Strain identifier

BacDive ID: 7338

Type strain: Yes

Species: Leifsonia xyli subsp. cynodontis

Strain Designation: TB1A

Strain history: CIP <- 1995, ATCC <- M.J. Davis: strain TBIA, Corynebacterium sp.

NCBI tax ID(s): 1389489 (strain), 31966 (subspecies)

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General

@ref: 12518

BacDive-ID: 7338

DSM-Number: 46306

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, plant pathogen

description: Leifsonia xyli subsp. cynodontis TB1A is an obligate aerobe, mesophilic plant pathogen that was isolated from bermudagrass.

NCBI tax id

NCBI tax idMatching level
31966subspecies
1389489strain

strain history

@refhistory
12518<- IMET <- M.J. Davis, TB1A
67770ICMP 8790 <-- M. J. Davis TB1A.
123999CIP <- 1995, ATCC <- M.J. Davis: strain TBIA, Corynebacterium sp.

doi: 10.13145/bacdive7338.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leifsonia
  • species: Leifsonia xyli subsp. cynodontis
  • full scientific name: Leifsonia xyli subsp. cynodontis (Davis et al. 1984) Evtushenko et al. 2000

  • synonyms

    @refsynonym
    20215Leifsonia cynodontis
    20215Clavibacter xyli subsp. cynodontis

@ref: 12518

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leifsonia

species: Leifsonia xyli subsp. cynodontis

full scientific name: Leifsonia xyli subsp. cynodontis (Davis et al. 1984) Evtushenko et al. 2000

strain designation: TB1A

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.725
69480100positive
123999nopositiverod-shaped

colony morphology

@refincubation periodcolony colormedium used
125183-7 days
2019310-14 daysLight ivory (1015)ISP 2
2019310-14 daysISP 3
2019310-14 daysZinc yellow (1018)ISP 4
2019310-14 daysISP 5
2019310-14 daysISP 7

multicellular morphology

@refmedium nameforms multicellular complex
20193ISP 2
20193ISP 3
20193ISP 4
20193ISP 5
20193no
20193ISP 2no
20193ISP 3no
20193ISP 4no
20193ISP 5no
20193ISP 7no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12518SC MEDIUM (DSMZ Medium 751)yeshttps://mediadive.dsmz.de/medium/751Name: SC MEDIUM (DSMZ Medium 751) Composition: Corn meal agar 17.0 g/l Soy peptone 8.0 g/l Bovine serum albumin 2.0 g/l Cysteine 1.0 g/l K2HPO4 1.0 g/l KH2PO4 1.0 g/l Glucose 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Hemin 0.015 g/l Distilled water
20193ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20193ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20193ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20193ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20193ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37046MEDIUM 111 - for ClavibacteryesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
123999CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111

culture temp

@refgrowthtypetemperaturerange
12518positivegrowth28mesophilic
37046positivegrowth30mesophilic
67770positivegrowth28mesophilic
123999positivegrowth30mesophilic
123999nogrowth37mesophilic
123999nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123999
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 100

halophily

  • @ref: 20193
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 12518
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2019317234glucose+
2019322599arabinose+
2019317992sucrose+
2019318222xylose+
2019317268myo-inositol+
2019329864mannitol+
2019328757fructose+
2019326546rhamnose+
2019316634raffinose+
2019362968cellulose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1239994853esculin-hydrolysis
123999606565hippurate-hydrolysis
12399917632nitrate-reduction
12399916301nitrite-reduction
123999132112sodium thiosulfate-builds gas from
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen+fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12399935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12399915688acetoin-
12399917234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
123999oxidase-
123999beta-galactosidase+3.2.1.23
123999alcohol dehydrogenase-1.1.1.1
123999gelatinase-
123999amylase+
123999DNase-
123999caseinase-3.4.21.50
123999catalase+1.11.1.6
123999tween esterase-
123999lecithinase-
123999lysine decarboxylase-4.1.1.18
123999ornithine decarboxylase-4.1.1.17
123999urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20193---+-----+--------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20193+++------++--------
123999-++-+----++---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20193------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123999-----------+/--------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123999---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost species
12518bermudagrassTaiwanTWNAsia
67770Bermuda grass (Cynodon dactylon)TaiwanTWNAsiaCynodon dactylon
123999Bermuda grass, Cynodon dactylonChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2936.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_671;97_777;98_901;99_2936&stattab=map
  • Last taxonomy: Leifsonia xyli
  • 16S sequence: AB016985
  • Sequence Identity:
  • Total samples: 47
  • soil counts: 6
  • aquatic counts: 1
  • animal counts: 37
  • plant counts: 3

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
12518yes1Risk group (German classification)
201931German classification
1239991Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Leifsonia xyli subsp. cynodontis gene for 16S rRNA, strain: JCM 9733
  • accession: AB016985
  • length: 1444
  • database: ena
  • NCBI tax ID: 31966

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leifsonia xyli subsp. cynodontis DSM 46306GCA_000470775completencbi1389489
66792Leifsonia xyli subsp. cynodontis DSM 463061389489.3completepatric1389489
66792Leifsonia xyli cynodontis DSM 463062554235749completeimg1389489

GC content

@refGC-contentmethod
1251866.0
6777066thermal denaturation, midpoint method (Tm)
6777069.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes81no
motileno90.728no
flagellatedno97.788no
gram-positiveyes89.95no
anaerobicno99.185no
aerobicyes79.254no
halophileno86.945no
spore-formingno94.773no
glucose-utilyes87.174yes
thermophileno96.741no
glucose-fermentno84.985yes

External links

@ref: 12518

culture collection no.: DSM 46306, ATCC 33973, IMET 11020, NCIB 11927, JCM 9733, CIP 104615, ICMP 8790, LMG 7552, NCIMB 11927, VKM Ac-2041

straininfo link

  • @ref: 76788
  • straininfo: 45192

literature

Pubmed-IDtitleauthorsjournalDOIyeartopicmeshtopic2
12501368Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate "Corynebacterium aquaticum" Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984.Suzuki KI, Suzuki M, Sasaki J, Park YH, Komagata KKJ Gen Appl Microbiol10.2323/jgam.45.2531999
19126716Leifsonia kribbensis sp. nov., isolated from soil.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.001925-02009PhylogenyActinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
24201198Complete Genome Sequence of Leifsonia xyli subsp. cynodontis Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses.Monteiro-Vitorello CB, Zerillo MM, Van Sluys MA, Camargo LE, Kitajima JPGenome Announc10.1128/genomeA.00915-132013Genetics

Reference

@idauthorscataloguedoi/urltitle
12518Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46306)https://www.dsmz.de/collection/catalogue/details/culture/DSM-46306
20193Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM46306.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
37046Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16543
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
76788Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45192.1StrainInfo: A central database for resolving microbial strain identifiers
123999Curators of the CIPCollection of Institut Pasteur (CIP 104615)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104615