Strain identifier

BacDive ID: 17241

Type strain: Yes

Species: Vibrio costicola

Strain history: CIP <- 1989, NCIMB <- 1960, M. Ingram <- N.E. Gibbons <- J. Robinson

NCBI tax ID(s): 51367 (species)

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General

@ref: 4352

BacDive-ID: 17241

DSM-Number: 11403

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, toxin production

description: Vibrio costicola DSM 11403 is an aerobe, mesophilic, Gram-negative bacterium that produces toxins and was isolated from bacon curing brine.

NCBI tax id

  • NCBI tax id: 51367
  • Matching level: species

strain history

@refhistory
4352<- ATCC <- P. Baumann <- NCIMB <- M. Ingraham <-J.M. Shewan <- N.E. Gibbons
67770CIP 103310 <-- NCIMB 701 <-- M. Ingram <-- J. M. Shewan <-- N. E. Gibbons.
118766CIP <- 1989, NCIMB <- 1960, M. Ingram <- N.E. Gibbons <- J. Robinson

doi: 10.13145/bacdive17241.20230509.8.1

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 costicola
  • full scientific name: Vibrio costicola corrig. Smith 1938 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Vibrio costicolus
    20215Salinivibrio costicola

@ref: 4352

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Salinivibrio

species: Salinivibrio costicola

full scientific name: Salinivibrio costicola (Smith 1938) Mellado et al. 1996 emend. Huang et al. 2000

type strain: yes

Morphology

cell morphology

  • @ref: 118766
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4352BACTO 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
4352SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
32825Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118766CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
4352positivegrowth25mesophilic
32825positivegrowth25mesophilic
47123positivegrowth30mesophilic
67770positivegrowth25mesophilic
118766positivegrowth15-37
118766nogrowth5psychrophilic
118766nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
47123aerobe
118766facultative anaerobe

compound production

  • @ref: 4352
  • compound: tetrodotoxin

halophily

@refsaltgrowthtested relationconcentration
47123NaClpositivegrowth3-5 %
118766NaClpositivegrowth0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
118766esculin-hydrolysis4853
118766glucose-fermentation17234
118766lactose-fermentation17716
118766nitrate-reduction17632
118766nitrite-reduction16301
118766sodium thiosulfate-builds gas from132112
118766glucose-degradation17234

metabolite production

  • @ref: 118766
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11876615688acetoin+
11876617234glucose+

enzymes

@refvalueactivityec
118766oxidase+
118766beta-galactosidase-3.2.1.23
118766alcohol dehydrogenase+1.1.1.1
118766gelatinase+/-
118766amylase-
118766DNase-
118766caseinase-3.4.21.50
118766catalase+1.11.1.6
118766tween esterase-
118766gamma-glutamyltransferase-2.3.2.2
118766lecithinase-
118766lipase-
118766lysine decarboxylase+4.1.1.18
118766ornithine decarboxylase-4.1.1.17
118766phenylalanine ammonia-lyase+4.3.1.24
118766protease-
118766tryptophan deaminase-
118766urease-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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    47123C12:00.212
    47123C14:01.214
    47123C16:05.716
    47123C18:00.218
    47123C13:0 ISO 2OH0.313.814
    47123C15:0 ANTEISO0.414.711
    47123C16:1 ω11c0.415.757
    47123C16:1 ω7c1015.819
    47123C17:0 iso 3OH13.218.161
    47123C18:1 ω7c /12t/9t517.824
    47123C19:0 CYCLO ω9c0.418.87
    47123Unidentified0.29.233
    47123Unidentified5.512.268
    47123Unidentified312.679
    47123Unidentified0.313.731
    47123Unidentified0.814.133
    47123Unidentified3.514.283
    47123Unidentified0.215.289
    47123Unidentified26.416.165
    47123Unidentified19.716.328
    47123unknown 12.4860.312.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118766-+++-+--+-++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118766+---+-----+++/-----+--+/-+-+/-+/-+/--+--++---+----------++/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118766++-+---+-++--------+-----------+-----------------+---------++--------------+--+-+--------++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4352bacon curing brineCanadaCANNorth America
47123Bacon curing brine
67770Cured meat
118766Food, Bacon curing brine

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Meat

taxonmaps

  • @ref: 69479
  • File name: preview.99_1660.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15915;96_827;97_1102;98_1313;99_1660&stattab=map
  • Last taxonomy: Salinivibrio
  • 16S sequence: X95527
  • Sequence Identity:
  • Total samples: 39
  • aquatic counts: 22
  • animal counts: 8
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43521Risk group (German classification)
1187662Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Salinivibrio costicola strain ATCC 33508 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequenceAF412998456ena51367
20218Salinivibrio costicola strain ATCC 33508 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequenceAF412999559ena51367
20218Salinivibrio costicola strain ATCC 33508 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequenceAF413000539ena51367
20218Salinivibrio costicola strain ATCC 33508 16S-23S ribosomal RNA intergenic spacer, partial sequenceAF413001315ena51367
20218Salinivibrio costicola strain ATCC 33508 16S-23S ribosomal RNA intergenic spacer, partial sequenceAF413002351ena51367
20218V.costicola (ATCC 35508T) gene for 16S ribosomal RNAX746991485ena51367
20218S.costicola 16S ribosomal RNA (strain NCIMB 701-T)X955271511ena51367
20218Vibrio costicola 16S rRNAD11200198ena51367
20218Vibrio costicola 16S rRNAD11249207ena51367
20218Vibrio costicola 16S rRNAD11298191ena51367

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinivibrio costicola subsp. costicola ATCC 33508 = LMG 116511269942.6wgspatric1269942
66792Salinivibrio costicola subsp. costicola ATCC 33508 = LMG 116511269942.3wgspatric1269942
66792Salinivibrio costicola costicola ATCC 335082551306522draftimg1269942
66792Salinivibrio costicola costicola ATCC 33508, LMG 116512579778798draftimg1269942
67770Salinivibrio costicola subsp. costicola ATCC 33508 = LMG 11651GCA_000565345contigncbi1269942
67770Salinivibrio costicola subsp. costicola ATCC 33508 = LMG 11651GCA_000390145contigncbi1269942

GC content

  • @ref: 67770
  • GC-content: 49.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.266no
gram-positiveno98.919no
anaerobicno98.273no
aerobicyes84.121yes
halophileyes67.865no
spore-formingno96.334no
glucose-utilyes90.948no
flagellatedyes84.582no
thermophileno97.507yes
glucose-fermentyes84.391no

External links

@ref: 4352

culture collection no.: DSM 11403, ATCC 33508, NCIMB 701, CCUG 20305, JCM 15095, BCRC 12910, CAIM 910, CCM 3575, CECT 4059, CGMCC 1.2322, CIP 103310, LMG 11651, LMG 6460, NCCB 77008

straininfo link

  • @ref: 86239
  • straininfo: 5062

literature

  • topic: Phylogeny
  • Pubmed-ID: 8782695
  • title: Analysis of 16S rRNA gene sequences of Vibrio costicola strains: description of Salinivibrio costicola gen. nov., comb. nov.
  • authors: Mellado E, Moore ER, Nieto JJ, Ventosa A
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-46-3-817
  • year: 1996
  • mesh: Base Sequence, DNA, Bacterial, Molecular Sequence Data, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Vibrio/*classification/genetics/metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4352Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11403)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11403
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32825Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15094
47123Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20305)https://www.ccug.se/strain?id=20305
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/
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
86239Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5062.1StrainInfo: A central database for resolving microbial strain identifiers
118766Curators of the CIPCollection of Institut Pasteur (CIP 103310)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103310