Xanthomonas cissicola (DSM 21306, ATCC 33616, CCM 2888)

Name: Xanthomonas cissicola (DSM 21306, ATCC 33616, CCM 2888)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13144

Type strain

Strain Designation PC1

Culture col. no. DSM 21306 ATCC 33616 CCM 2888 CCUG 18839 CIP 106723 7 more

NCBI tax ID(s) 86186

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- CCM <- M. Goto, Shizuoka University, Japan JCM <-- CIP 106723 <-- CCM 2888 <-- M. Goto PC1. CIP <- 2000, CCM <- M. Goto: strain PC1, Agrobacterium sp.

Links

Xanthomonas cissicola PC1 is an obligate aerobe, Gram-negative, motile plant pathogen that was isolated from Leaf spot of Cissus japonica.

Gram-negative motile rod-shaped obligate aerobe plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92385

LMG 2167,ATCC 33616,CCM 2888,ICMP 4289,ICMP 8561,NCPPB 2982,PDDCC 4289,CCUG 18839,CIP 106723,CIP 105155,CFBP 2432,LMG 21719,BCRC 15826,CCRC 15826,KACC 10136,JCM 13362,DSM 21306

@ref 20215

Last LPSN update 2026-05-29 08:27:58

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas cissicola

Full scientific name Xanthomonas cissicola (Takimoto 1939) Rudra and Gupta 2021

Synonyms (2)

Pseudomonas cissicola
"Aplanobacter cissicola"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118291	negative	rod-shaped
125438	negative		98.5
125439	negative		97.95

Pigmentation

@ref	Production	Name
118291		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15429	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
40329	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118291	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
15429	positive	growth	28
40329	positive	growth	25
67770	positive	growth	25
118291	positive	growth	25-30
118291	negative	growth	5
118291	negative	growth	10
118291	negative	growth	37
118291	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
118291	obligate aerobe
125439	obligate aerobe	99.552

Spore formation

@ref	Spore formation	Confidence
125439		99.573

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118291	NaCl	positive	growth	0 %
118291	NaCl		growth	4 %
118291	NaCl		growth	6 %
118291	NaCl		growth	8 %
118291	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
118291	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
118291	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
118291	17632 ChEBI	nitrate	-	reduction
118291	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
118291	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
118291	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
118291	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118291	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118291	amylase	+
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
118291	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118291	caseinase	+	3.4.21.50
118291	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
118291	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118291	gelatinase	+
68369	gelatinase	+		from API 20NE
118291	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118291	lipase	+
68382	lipase (C 14)	+		from API zym
118291	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118291	ornithine decarboxylase	-	4.1.1.17
118291	oxidase	-
118291	protease	+
68382	trypsin	+	3.4.21.4	from API zym
118291	tryptophan deaminase	-
118291	tween esterase	+
118291	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

Fatty acid profile

Metadata FA analysis

@ref

46911

Fatty acid	Percentage	ECL
C15:0 ISO	42.6	14.621
C16:1 ω7c	19.4	15.819
C15:0 ANTEISO	8	14.711
C16:0 10-methyl	7.1	16.433
C17:0 iso	5.3	16.629
C16:0	3.5	16
C11:0 ISO 3OH	3.2	12.09
C13:0 ISO 3OH	2.3	14.11
C14:0	2	14
unknown 11.798	1.9	11.798
C15:0	1.8	15
C10:0 3OH	1.7	11.423
C16:1 ω9c	1.3	15.774

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
118291	-	+	+	+	+	+	+	+	+	-	+	+	-	+	-	-	+	+	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
46911	-	-	-	-	-	+	+	+	+	-	+	-	+	-	-	-	-	+	+	-	-

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
118291	not determinedn.d.	+	+	+	+	+	-	+	+	-	-	-	-	-	-	-	+	+	-	+	-	-	+	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	+	+	-	+	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent	Isolation date
15429	Leaf spot of Cissus japonica	Cissus japonica
46911	Leaf spot		Japan	JPN	Asia
67770	Leaf spot of Cissus japonica	Cissus japonica	Japan	JPN	Asia
118291	Plant, Leaf spot of Cissus japonica		Japan	JPN	Asia	1974

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
15429		1	Risk group (German classification) According to TRBA 466
118291		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
67770	ASM201922v1 assembly for Xanthomonas cissicola LMG21719	contig	GCA_002019225	86186.3	2791355361	86186	16.57
67770	ASM880157v1 assembly for Xanthomonas cissicola CCUG 18839	contig	GCA_008801575	86186.4		86186	16.27

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15429	[Pseudomonas] cissicola gene for 16S rRNA, strain: ATCC 33616	AB021399	1503		86186

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM201922v1 assembly for Xanthomonas cissicola LMG21719
BV-BRC: 86186.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.55	no
125439	gram_stain	BacteriaNetⓘ	negative	97.95	no
125439	spore_formation	BacteriaNetⓘ	no	99.57	no
125439	motility	BacteriaNetⓘ	yes	79.19	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Pseudomonas] cissicola strain LMG21719
PATRIC: 86186.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	97.74	no
125438	aerobic	aerobicⓘ	yes	86.04	yes
125438	spore-forming	spore-formingⓘ	no	86.69	no
125438	thermophilic	thermophileⓘ	no	98.98	no
125438	flagellated	motile2+ⓘ	yes	67.34	no

Literature

References

#15429	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21306
#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 )
#40329	; Curators of the CIP;
#46911	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 18839
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#118291	Collection of Institut Pasteur ; Curators of the CIP; CIP 106723
#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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