Strain identifier

BacDive ID: 17312

Type strain: Yes

Species: Vibrio litoralis

Strain Designation: MANO22D, Mano22 deep

Strain history: CIP <- 2007, DSMZ <- Y. D. Nam, KRIBB, Daejon, Korea: strain MANO22D

NCBI tax ID(s): 1123493 (strain), 335972 (species)

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General

@ref: 7109

BacDive-ID: 17312

DSM-Number: 17657

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

description: Vibrio litoralis MANO22D is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
335972species
1123493strain

strain history

@refhistory
7109<- Y.-D. Nam, KRIBB, Korea; Mano 22d
67771<- YD Nam, KRIBB
120636CIP <- 2007, DSMZ <- Y. D. Nam, KRIBB, Daejon, Korea: strain MANO22D

doi: 10.13145/bacdive17312.20230509.8.1

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 litoralis
  • full scientific name: Vibrio litoralis Nam et al. 2007

@ref: 7109

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio litoralis

full scientific name: Vibrio litoralis Nam et al. 2007

strain designation: MANO22D, Mano22 deep

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31921negative2.5 µm0.7 µmrod-shapedyes
67771negative
69480negative99.978
120636negativerod-shapedno

pigmentation

  • @ref: 31921
  • production: yes

multimedia

  • @ref: 7109
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_17657.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7109BACTO 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
37650Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120636CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7109positivegrowth28mesophilic
31921positivegrowth4-45
31921positiveoptimum27.5mesophilic
37650positivegrowth30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31921positivegrowth4.1-8.8alkaliphile
31921positiveoptimum6.9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31921facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.974

halophily

@refsaltgrowthtested relationconcentration
31921NaClpositivegrowth01-12 %
31921NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3192116449alanine+carbon source
3192122599arabinose+carbon source
3192116947citrate+carbon source
3192128260galactose+carbon source
3192124265gluconate+carbon source
3192117234glucose+carbon source
3192117754glycerol+carbon source
3192117596inosine+carbon source
3192125115malate+carbon source
3192117306maltose+carbon source
3192129864mannitol+carbon source
3192137684mannose+carbon source
31921506227N-acetylglucosamine+carbon source
3192126271proline+carbon source
3192153426tween 80+carbon source
3192117632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12063617632nitrate+reduction
12063616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12063635581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31921catalase+1.11.1.6
31921cytochrome oxidase+1.9.3.1
31921urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120636oxidase+
120636catalase+1.11.1.6
120636urease-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
120636-++--+-+--++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7109+-+-----------++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7109seawaterYellow SeaRepublic of KoreaKORAsia
67771From sea waterWest SeaRepublic of KoreaKORAsia
120636Environment, SeawaterChung NamRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_42716.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_982;97_1142;98_1364;99_42716&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: DQ097523
  • Sequence Identity:
  • Total samples: 134
  • soil counts: 4
  • aquatic counts: 62
  • animal counts: 66
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71091Risk group (German classification)
1206362Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7109
  • description: Vibrio litoralis strain MANO22D 16S ribosomal RNA gene, partial sequence
  • accession: DQ097523
  • length: 1441
  • database: ena
  • NCBI tax ID: 335972

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio litoralis DSM 17657GCA_000426765scaffoldncbi1123493
66792Vibrio litoralis DSM 176571123493.3wgspatric1123493
66792Vibrio litoralis DSM 176572524614821draftimg1123493

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno54.978yes
flagellatedno74.772no
gram-positiveno98.858no
anaerobicno99.349yes
aerobicyes86.665no
halophileyes80.515no
spore-formingno97.342no
glucose-utilyes91.992no
thermophileno99.768no
glucose-fermentyes89.814no

External links

@ref: 7109

culture collection no.: DSM 17657, CAIM 315, CIP 109585, KCTC 12520

straininfo link

  • @ref: 86312
  • straininfo: 297374

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329785Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea.Nam YD, Chang HW, Park JR, Kwon HY, Quan ZX, Park YH, Kim BC, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.64653-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Vibrio/*classification/genetics/isolation & purification/physiologyGenetics
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
Phylogeny27199227Vibrio algivorus sp. nov., an alginate- and agarose-assimilating bacterium isolated from the gut flora of a turban shell marine snail.Doi H, Chinen A, Fukuda H, Usuda YInt J Syst Evol Microbiol10.1099/ijsem.0.0011652016Alginates, Animals, Aquatic Organisms/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gastrointestinal Microbiome, Glucuronic Acid, Hexuronic Acids, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sepharose, Sequence Analysis, DNA, Snails/*microbiology, Ubiquinone/chemistry, Vibrio/*classification/genetics/isolation & purificationTranscriptome
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
Phylogeny34874245Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus.Moon YL, Park JSInt J Syst Evol Microbiol10.1099/ijsem.0.0051362021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mytilus/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Vibrio/classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7109Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17657)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17657
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
31921Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2817828776041
37650Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7344
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
86312Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297374.1StrainInfo: A central database for resolving microbial strain identifiers
120636Curators of the CIPCollection of Institut Pasteur (CIP 109585)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109585