Name: Xanthomonas hortorum A960701
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17599

Type strain:

Species: Xanthomonas hortorum

Strain Designation: A960701

Culture col. no.: DSM 16794, CFBP 4188, CIP 106774

Strain history: CIP <- 2000, CFBP <- J.L. Tanguy: strain A960701

Other strains from Xanthomonas hortorum

X. hortorum DSM 19143, ICMP 453, LMG 733, NCPPB ... (type strain)
X. hortorum DSM 50857
X. hortorum DSM 50858
X. hortorum 1248/9, DSM 50859

Section

Xanthomonas hortorum A960701 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from Cynara scolymus.

Gram-negative
motile
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Xanthomonas*
	Species	**Xanthomonas hortorum**
	Full Scientific Name (LPSN)	Xanthomonas hortorum Vauterin et al. 1995

	Synonym	Xanthomonas cynarae
	Synonym	Xanthomonas gardneri

Information on morphological and physiological properties Morphology

[Ref.: #118830]	Gram stain	negative

[Ref.: #118830]	Cell shape	rod-shaped

[Ref.: #118830]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6606]

Culture medium

YPGA (DSMZ Medium 1015)

[Ref.: #6606]

Culture medium growth

[Ref.: #6606]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6606]

Culture medium composition

expand / minimize

[Ref.: #39578]

Culture medium

MEDIUM 29- Brain heart agar

[Ref.: #39578]

Culture medium growth

[Ref.: #39578]

Culture medium composition

expand / minimize

[Ref.: #118830]

Culture medium

CIP Medium 29

[Ref.: #118830]

Culture medium growth

[Ref.: #118830]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6606]		growth	28 °C
[Ref.: #39578]		growth	30 °C
[Ref.: #118830]		growth	5-30 °C
[Ref.: #118830]	no	growth	37 °C
[Ref.: #118830]	no	growth	41 °C

[Ref.: #6606]	Temperature range	mesophilic
[Ref.: #39578]	Temperature range	mesophilic
[Ref.: #118830]	Temperature range	mesophilic
[Ref.: #118830]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #118830]

Oxygen tolerance

obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #118830]	NaCl		growth	0-6	%
[Ref.: #118830]	NaCl	no	growth	8	%
[Ref.: #118830]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118830]	citrate ChEBI	+	carbon source
[Ref.: #118830]	esculin ChEBI	+	hydrolysis
[Ref.: #118830]	nitrate ChEBI	-	reduction
[Ref.: #118830]	nitrate ChEBI	-	respiration
[Ref.: #118830]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #118830]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #118830]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118830]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[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.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #118830]	amylase	+
[Ref.: #118830]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118830]	caseinase	+	3.4.21.50
[Ref.: #118830]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #118830]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118830]	gelatinase	+/-
[Ref.: #118830]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #118830]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118830]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118830]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118830]	oxidase	-
[Ref.: #118830]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118830]	tryptophan deaminase	-
[Ref.: #118830]	tween esterase	+
[Ref.: #118830]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	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
[Ref.: #118830]	1830	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.: #118830]	9796	-	+	+	+	-	+	+	-	+	+	+	+	-	+	-	-	+	+	-	-

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

[Ref.: #6606]	Sample type/isolated from	Cynara scolymus
[Ref.: #6606]	Host species	Cynara scolymus
[Ref.: #6606]	Geographic location (country and/or sea, region)	Brittany
[Ref.: #6606]	Country	France
[Ref.: #6606]	Country ISO 3 Code	FRA
[Ref.: #6606]	Continent	Europe

[Ref.: #118830]	Sample type/isolated from	Cynara scolymus
[Ref.: #118830]	Geographic location (country and/or sea, region)	Brittany
[Ref.: #118830]	Country	France
[Ref.: #118830]	Country ISO 3 Code	FRA
[Ref.: #118830]	Continent	Europe
[Ref.: #118830]	Isolation date	1996
* 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 AF208315 (>99% sequence identity) for Xanthomonas from Microbeatlas

Aquatic Samples	6826
Soil Samples	10026
Animal Samples	28252
Plant Samples	7048
Total Samples	52152

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

[Ref.: #6606]	Pathogenicity (plant)	yes
[Ref.: #6606]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118830]	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.: #6606]	Xanthomonas cynarae 16S ribosomal RNA gene, partial sequence	AF208315	1552	ENA	109214 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Xanthomonas hortorum pv. cynarae CFBP4188	GCA_002939985	scaffold	GenBank	2754057 tax ID	*
[Ref.: #66792]	Xanthomonas cynarae strain CFBP4188	109214.3	wgs	PATRIC	2754057 tax ID	*
[Ref.: #66792]	Xanthomonas cynarae CFBP4188	2878089750	draft	JGI IMG/M	109214 tax ID	*
[Ref.: #66792]	Xanthomonas hortorum pv. cynarae CFBP 4188	GCA_021352995	scaffold	GenBank	2754057 tax ID	*

[Ref.: #6606]

GC-content

63 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Xanthomonas hortorum pv. cynarae CFBP4188 NCBI: GCA_002939985.1
[Ref.: #69480]	flagellated	no	86.221	no
[Ref.: #69480]	gram-positive	no	97.845	no
[Ref.: #69480]	anaerobic	no	99.181	no
[Ref.: #69480]	aerobic	yes	94.401	no
[Ref.: #69480]	halophile	no	94.649	no
[Ref.: #69480]	spore-forming	no	95.004	no
[Ref.: #69480]	glucose-util	yes	93.563	no
[Ref.: #69480]	thermophile	no	99.477	yes
[Ref.: #69480]	motile	yes	80.105	no
[Ref.: #69480]	glucose-ferment	no	90.464	no

Availability in culture collections External links

[Ref.: #6606]

Culture collection no.

DSM 16794, CFBP 4188, CIP 106774

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Xanthomonas gardneri (ex Sutic 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trebaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses.	Timilsina S, Kara S, Jacques MA, Potnis N, Minsavage GV, Vallad GE, Jones JB, Fischer-Le Saux M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003104	2018	*
Phylogeny	Genomic and phenotypic characterization of Xanthomonas cynarae sp. nov., a new species that causes bacterial bract spot of artichoke (Cynara scolymus L.).	Trebaol G, Gardan L, Manceau C, Tanguy JL, Tirilly Y, Boury S	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1471	2000	*

References

#6606

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16794

#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 )

#39578 ; 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) .

#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) .

#118830 Collection of Institut Pasteur ; Curators of the CIP; CIP 106774
* These data were automatically processed and therefore are not curated

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Xanthomonas hortorum pv. cynarae CFBP4188

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