Xanthomonas cassavae (DSM 18958, ICMP 204, LMG 673)

Name: Xanthomonas cassavae (DSM 18958, ICMP 204, LMG 673)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17606

Type strain

Strain Designation VdM 147, ZD1

Culture col. no. DSM 18958 ICMP 204 LMG 673 NCPPB 101 VdM 147 2 more

NCBI tax ID(s) 1219375 56450

Special Collections DSMZ

Links

Xanthomonas cassavae VdM 147 is a mesophilic plant pathogen that was isolated from Manihot esculenta, leaf spots.

mesophilic plant pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 5374

LMG 673,ICMP 204,NCPPB 101,PDDCC 204,DSM 18958,CFBP 4642

@ref 20215

Last LPSN update 2025-12-16 09:51:08

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas cassavae

Full scientific name Xanthomonas cassavae (ex Wiehe and Dowson 1953) Vauterin et al. 1995

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.8
125438	negative	98.75

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7804	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7804	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
125439		97.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
7804	Manihot esculenta, leaf spots	Manihot esculenta	Malawi	MWI	Africa

Taxonmaps

69479

Global distribution of 16S sequence Y10762 (>99% sequence identity) for Xanthomonas from Microbeatlas

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

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
7804		1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	20120625 assembly for Xanthomonas cassavae CFBP 4642	chromosome	GCA_000454545	1219375.3	2551306373	1219375	72.35
66792	ASM2078389v1 assembly for Xanthomonas cassavae CFBP 4642 NCPPB 101	contig	GCA_020783895	1219375.13	8118484188	1219375	41.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Xanthomonas cassavae strain LMG673 16S-23S ribosomal RNA intergenic spacer, complete sequence	AF209756	513		1219375
7804	X.cassavae 16S rRNA gene	Y10762	1502		1219375

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xanthomonas cassavae CFBP 4642 NCPPB 101
NCBI: GCA_020783895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.50	no
125439	motility	BacteriaNetⓘ	yes	82.10	no
125439	gram_stain	BacteriaNetⓘ	negative	97.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xanthomonas cassavae CFBP 4642
PATRIC: 1219375.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.75	no
125438	anaerobic	anaerobicⓘ	no	98.17	no
125438	spore-forming	spore-formingⓘ	no	88.86	no
125438	aerobic	aerobicⓘ	yes	80.59	no
125438	thermophilic	thermophileⓘ	no	96.98	yes
125438	flagellated	motile2+ⓘ	yes	68.19	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft Genome Sequence of the Xanthomonas cassavae Type Strain CFBP 4642.	Bolot S, Munoz Bodnar A, Cunnac S, Ortiz E, Szurek B, Noel LD, Arlat M, Jacques MA, Gagnevin L, Portier P, Fischer-Le Saux M, Carrere S, Koebnik R.	Genome Announc	10.1128/genomea.00679-13	2013
Metabolism	Antimicrobial activity of some macrophytes from Lake Manzalah (Egypt).	Fareed MF, Haroon AM, Rabeh SA.	Pak J Biol Sci	10.3923/pjbs.2008.2454.2463	2008
Phylogeny	Application of whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification and clustering analysis of pantoea species.	Rezzonico F, Vogel G, Duffy B, Tonolla M.	Appl Environ Microbiol	10.1128/aem.03112-09	2010
	Pathological and Molecular Characterization of Xanthomonas campestris Strains Causing Diseases of Cassava (Manihot esculenta).	Verdier V, Boher B, Maraite H, Geiger JP.	Appl Environ Microbiol	10.1128/aem.60.12.4478-4486.1994	1994

References

#7804	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18958
#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 )
#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) .
#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 .
#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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Xanthomonas cassavae (DSM 18958, ICMP 204, LMG 673)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000454545

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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