Strain identifier

BacDive ID: 133177

Type strain: Yes

Species: Vibrio cidicii

Strain Designation: 2756-81

Strain history: CIP <- 2016, Y. Boucher, Alberta Univ., Edmonton, Alberta, Canada: strain 2756-81

NCBI tax ID(s): 1763883 (species)

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General

@ref: 24954

BacDive-ID: 133177

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Vibrio cidicii 2756-81 is a psychrophilic, Gram-negative, motile bacterium that forms circular colonies and was isolated from river water.

NCBI tax id

  • NCBI tax id: 1763883
  • Matching level: species

strain history

  • @ref: 118281
  • history: CIP <- 2016, Y. Boucher, Alberta Univ., Edmonton, Alberta, Canada: strain 2756-81

doi: 10.13145/bacdive133177.20230509.8.1

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 cidicii
  • full scientific name: Vibrio cidicii Orata et al. 2016

@ref: 24954

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales

family: Vibrionaceae

genus: Vibrio

species: Vibrio cidicii

strain designation: 2756-81

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
24954negative1.48-1.68 µm0.64-0.78 µmrod-shapedyes
118281negativerod-shapedyes

colony morphology

@refcolony colorcolony shapemedium used
24954creamcircularTSB agar
24954yellowTCBS agar

Culture and growth conditions

culture medium

@refnamegrowthlink
24954TSB agaryes
24954TCBS agaryes
118281CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
24954nogrowth4psychrophilic
24954nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
24954NaClpositivegrowth0-6.5 %
24954NaClinconsistentgrowth8 %
24954NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
24954169971,2-propandiol-carbon source
24954181014-hydroxyphenylacetic acid-carbon source
2495417128adipate-carbon source
2495415963ribitol-builds acid from
2495418333D-arabitol-builds acid from
2495418333D-arabitol-carbon source
2495429990D-aspartate-carbon source
2495418024D-galacturonic acid-carbon source
2495417784D-glucosaminic acid-carbon source
2495417634D-glucose-builds gas from
2495416523D-serine-carbon source
2495416398D-threonine-carbon source
2495465327D-xylose-builds acid from
2495427689decanoate-carbon source
2495417113erythritol-builds acid from
2495417113erythritol-carbon source
2495416000ethanolamine-carbon source
2495416537galactarate-builds acid from
2495416813galactitol-builds acid from
2495432323glucuronamide-carbon source
2495417754glycerol-builds acid from
2495436655glyoxylate-carbon source
2495417268myo-inositol-builds acid from
2495417268myo-inositol-carbon source
2495430849L-arabinose-builds acid from
2495416467L-arginine-carbon source
2495418287L-fucose-carbon source
2495417716lactose-builds acid from
2495425094lysine-carbon source
2495415792malonate-carbon source
2495428053melibiose-builds acid from
2495430928meso-tartrate-carbon source
2495455507methyl alpha-D-galactoside-carbon source
2495418257ornithine-carbon source
2495418401phenylacetate-carbon source
2495450048phenylethylamine-carbon source
2495416634raffinose-builds acid from
2495416634raffinose-carbon source
2495453258sodium citrate-carbon source
2495462517tricarballylate-carbon source
2495415760tyramine-carbon source
2495416199urea-hydrolysis
2495416199urea-carbon source
2495415588D-malate+carbon source
2495415588D-malate+energy source
2495415589L-malate+carbon source
2495415589L-malate+energy source
24954172562-deoxyadenosine+carbon source
24954172562-deoxyadenosine+energy source
24954645522-hydroxybutyrate+carbon source
24954645522-hydroxybutyrate+energy source
24954167632-oxobutanoate+carbon source
24954167632-oxobutanoate+energy source
24954309162-oxoglutarate+carbon source
24954309162-oxoglutarate+energy source
2495430089acetate+carbon source
2495430089acetate+energy source
2495413705acetoacetate+carbon source
2495413705acetoacetate+energy source
2495415688acetoin+builds acid from
2495416335adenosine+carbon source
2495416335adenosine+energy source
2495473673alpha-hydroxyglutarate-gamma-lactone+carbon source
2495473673alpha-hydroxyglutarate-gamma-lactone+energy source
2495473706bromosuccinate+carbon source
2495473706bromosuccinate+energy source
2495417057cellobiose+builds acid from
2495417057cellobiose+carbon source
2495417057cellobiose+energy source
2495416947citrate+carbon source
2495416947citrate+energy source
2495415570D-alanine+carbon source
2495415570D-alanine+energy source
2495415824D-fructose+carbon source
2495415824D-fructose+energy source
2495478697D-fructose 6-phosphate+carbon source
2495478697D-fructose 6-phosphate+energy source
249548391D-gluconate+carbon source
249548391D-gluconate+energy source
2495417634D-glucose+builds acid from
2495417634D-glucose+carbon source
2495417634D-glucose+energy source
2495414314D-glucose 6-phosphate+carbon source
2495414314D-glucose 6-phosphate+energy source
2495417306maltose+carbon source
2495417306maltose+energy source
2495416899D-mannitol+carbon source
2495416899D-mannitol+energy source
2495416024D-mannose+carbon source
2495416024D-mannose+energy source
2495427605D-psicose+carbon source
2495427605D-psicose+energy source
2495416988D-ribose+carbon source
2495416988D-ribose+energy source
2495465327D-xylose+carbon source
2495465327D-xylose+energy source
2495416991dna+carbon source
2495416991dna+energy source
249544853esculin+hydrolysis
249544853esculin+carbon source
249544853esculin+energy source
2495415740formate+carbon source
2495415740formate+energy source
2495429806fumarate+carbon source
2495429806fumarate+energy source
249545291gelatin+hydrolysis
249545291gelatin+carbon source
249545291gelatin+energy source
2495417234glucose+fermentation
2495429042glucose 1-phosphate+carbon source
2495429042glucose 1-phosphate+energy source
2495417754glycerol+carbon source
2495417754glycerol+energy source
2495414336glycerol 1-phosphate+carbon source
2495414336glycerol 1-phosphate+energy source
2495473804glycyl L-aspartic acid+carbon source
2495473804glycyl L-aspartic acid+energy source
2495417596inosine+carbon source
2495417596inosine+energy source
2495416977L-alanine+carbon source
2495416977L-alanine+energy source
2495473786L-alanylglycine+carbon source
2495473786L-alanylglycine+energy source
2495417196L-asparagine+carbon source
2495417196L-asparagine+energy source
2495429991L-aspartate+carbon source
2495429991L-aspartate+energy source
2495429985L-glutamate+carbon source
2495429985L-glutamate+energy source
2495418050L-glutamine+carbon source
2495418050L-glutamine+energy source
2495462320L-lyxose+carbon source
2495462320L-lyxose+energy source
2495417203L-proline+carbon source
2495417203L-proline+energy source
2495462345L-rhamnose+builds acid from
2495462345L-rhamnose+carbon source
2495462345L-rhamnose+energy source
2495417115L-serine+carbon source
2495417115L-serine+energy source
2495416857L-threonine+carbon source
2495416857L-threonine+energy source
2495416828L-tryptophan+carbon source
2495416828L-tryptophan+energy source
2495424996lactate+carbon source
2495424996lactate+energy source
2495425115malate+carbon source
2495425115malate+energy source
2495417306maltose+builds acid from
2495461993maltotriose+carbon source
2495461993maltotriose+energy source
2495429864mannitol+builds acid from
2495437684mannose+builds acid from
24954320055methyl beta-D-glucopyranoside+carbon source
24954320055methyl beta-D-glucopyranoside+energy source
2495451850methyl pyruvate+carbon source
2495451850methyl pyruvate+energy source
2495475146monomethyl succinate+carbon source
2495475146monomethyl succinate+energy source
24954506227N-acetylglucosamine+carbon source
24954506227N-acetylglucosamine+energy source
2495473784glycyl-l-glutamate+carbon source
2495473784glycyl-l-glutamate+energy source
2495417632nitrate+reduction
2495428044phenylalanine+carbon source
2495428044phenylalanine+energy source
2495432032potassium gluconate+carbon source
2495432032potassium gluconate+energy source
2495417272propionate+carbon source
2495417272propionate+energy source
2495415361pyruvate+carbon source
2495415361pyruvate+energy source
2495430031succinate+carbon source
2495430031succinate+energy source
2495417992sucrose+builds acid from
2495417992sucrose+carbon source
2495417992sucrose+energy source
2495417748thymidine+carbon source
2495417748thymidine+energy source
2495427082trehalose+builds acid from
2495427082trehalose+carbon source
2495427082trehalose+energy source
2495427897tryptophan+energy source
2495453423tween 40+carbon source
2495453423tween 40+energy source
2495453426tween 80+carbon source
2495453426tween 80+energy source
2495416704uridine+carbon source
2495416704uridine+energy source

metabolite production

@refChebi-IDmetaboliteproduction
2495415688acetoinno
2495435581indoleyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
2495417234glucose+
2495415688acetoin-
2495435581indole+

enzymes

@refvalueactivityec
24954arginine dihydrolase-3.5.3.6
24954cytochrome oxidase+1.9.3.1
24954DNase+
24954lysine decarboxylase-4.1.1.18
24954ornithine decarboxylase-4.1.1.17
24954phenylalanine deaminase+4.3.1.5
24954tryptophan deaminase+4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typeisolation dategeographic locationcountryorigin.countrycontinent
24954river water1981
118281Environment, River water2015-06-24Atlanta, GeorgiaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

Safety information

risk assessment

  • @ref: 118281
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24954
  • description: 16S rRNA
  • accession: KJ807108
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio cidicii 2756-81GCA_009763805completencbi1763883
66792Vibrio cidicii 2756-81GCA_001597655contigncbi1763883
66792Vibrio cidicii 2756-812690315852draftimg1763883

GC content

  • @ref: 24954
  • GC-content: 47.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.332yes
flagellatedyes90.599no
gram-positiveno98.899no
anaerobicno96.329no
aerobicyes84.567no
halophileno57.327no
spore-formingno94.115no
glucose-utilyes88.323yes
thermophileno99.242no
glucose-fermentyes87.853yes

External links

@ref: 24954

culture collection no.: LMG 29267, CIP 111013

straininfo link

  • @ref: 91386
  • straininfo: 412576

literature

  • topic: Phylogeny
  • Pubmed-ID: 27468862
  • title: Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis.
  • authors: Orata FD, Xu Y, Gladney LM, Rishishwar L, Case RJ, Boucher Y, Jordan IK, Tarr CL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001327
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vibrio/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24954F. D. X. Orata, Yue,Gladney, Lori M.,Rishishwar, Lavanya,Case, Rebecca J.,Boucher, Yan,Jordan, I. King,Tarr, Cheryl L.Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis10.1099/ijsem.0.001327IJSEM 66: 4148-4155 201627468862
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
91386Reimer, 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 identifiers10.60712/SI-ID412576.1
118281Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111013Collection of Institut Pasteur (CIP 111013)