Name: Rathayibacter rathayi CE4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7482

Type strain:

Species: Rathayibacter rathayi

Strain Designation: CE4

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

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

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

SI-ID 13617

LMG 7288, ICMP 2574, NCPPB 2980, PDDCC 2574, CIP 104036, VKM Ac-1601, JCM 9307, IMI 347340, CECT 4210, CFBP 2406, DSM 7485

Special Collections

Other strains from Rathayibacter rathayi

Section

When using BacDive for research please cite our paper

Rathayibacter rathayi CE4 is a facultative anaerobe, mesophilic, Gram-positive plant pathogen that was isolated from Dactylis glomerata.

Gram-positive
rod-shaped
facultative anaerobe
mesophilic
plant pathogen
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Rathayibacter*
	Species	**Rathayibacter rathayi**
	Full Scientific Name (LPSN)	Rathayibacter rathayi (Smith 1913) Zgurskaya et al. 1993

	Synonym	Corynebacterium rathayi
	Synonym	"Aplanobacter* rathayi"*
	Synonym	Clavibacter rathayi

Information on morphological and physiological properties Morphology

[Ref.: #122141]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %92.118
[Ref.: #125439]	Gram stain	positive Confidence in %97.1

[Ref.: #122141]	Cell shape	rod-shaped

[Ref.: #122141]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %90.5

[Ref.: #19726]	Colony color	Ivory
[Ref.: #19726]	Incubation period	10-14 days
[Ref.: #19726]	Cultivation medium used	5006

[Ref.: #19726]	Colony color	Ivory
[Ref.: #19726]	Incubation period	10-14 days
[Ref.: #19726]	Cultivation medium used	5425

[Ref.: #19726]	Colony color	Ivory
[Ref.: #19726]	Incubation period	10-14 days
[Ref.: #19726]	Cultivation medium used	5428

[Ref.: #19726]	Colony color	Ivory
[Ref.: #19726]	Incubation period	10-14 days
[Ref.: #19726]	Cultivation medium used	5530

[Ref.: #19726]	Colony color	Ivory
[Ref.: #19726]	Incubation period	10-14 days
[Ref.: #19726]	Cultivation medium used	ISP 2

[Ref.: #19726]	Multicellular complex forming ability	no
[Ref.: #19726]	Medium Name (multicellularity)	ISP 2

[Ref.: #19726]	Multicellular complex forming ability	no
[Ref.: #19726]	Medium Name (multicellularity)	5006

[Ref.: #19726]	Multicellular complex forming ability	no
[Ref.: #19726]	Medium Name (multicellularity)	5425

[Ref.: #19726]	Multicellular complex forming ability	no
[Ref.: #19726]	Medium Name (multicellularity)	5530

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19726]

Culture medium

ISP 2

[Ref.: #19726]

Culture medium growth

[Ref.: #19726]

Culture medium composition

expand / minimize

[Ref.: #19726]

Culture medium

5006

[Ref.: #19726]

Culture medium growth

[Ref.: #19726]

Culture medium composition

expand / minimize

[Ref.: #19726]

Culture medium

5425

[Ref.: #19726]

Culture medium growth

[Ref.: #19726]

Culture medium composition

expand / minimize

[Ref.: #19726]

Culture medium

5428

[Ref.: #19726]

Culture medium growth

[Ref.: #19726]

Culture medium

5530

[Ref.: #19726]

Culture medium growth

[Ref.: #3184]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #3184]

Culture medium growth

[Ref.: #3184]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3184]

Culture medium composition

expand / minimize

[Ref.: #35609]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #35609]

Culture medium growth

[Ref.: #35609]

Culture medium composition

expand / minimize

[Ref.: #122141]

Culture medium

CIP Medium 72

[Ref.: #122141]

Culture medium growth

[Ref.: #122141]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122141]

Culture medium

CIP Medium 111

[Ref.: #122141]

Culture medium growth

[Ref.: #122141]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #3184]	growth	28 °C
[Ref.: #35609]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122141]

Oxygen tolerance

facultative anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #19726]		NaCl		maximum	5	%

[Ref.: #3184]	Murein short key	B07
[Ref.: #3184]	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.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne, API 20E
[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.: #122141]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #122141]	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.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne, API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #122141]	indole ChEBI	no
[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.: #68379]	alkaline phosphatase	+	3.1.3.1	* from 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.: #122141]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68368]	gelatinase	-		* from API 20E, API Coryne
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[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.: #122141]	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.: #122141]	urease	-	3.5.1.5
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E, API Coryne
[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.: #19726]	507	-	+	+	+	+	-	+	-	-	-	-	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.: #19726]	272	+	-	-	+	-	-	-	-	-	+	-	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.: #19726]	550	not determinedn.d.	+	-	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-
[Ref.: #122141]	7775	-	-	-	-	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #3184]	Sample type/isolated from	Dactylis glomerata
[Ref.: #3184]	Host species	Dactylis glomerata
[Ref.: #3184]	Country	New Zealand
[Ref.: #3184]	Country ISO 3 Code	NZL
[Ref.: #3184]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Cooksfoot (Dactylis glomerata)
[Ref.: #67770]	Host species	Dactylis glomerata
[Ref.: #67770]	Country	New Zealand
[Ref.: #67770]	Country ISO 3 Code	NZL
[Ref.: #67770]	Continent	Australia and Oceania

[Ref.: #122141]	Sample type/isolated from	Dactylis glomerata
[Ref.: #122141]	Country	New Zealand
[Ref.: #122141]	Country ISO 3 Code	NZL
[Ref.: #122141]	Continent	Australia and Oceania
* 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 X77439 (>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.: #3184]	Pathogenicity (plant)	yes
[Ref.: #3184]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19726]	Biosafety level	1	Risk group (German classification)
[Ref.: #122141]	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.: #3184]	R.rathayi (DSM 7485) 16S rRNA gene	X77439	1474	GenBank ENA	33887 tax ID
[Ref.: #124043]	Pseudomonas putida strain mipp_04 16S ribosomal RNA gene, partial sequence.	KT760415	1016	GenBank ENA	33887 tax ID	*
[Ref.: #124043]	Pseudomonas putida strain mipp_04 16S ribosomal RNA gene, partial sequence.	KT760416	1016	GenBank ENA	33887 tax ID	*
[Ref.: #124043]	Pseudomonas putida strain mipp_04 16S ribosomal RNA gene, partial sequence.	KT760417	1016	GenBank ENA	33887 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 rathayi NCPPB 2980 = VKM Ac-1601	GCA_900215645	scaffold	GenBank ENA	1328865 tax ID
[Ref.: #67770]	Rathayibacter rathayi DSM 7485	GCA_007828845	contig	GenBank ENA	33887 tax ID
[Ref.: #66792]	Rathayibacter rathayi NCPPB 2980 = VKM Ac-1601	1328865.4	wgs	PATRIC	1328865 tax ID	*
[Ref.: #66792]	Rathayibacter rathayi strain DSM 7485	33887.27	complete	PATRIC	33887 tax ID	*
[Ref.: #66792]	Rathayibacter rathayi strain DSM 7485	33887.29	wgs	PATRIC	33887 tax ID	*
[Ref.: #66792]	Rathayibacter rathayi DSM 7485	2840627797	complete	JGI IMG/M	33887 tax ID	*

[Ref.: #67770]

GC-content

67 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rathayibacter rathayi DSM 7485 NCBI: GCA_004011095.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	92.118	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.954	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.543	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	76.958	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.929	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	90.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rathayibacter rathayi strain DSM 7485 PATRIC: 33887.27
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	63.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	82.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	97.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	microaerophile	69.6

Availability in culture collections 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

[Ref.: #76927]

SI-ID 13617

References

#3184

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7485

#19726

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 )

#35609 ; Curators of the CIP;

#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 .

#76927

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-ID13617.1 )

#122141 Collection of Institut Pasteur ; Curators of the CIP; CIP 104036

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Rathayibacter rathayi DSM 7485

Rathayibacter rathayi strain DSM 7485

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