Name: Xanthomonas cissicola PC1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13144

Type strain:

Species: Xanthomonas cissicola

Strain Designation: PC1

Culture col. no.: DSM 21306, ATCC 33616, CCM 2888, CCUG 18839, CIP 106723, ICMP 8561, LMG 2167, NCPPB 2982, JCM 13362, CIP 105155, LMG 21719

Strain history: CIP <- 2000, CCM <- M. Goto: strain PC1, Agrobacterium sp.

NCBI tax ID(s): 86186 (species)

Section

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

motile
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 cissicola**
	Full Scientific Name (LPSN)	Xanthomonas cissicola (Takimoto 1939) Rudra and Gupta 2021

	Synonym	"Aplanobacter* cissicola"*
	Synonym	Pseudomonas cissicola

Information on morphological and physiological properties Morphology

[Ref.: #118291]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #118291]	Cell shape	rod-shaped

[Ref.: #118291]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.664

[Ref.: #118291]	Pigment production	no
[Ref.: #118291]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15429]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15429]

Culture medium growth

[Ref.: #15429]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15429]

Culture medium composition

expand / minimize

[Ref.: #40329]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #40329]

Culture medium growth

[Ref.: #40329]

Culture medium composition

expand / minimize

[Ref.: #118291]

Culture medium

CIP Medium 72

[Ref.: #118291]

Culture medium growth

[Ref.: #118291]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #15429]		growth	28 °C
[Ref.: #40329]		growth	25 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #118291]		growth	25-30 °C
[Ref.: #118291]	no	growth	5 °C
[Ref.: #118291]	no	growth	10 °C
[Ref.: #118291]	no	growth	37 °C
[Ref.: #118291]	no	growth	41 °C

[Ref.: #15429]	Temperature range	mesophilic
[Ref.: #40329]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #118291]	Temperature range	mesophilic
[Ref.: #118291]	Temperature range	psychrophilic
[Ref.: #118291]	Temperature range	mesophilic
[Ref.: #118291]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #118291]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Salt	Tested relation		Salt conc.
[Ref.: #118291]	NaCl		growth	0	%
[Ref.: #118291]	NaCl	no	growth	4	%
[Ref.: #118291]	NaCl	no	growth	6	%
[Ref.: #118291]	NaCl	no	growth	8	%
[Ref.: #118291]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #118291]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #118291]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #118291]	nitrate ChEBI	-	reduction
[Ref.: #118291]	nitrate ChEBI	-	respiration
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #118291]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #118291]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #118291]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118291]	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.: #118291]	amylase	+
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #118291]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE, API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118291]	caseinase	+	3.4.21.50
[Ref.: #118291]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #118291]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118291]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #118291]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #118291]	lipase	+
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #118291]	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.: #118291]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118291]	oxidase	-
[Ref.: #118291]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118291]	tryptophan deaminase	-
[Ref.: #118291]	tween esterase	+
[Ref.: #118291]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #46911]	7361	-	-	-	-	-	+	+	+	+	-	+	-	+	-	-	-	-	+	+	-	-

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.: #118291]	1797	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.: #118291]	9754	-	+	+	+	+	+	+	+	+	-	+	+	-	+	-	-	+	+	-	-

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

[Ref.: #15429]	Sample type/isolated from	Leaf spot of Cissus japonica
[Ref.: #15429]	Host species	Cissus japonica

[Ref.: #46911]	Sample type/isolated from	Leaf spot
[Ref.: #46911]	Country	Japan
[Ref.: #46911]	Country ISO 3 Code	JPN
[Ref.: #46911]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Leaf spot of Cissus japonica
[Ref.: #67770]	Host species	Cissus japonica
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #118291]	Sample type/isolated from	Plant, Leaf spot of Cissus japonica
[Ref.: #118291]	Country	Japan
[Ref.: #118291]	Country ISO 3 Code	JPN
[Ref.: #118291]	Continent	Asia
[Ref.: #118291]	Isolation date	1974
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #15429]	Pathogenicity (plant)	yes
[Ref.: #15429]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118291]	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.: #15429]	[Pseudomonas] cissicola gene for 16S rRNA, strain: ATCC 33616	AB021399	1503	ENA	86186 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Xanthomonas cissicola LMG21719	GCA_002019225	contig	GenBank	86186 tax ID
[Ref.: #67770]	Xanthomonas cissicola CCUG 18839	GCA_008801575	contig	GenBank	86186 tax ID
[Ref.: #66792]	[Pseudomonas] cissicola strain LMG21719	86186.3	wgs	PATRIC	86186 tax ID	*
[Ref.: #66792]	[Pseudomonas] cissicola strain CCUG 18839	86186.4	wgs	PATRIC	86186 tax ID	*
[Ref.: #66792]	Pseudomonas cissicola LMG21719	2791355361	draft	JGI IMG/M	86186 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: [Pseudomonas] cissicola strain CCUG 18839 PATRIC: 86186.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Pseudomonas] cissicola strain LMG21719 PATRIC: 86186.3
[Ref.: #69480]	motile	yes	79.613	no
[Ref.: #69480]	flagellated	no	84.016	no
[Ref.: #69480]	gram-positive	no	98.084	no
[Ref.: #69480]	anaerobic	no	99.057	no
[Ref.: #69480]	halophile	no	95.185	no
[Ref.: #69480]	spore-forming	no	95.052	no
[Ref.: #69480]	glucose-util	yes	94.112	no
[Ref.: #69480]	aerobic	yes	95.407	no
[Ref.: #69480]	thermophile	no	98.967	yes
[Ref.: #69480]	glucose-ferment	no	90.22	yes

Availability in culture collections External links

[Ref.: #15429]

Culture collection no.

DSM 21306, ATCC 33616, CCM 2888, CCUG 18839, CIP 106723, ICMP 8561, LMG 2167, NCPPB 2982, JCM 13362, CIP 105155, LMG 21719

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

#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;

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#118291 Collection of Institut Pasteur ; Curators of the CIP; CIP 106723
* These data were automatically processed and therefore are not curated

Change proposal

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[Pseudomonas] cissicola strain CCUG 18839

[Pseudomonas] cissicola strain LMG21719

Change proposal

Change proposal