Strain identifier

BacDive ID: 17599

Type strain: Yes

Species: Xanthomonas hortorum

Strain Designation: A960701

Strain history: CIP <- 2000, CFBP <- J.L. Tanguy: strain A960701

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General

@ref: 6606

BacDive-ID: 17599

DSM-Number: 16794

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen

description: Xanthomonas hortorum A960701 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from Cynara scolymus.

strain history

@refhistory
6606<- CFBP <- J.-L. Tanguy; A960701
118830CIP <- 2000, CFBP <- J.L. Tanguy: strain A960701

doi: 10.13145/bacdive17599.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Xanthomonas
  • species: Xanthomonas hortorum
  • full scientific name: Xanthomonas hortorum Vauterin et al. 1995

  • synonyms

    @refsynonym
    20215Xanthomonas cynarae
    20215Xanthomonas gardneri

@ref: 6606

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Xanthomonas

species: Xanthomonas cynarae

full scientific name: Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019

strain designation: A960701

type strain: yes

Morphology

cell morphology

  • @ref: 118830
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6606YPGA (DSMZ Medium 1015)yeshttps://mediadive.dsmz.de/medium/1015Name: YPGA (DSMZ Medium 1015) Composition: Agar 15.0 g/l Glucose 7.0 g/l Bacto peptone 7.0 g/l Yeast extract 7.0 g/l Distilled water
39578MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
118830CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
6606positivegrowth28mesophilic
39578positivegrowth30mesophilic
118830positivegrowth5-30
118830nogrowth37mesophilic
118830nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118830
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118830NaClpositivegrowth0-6 %
118830NaClnogrowth8 %
118830NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11883016947citrate+carbon source
1188304853esculin+hydrolysis
11883017632nitrate-reduction
11883016301nitrite-reduction
11883017632nitrate-respiration

antibiotic resistance

  • @ref: 118830
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118830
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118830oxidase-
118830beta-galactosidase+3.2.1.23
118830alcohol dehydrogenase-1.1.1.1
118830gelatinase+/-
118830amylase+
118830DNase+
118830caseinase+3.4.21.50
118830catalase+1.11.1.6
118830tween esterase+
118830lecithinase-
118830lipase+
118830lysine decarboxylase-4.1.1.18
118830ornithine decarboxylase-4.1.1.17
118830protease+
118830tryptophan deaminase-
118830urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118830-+++-++-++++-+--++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118830+++++--+----+--+--+-----+------+-------+------+--+---+-----+---------------+---++---------+-+--+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
6606Cynara scolymusCynara scolymusBrittanyFranceFRAEurope
118830Cynara scolymusBrittanyFranceFRAEurope1996

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_92.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_73;97_76;98_83;99_92&stattab=map
  • Last taxonomy: Xanthomonas
  • 16S sequence: AF208315
  • Sequence Identity:
  • Total samples: 52152
  • soil counts: 10026
  • aquatic counts: 6826
  • animal counts: 28252
  • plant counts: 7048

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
6606yes1Risk group (German classification)
1188301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6606
  • description: Xanthomonas cynarae 16S ribosomal RNA gene, partial sequence
  • accession: AF208315
  • length: 1552
  • database: ena
  • NCBI tax ID: 109214

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthomonas hortorum pv. cynarae CFBP4188GCA_002939985scaffoldncbi2754057
66792Xanthomonas cynarae strain CFBP4188109214.3wgspatric2754057
66792Xanthomonas cynarae CFBP41882878089750draftimg109214
66792Xanthomonas hortorum pv. cynarae CFBP 4188GCA_021352995scaffoldncbi2754057

GC content

  • @ref: 6606
  • GC-content: 63
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno86.221no
gram-positiveno97.845no
anaerobicno99.181no
aerobicyes94.401no
halophileno94.649no
spore-formingno95.004no
glucose-utilyes93.563no
thermophileno99.477yes
motileyes80.105no
glucose-fermentno90.464no

External links

@ref: 6606

culture collection no.: DSM 16794, CFBP 4188, CIP 106774

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10939652Genomic and phenotypic characterization of Xanthomonas cynarae sp. nov., a new species that causes bacterial bract spot of artichoke (Cynara scolymus L.).Trebaol G, Gardan L, Manceau C, Tanguy JL, Tirilly Y, Boury SInt J Syst Evol Microbiol10.1099/00207713-50-4-14712000Base Composition, Cloning, Molecular, DNA, Bacterial, *Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Plants/*microbiology, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Xanthomonas/chemistry/classification/*geneticsEnzymology
Phylogeny30457512Reclassification of Xanthomonas gardneri (ex Sutic 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trebaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses.Timilsina S, Kara S, Jacques MA, Potnis N, Minsavage GV, Vallad GE, Jones JB, Fischer-Le Saux MInt J Syst Evol Microbiol10.1099/ijsem.0.0031042018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Genome, Bacterial, Multilocus Sequence Typing, *Phylogeny, Plant Diseases/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xanthomonas/*classificationGenetics

Reference

@idauthorscataloguedoi/urltitle
6606Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16794)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16794
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
39578Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18941
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
118830Curators of the CIPCollection of Institut Pasteur (CIP 106774)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106774