Cite this strain

Xanthomonas codiaei (DSM 18812, CFBP 4690, ICMP 9513)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17607

Type strain

Culture col. no. DSM 18812 CFBP 4690 ICMP 9513 LMG 8678

NCBI tax ID(s) 56463

Special Collections DSMZ

Links

Name and taxonomic classification

Xanthomonas codiaei DSM 18812 is a mesophilic, Gram-negative plant pathogen that was isolated from Codiacum variegatum.

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

SI-ID 5924

LMG 8678, ICMP 9513, ATCC 700187, KACC 10909, DSM 18812, CFBP 4690, NCPPB 4350

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

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Xanthomonas

Species Xanthomonas codiaei

Full scientific name Xanthomonas codiaei Vauterin et al. 1995

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.75
125439	negative	98.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7712	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
7712	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		90.423
125439		97.9

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)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
7712	Codiacum variegatum	Codiacum variegatum	Florida	USA	USA	North America

Safety information

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
7712		1	Risk group (German classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Xanthomonas codiaei 16S ribosomal RNA gene, partial sequence and 16S-23S ribosomal RNA intergenic spacer, complete sequence	AF260971	578	56463
20218	Xanthomonas codiaei clone K0906 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence	HM181910	615	56463
7712	X.codiaei 16S rRNA gene	Y10765	1502	56463

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Xanthomonas codiaei CFBP4690	GCA_002939785	contig		56463
66792	Xanthomonas codiaei strain CFBP4690	56463.3	wgs	PATRIC	56463
66792	Xanthomonas codiaei CFBP4690	2880484841	draft	JGI IMG/M	56463

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Xanthomonas codiaei CFBP4690
NCBI: GCA_002939785

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	yes	87.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from Diaspora project based on:
Xanthomonas codiaei strain CFBP4690
PATRIC: 56463.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.75	no
125438	anaerobic	anaerobicⓘ	no	98.23	no
125438	spore-forming	spore-formingⓘ	no	90.42	no
125438	aerobic	aerobicⓘ	yes	86.08	no
125438	thermophilic	thermophileⓘ	no	99.98	no
125438	flagellated	motile2+ⓘ	yes	74.80	no

External links

Straininfo Link

@ref	Straininfo	Culture collections
86600	5924	LMG 8678, ICMP 9513, ATCC 700187, KACC 10909, DSM 18812, CFBP 4690, NCPPB 4350

Culture collection no.

Culture collection no.
DSM 18812
CFBP 4690
ICMP 9513
LMG 8678

References

#7712	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18812
#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) .
#86600	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-ID5924.1 )
#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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