Cite this strain

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 1 more

NCBI tax ID(s) 1219375 56450

Special Collections DSMZ

Links

Name and taxonomic classification

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

Gram-negative mesophilic plant pathogen genome sequence 16S sequence Bacteria

SI-ID 5374

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

Last LPSN update 2024-12-09 10:45:03

Domain Bacteria

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

Spore formation

@ref	Spore formation	Confidence
125439		97.5

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.4

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

Safety information

Risk assessment

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

Sequence information

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 sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Xanthomonas cassavae CFBP 4642 NCPPB 101	GCA_020783895	contig		1219375
66792	Xanthomonas cassavae CFBP 4642	1219375.3	complete	PATRIC	1219375

Genome-based predictions

Predictions

Predictions from Diaspora project 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 Diaspora project 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

External links

Straininfo Link

@ref	Straininfo	Culture collections
86599	5374	LMG 673, ICMP 204, NCPPB 101, PDDCC 204, DSM 18958, CFBP 4642

Culture collection no.

Culture collection no.
DSM 18958
ICMP 204
LMG 673
NCPPB 101
VdM 147
ZD1

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 .
#86599	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID5374.1 )
#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 .

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