
[Ref.: #19725]	Cultivation medium used	5425

[Ref.: #19725]	Colony color	Cream
[Ref.: #19725]	Incubation period	10-14 days
[Ref.: #19725]	Cultivation medium used	5428

[Ref.: #19725]	Colony color	Cream
[Ref.: #19725]	Incubation period	10-14 days
[Ref.: #19725]	Cultivation medium used	5530

[Ref.: #19725]	Colony color	Cream
[Ref.: #19725]	Incubation period	10-14 days
[Ref.: #19725]	Cultivation medium used	ISP 2

[Ref.: #19725]	Multicellular complex forming ability	no
[Ref.: #19725]	Medium Name (multicellularity)	ISP 2

[Ref.: #19725]	Multicellular complex forming ability	no
[Ref.: #19725]	Medium Name (multicellularity)	5006

[Ref.: #19725]	Multicellular complex forming ability	no
[Ref.: #19725]	Medium Name (multicellularity)	5425

[Ref.: #19725]	Multicellular complex forming ability	no
[Ref.: #19725]	Medium Name (multicellularity)	5530

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3183]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #3183]

Culture medium growth

[Ref.: #3183]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3183]

Culture medium composition

expand / minimize

[Ref.: #19725]

Culture medium

ISP 2

[Ref.: #19725]

Culture medium growth

[Ref.: #19725]

Culture medium composition

expand / minimize

[Ref.: #19725]

Culture medium

5006

[Ref.: #19725]

Culture medium growth

[Ref.: #19725]

Culture medium composition

expand / minimize

[Ref.: #19725]

Culture medium

5425

[Ref.: #19725]

Culture medium growth

[Ref.: #19725]

Culture medium composition

expand / minimize

[Ref.: #19725]

Culture medium

5428

[Ref.: #19725]

Culture medium growth

[Ref.: #19725]

Culture medium

5530

[Ref.: #19725]

Culture medium growth

[Ref.: #34459]

Culture medium

MEDIUM 29- Brain heart agar

[Ref.: #34459]

Culture medium growth

[Ref.: #34459]

Culture medium composition

expand / minimize

[Ref.: #120281]

Culture medium

CIP Medium 29

[Ref.: #120281]

Culture medium growth

[Ref.: #120281]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #3183]	growth	28 °C
[Ref.: #34459]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #3183]	Temperature range	mesophilic
[Ref.: #34459]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120281]

Oxygen tolerance

obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #19725]		NaCl		maximum	5	%

[Ref.: #3183]	Murein short key	B07
[Ref.: #3183]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #67770]

Observation

quinones: MK-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E, API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #120281]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #120281]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E, API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #120281]	indole ChEBI	yes
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #120281]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne, API 20E
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #120281]	oxidase	-
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #120281]	urease	-	3.5.1.5
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne, API 20E
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #19725]	506	-	+	+	+	+	-	+	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #19725]	271	-	-	+	-	-	-	-	-	-	+	-	not determinedn.d.	-	-	-	-	-	-	+	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19725]	549	not determinedn.d.	-	-	+	+	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-
[Ref.: #120281]	7776	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #3183]	Sample type/isolated from	Triticum aestivum
[Ref.: #3183]	Host species	Triticum aestivum
[Ref.: #3183]	Country	Iran
[Ref.: #3183]	Country ISO 3 Code	IRN
[Ref.: #3183]	Continent	Asia

[Ref.: #47876]	Sample type/isolated from	Triticum aestivum (Aestivum group)
[Ref.: #47876]	Sampling date	1966
[Ref.: #47876]	Country	Iran
[Ref.: #47876]	Country ISO 3 Code	IRN
[Ref.: #47876]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Wheat (Triticum aestivum)
[Ref.: #67770]	Host species	Triticum aestivum
[Ref.: #67770]	Country	Iran
[Ref.: #67770]	Country ISO 3 Code	IRN
[Ref.: #67770]	Continent	Asia

[Ref.: #120281]	Sample type/isolated from	Food, Wheat, Triticum aesticum
[Ref.: #120281]	Country	Iran
[Ref.: #120281]	Country ISO 3 Code	IRN
[Ref.: #120281]	Continent	Asia
[Ref.: #120281]	Isolation date	1966
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC188341 (>99% sequence identity) for Rathayibacter from Microbeatlas

Aquatic Samples	712
Soil Samples	2646
Animal Samples	2197
Plant Samples	2536
Total Samples	8091

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #3183]	Pathogenicity (plant)	yes
[Ref.: #3183]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19725]	Biosafety level	1	Risk group (German classification)
[Ref.: #120281]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Rathayibacter iranicus partial 16S rRNA gene, type strain DSM 7484	AM410684	1270	ENA	59737 tax ID	*
[Ref.: #20218]	Rathayibacter iranicus 16S ribosomal RNA gene, partial sequence	U96184	1270	ENA	59737 tax ID	*
[Ref.: #20218]	Rathayibacter iranicus partial 16S rRNA gene, strain LMG3677T	FR728296	442	ENA	59737 tax ID	*
[Ref.: #20218]	Rathayibacter iranicus strain VKM Ac-1602 16S ribosomal RNA gene, partial sequence	KC188341	1489	ENA	59737 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rathayibacter iranicus NCCPB 2253	GCA_004011115	complete	GenBank	59737 tax ID
[Ref.: #67770]	Rathayibacter iranicus DSM 7484	GCA_002933035	scaffold	GenBank	59737 tax ID
[Ref.: #67770]	Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602	GCA_003149025	scaffold	GenBank	1328868 tax ID
[Ref.: #66792]	Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602	GCA_009806955	contig	GenBank	1328868 tax ID	*
[Ref.: #66792]	Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602	1328868.4	wgs	PATRIC	1328868 tax ID	*
[Ref.: #66792]	Rathayibacter iranicus strain DSM 7484	59737.5	wgs	PATRIC	59737 tax ID	*

[Ref.: #67770]	GC-content	63 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	66 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602 PATRIC: 1328868.4
[Ref.: #69480]	motile	no	93.31	no
[Ref.: #69480]	gram-positive	yes	94.005	no
[Ref.: #69480]	anaerobic	no	99.36	no
[Ref.: #69480]	halophile	no	86.897	no
[Ref.: #69480]	spore-forming	no	93.835	no
[Ref.: #69480]	glucose-util	yes	86.58	no
[Ref.: #69480]	aerobic	yes	90.154	no
[Ref.: #69480]	flagellated	no	97.84	no
[Ref.: #69480]	thermophile	no	98.824	no
[Ref.: #69480]	glucose-ferment	no	89.745	yes

Availability in culture collections 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

[Ref.: #76930]

SI-ID 1754

Literature:

	Title	Authors	Journal	DOI	Year
	New glycopolymers containing both D- and L-rhamnopyranoses from Rathayibacter iranicus VKM Ac-1602(T) cell wall.	Dmitrenok AS, Shashkov AS, Streshinskaya GM, Tul'skaya EM, Potekhina NV, Senchenkova SN, Dorofeeva LV, Evtushenko LI	Carbohydr Res	10.1016/j.carres.2019.06.007	2019	*

References

#3183

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7484

#19725

Wink, J.: 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.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#34459 ; Curators of the CIP;
#47876 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 23897

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#76930

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID1754.1 )

#120281 Collection of Institut Pasteur ; Curators of the CIP; CIP 104037
* These data were automatically processed and therefore are not curated

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Search for species Rathayibacter iranicus in external resources:
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Rathayibacter iranicus NCPPB 2253 = VKM Ac-1602

Change proposal

Change proposal