Strain identifier

BacDive ID: 17353

Type strain: Yes

Species: Vibrio casei

Strain Designation: WS 4539, TF11-505

Strain history: CIP <- 2010, DSMZ

NCBI tax ID(s): 1255579 (strain), 673372 (species)

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General

@ref: 16186

BacDive-ID: 17353

DSM-Number: 22364

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Vibrio casei WS 4539 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from surface of a French smear ripened cheese .

NCBI tax id

NCBI tax idMatching level
673372species
1255579strain

strain history

@refhistory
352282010, DSMZ
16186<- S. Scherer, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; TF11-505 <- A. Bleicher
117201CIP <- 2010, DSMZ

doi: 10.13145/bacdive17353.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio casei
  • full scientific name: Vibrio casei Bleicher et al. 2010

@ref: 16186

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio casei

full scientific name: Vibrio casei Bleicher et al. 2010

strain designation: WS 4539, TF11-505

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29589negative1.5-1.8 µm0.6-1.2 µmrod-shapedyes
69480negative99.962
117201negativerod-shapedyes

pigmentation

  • @ref: 29589
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16186BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
35228Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
117201CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16186positivegrowth28mesophilic
29589positivegrowth02-30
29589positiveoptimum30mesophilic
35228positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29589positivegrowth6-8.5alkaliphile
29589positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29589facultative anaerobe
117201facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.988

halophily

@refsaltgrowthtested relationconcentration
29589NaClpositivegrowth02-10 %
29589NaClpositiveoptimum02-10 %

observation

  • @ref: 29589
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2958922599arabinose+carbon source
2958916947citrate+carbon source
2958924265gluconate+carbon source
2958917234glucose+carbon source
2958925115malate+carbon source
2958917306maltose+carbon source
2958929864mannitol+carbon source
2958937684mannose+carbon source
295894853esculin+hydrolysis
2958917632nitrate+reduction
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
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
6837115824D-fructose+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
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11720117632nitrate+reduction
11720116301nitrite-reduction

metabolite production

  • @ref: 117201
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29589catalase+1.11.1.6
29589cytochrome oxidase+1.9.3.1
117201oxidase+
117201catalase+1.11.1.6
117201urease-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
117201-+++-+----+--+---+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117201---+/-------+++--------+-----++-+/------------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16186surface of a French smear ripened cheese (TF11)FreisingGermanyDEUEurope
117201Food, Surfaces of two French red smear soft cheesesBulgnévilleFranceFRAEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_60012.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_26454;97_33206;98_42638;99_60012&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: FJ968722
  • Sequence Identity:
  • Total samples: 102
  • soil counts: 1
  • aquatic counts: 50
  • animal counts: 49
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
161861Risk group (German classification)
1172012Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16186
  • description: Vibrio casei strain WS 4539 16S ribosomal RNA gene, partial sequence
  • accession: FJ968722
  • length: 1519
  • database: ena
  • NCBI tax ID: 1255579

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio casei DSM 22364GCA_002218025completencbi673372
66792Vibrio casei strain DSM 22364673372.5wgspatric673372
66792Vibrio casei DSM 223642860767601completeimg673372

GC content

@refGC-contentmethod
1618641.8high performance liquid chromatography (HPLC)
2958941.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes77.337no
flagellatedyes77.337no
gram-positiveno98.595yes
gram-positiveno98.595yes
anaerobicno99.324yes
anaerobicno99.324yes
aerobicyes92.698no
aerobicyes92.698no
halophileyes67.916no
halophileyes67.916no
spore-formingno96.158no
spore-formingno96.158no
thermophileno99.439yes
thermophileno99.439yes
glucose-utilyes92.941no
glucose-utilyes92.941no
motileyes87.152no
motileyes87.152no
glucose-fermentyes89.13no
glucose-fermentyes89.13no

External links

@ref: 16186

culture collection no.: DSM 22364, LMG 25240, CIP 110169

straininfo link

  • @ref: 86354
  • straininfo: 361404

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19749036Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses.Bleicher A, Neuhaus K, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.016493-02009Cheese/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Oxidoreductases/genetics/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Vibrio/*classification/enzymology/genetics/*isolation & purification, beta-Galactosidase/genetics/metabolismEnzymology
Phylogeny29676719Vibrio gangliei sp. nov., a novel member of Vibrionaceae isolated from sawdust in a pigpen.Meng YC, Liu HC, Zhou YG, Cai M, Kang YInt J Syst Evol Microbiol10.1099/ijsem.0.0027792018Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Housing, Animal, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Swine, Vibrio/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16186Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22364)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22364
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
29589Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2598128776041
35228Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7998
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)
68371Automatically annotated from API 50CH acid
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86354Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID361404.1StrainInfo: A central database for resolving microbial strain identifiers
117201Curators of the CIPCollection of Institut Pasteur (CIP 110169)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110169