Rathayibacter toxicus (DSM 7488, ATCC 49908, ICMP 9525)

Name: Rathayibacter toxicus (DSM 7488, ATCC 49908, ICMP 9525)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7483

Type strain

Strain Designation CS14

Culture col. no. DSM 7488 ATCC 49908 ICMP 9525 NCPPB 3552 CS14 3 more

NCBI tax ID(s) 1123052 145458

Special Collections DSMZ JCM CIP Wink compendium

History DSMZ <- NCPPB <- I.T. Riley, CS14 JCM <-- ICMP 9525 <-- I. T. Riley CS14. CIP <- 1995, ATCC <- I.T. Riley

Links

Rathayibacter toxicus CS14 is a Gram-positive, rod-shaped bacterium that was isolated from annual ryegrass.

Gram-positive rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 2091

ATCC 49908,ICMP 9525,NCPPB 3552,CIP 104617,DSM 7488,JCM 9669

@ref 20215

Last LPSN update 2026-05-29 08:26:39

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Rathayibacter

Species Rathayibacter toxicus

Full scientific name Rathayibacter toxicus (Riley and Ophel 1992) Sasaki et al. 1998

Synonyms (1)

Clavibacter toxicus

BacDive ID	Other strains from **Rathayibacter toxicus** (1)	Type strain
105494	R. toxicus STH00001(ZIMET), CS14, ICMB9525, HKI 0001

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123568	positive	rod-shaped
125439			98.308
125439	positive		97.28
125438			92
125438	positive		91.611

Colony morphology

@ref	Colony color	Incubation period	Medium used
20201	Golden yellow (1004)	10-14 days	5006
20201	Golden yellow (1004)	10-14 days	ISP 2
20201	Golden yellow (1004)	10-14 days	ISP 4
20201	Golden yellow (1004)	10-14 days	ISP 5
20201	Golden yellow (1004)	10-14 days	ISP 6
20201	Golden yellow (1004)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20201		5006
20201		ISP 2
20201		ISP 4
20201		ISP 5
20201		ISP 6
20201		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3187	DOEPEL MEDIUM (DSMZ Medium 698)	Medium recipe at MediaDive	Name: DOEPEL MEDIUM (DSMZ Medium 698) Composition: Yeast extract 8.0 g/l Casein hydrolysate 8.0 g/l Glucose 5.0 g/l K2HPO4 2.0 g/l MgSO4 0.3 g/l Distilled water
20201	5006		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
20201	ISP 2		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
20201	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20201	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20201	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20201	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
39068	MEDIUM 111 - for Clavibacter		Distilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
123568	CIP Medium 111	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3187	positive	growth	28
20201	positive	optimum	28
39068	positive	growth	30
67770	positive	growth	30
123568	positive	growth	30
123568	negative	growth	10
123568	negative	growth	37
123568	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	95.559

Spore formation

@ref	Spore formation	Confidence
125439		97.517

Murein

@ref	Murein short key	Type
3187	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Observation

67770

Observationquinones: MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
123568	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
123568	17632 ChEBI	nitrate	-	reduction
123568	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
123568	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
123568	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	+			from API 20E
123568	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123568	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
123568	beta-galactosidase	-	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
123568	caseinase	-	3.4.21.50
123568	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
123568	DNase	-
68382	esterase lipase (C 8)	+		from API zym
123568	gelatinase	-
68379	gelatinase	-		from API Coryne
68368	gelatinase	-		from API 20E
123568	lecithinase	-
68382	lipase (C 14)	-		from API zym
123568	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
123568	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
123568	oxidase	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
123568	tween esterase	-
123568	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	lipoate biosynthesis	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	pentose phosphate pathway	90.91	10 of 11
66794	valine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	factor 420 biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	ppGpp biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	metabolism of disaccharids	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	degradation of sugar alcohols	68.75	11 of 16
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	pyrimidine metabolism	66.67	30 of 45
66794	alanine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	citric acid cycle	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	Entner Doudoroff pathway	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	cysteine metabolism	55.56	10 of 18
66794	tryptophan metabolism	55.26	21 of 38
66794	lipid metabolism	54.84	17 of 31
66794	arginine metabolism	54.17	13 of 24
66794	histidine metabolism	51.72	15 of 29
66794	glycine metabolism	50	5 of 10
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	oxidative phosphorylation	49.45	45 of 91
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	glutathione metabolism	42.86	6 of 14
66794	propanol degradation	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	bacilysin biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	urea cycle	38.46	5 of 13
66794	d-xylose degradation	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	arachidonic acid metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
20201	-	-	-	-	-	-	-	-	-	+	-	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

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
20201	-	-	-	-	-	-	+	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
20201	not determinedn.d.	-	-	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-
123568	-	-	+	+	-	+	-	-	-	-	+	-	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
123568	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
123568	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
3187	annual ryegrass			Australia	AUS	Australia and Oceania
67770	Seed gall of Lolium rigidum	Lolium rigidum	Murray Bridge, South Australia	Australia	AUS	Australia and Oceania
123568	Animal, Nematode, galls on rye grass		Murray bridge	Australia	AUS	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence LC066140 (>99% sequence identity) for Rathayibacter toxicus subclade from Microbeatlas

Aquatic Samples	82
Soil Samples	951
Animal Samples	127
Plant Samples	184
Total Samples	1344

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3187	1	Risk group (German classification) According to TRBA 466
20201	1	German classification According to TRBA 466
123568	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM1477018v1 assembly for Rathayibacter toxicus FH79	complete	GCA_014770185	145458.45	8121190580	145458	97.83
67770	ASM42532v1 assembly for Rathayibacter toxicus DSM 7488	scaffold	GCA_000425325	1123052.5	2524023208	1123052	72.63

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Rathayibacter toxicus gene for 16S rRNA, partial sequence	D84127	1477	145458
67770	Rathayibacter toxicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 9669	LC066140	1463	145458
124043	Rathayibacter toxicus strain VKM Ac-1600 16S ribosomal RNA gene, partial sequence.	KX758073	1405	145458

GC content

@ref	GC-content (mol%)	Method
3187	67.0	thermal denaturation, midpoint method (Tm)
67770	67	thermal denaturation, midpoint method (Tm)
67770	60	high performance liquid chromatography (HPLC)
67770	61.5	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1477018v1 assembly for Rathayibacter toxicus FH79
NCBI: GCA_014770185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.56	no
125439	gram_stain	BacteriaNetⓘ	positive	97.28	no
125439	motility	BacteriaNetⓘ	no	98.31	no
125439	spore_formation	BacteriaNetⓘ	no	97.52	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rathayibacter toxicus DSM 7488
PATRIC: 1123052.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.61	no
125438	anaerobic	anaerobicⓘ	no	95.07	no
125438	spore-forming	spore-formingⓘ	no	86.52	no
125438	aerobic	aerobicⓘ	yes	77.45	no
125438	thermophilic	thermophileⓘ	no	92.36	yes
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium.	Arif M, Busot GY, Mann R, Rodoni B, Liu S, Stack JP.	PLoS One	10.1371/journal.pone.0156182	2016
Genetics	Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus.	Yasuhara-Bell J, Arif M, Busot GY, Mann R, Rodoni B, Stack JP.	Microorganisms	10.3390/microorganisms8030366	2020
	A study on the antioxidant and antimicrobial activities in the chloroformic and methanolic extracts of 6 important medicinal plants collected from North of Iran.	Hadadi Z, Nematzadeh GA, Ghahari S.	BMC Chem	10.1186/s13065-020-00683-5	2020
	Erratum to: "Rhamnose-Containing Cell Wall Glycopolymers from Rathayibacter toxicus VKM Ac-1600 and "Rathayibacter tanaceti" VKM Ac-2596" [Biochemistry (Moscow), 83, 717 (2018)].	Shashkov AS, Tul'skaya EM, Dmitrenok AS, Streshinskaya GM, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LI	Biochemistry (Mosc)	10.1134/S0006297918070106	2018
Metabolism	Rhamnose-Containing Cell Wall Glycopolymers from Rathayibacter toxicus VKM Ac-1600 and "Rathayibacter tanaceti" VKM Ac-2596.	Shashkov AS, Tul'skaya EM, Dmitrenok AS, Streshinskaya GM, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LI	Biochemistry (Mosc)	10.1134/S0006297918060093	2018

References

#3187	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7488
#20201	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 )
#39068	; Curators of the CIP;
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68371	Automatically annotated from API 50CH acid .
#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 .
#123568	Collection of Institut Pasteur ; Curators of the CIP; CIP 104617
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Rathayibacter toxicus (DSM 7488, ATCC 49908, ICMP 9525)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

API coryne

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014770185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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