Strain identifier

BacDive ID: 17355

Type strain: Yes

Species: Vibrio atypicus

Strain history: <- LMG <- Y. Wang, Department of Marine Biology, Ocean University of China, Qingdao

NCBI tax ID(s): 558271 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17984

BacDive-ID: 17355

DSM-Number: 25292

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

description: Vibrio atypicus DSM 25292 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from digestive tract of healthy Chinese prawns Penaeus chinensis O'sbeck.

NCBI tax id

  • NCBI tax id: 558271
  • Matching level: species

strain history

  • @ref: 17984
  • history: <- LMG <- Y. Wang, Department of Marine Biology, Ocean University of China, Qingdao

doi: 10.13145/bacdive17355.20250331.9.3

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 atypicus
  • full scientific name: Vibrio atypicus Wang et al. 2010

@ref: 17984

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio atypicus

full scientific name: Vibrio atypicus Wang et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29609negative1-1.5 µm0.5-0.7 µmrod-shapedyes
125439negative99.7
125438yes91.216
125438negative99.917

pigmentation

  • @ref: 29609
  • production: no

multimedia

  • @ref: 17984
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25292.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 17984
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
17984positivegrowth28
29609positivegrowth16-30
29609positiveoptimum20

culture pH

@refabilitytypepHPH range
29609positivegrowth07-10alkaliphile
29609positiveoptimum08-09

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29609facultative anaerobe
125439obligate aerobe98

spore formation

@refspore formationconfidence
29609no
125439no99.8

halophily

@refsaltgrowthtested relationconcentration
29609NaClpositivegrowth0.5-7 %
29609NaClpositiveoptimum01-03 %

observation

  • @ref: 29609
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2960917057cellobiose+carbon source
2960917234glucose+carbon source
2960929864mannitol+carbon source
2960917992sucrose+carbon source
2960917632nitrate+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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
29609cytochrome oxidase+1.9.3.1
29609urease+3.5.1.5
68369urease+3.5.1.5
68369arginine dihydrolase+3.5.3.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
17984+-++++++---+-++--+--+

Isolation, sampling and environmental information

isolation

  • @ref: 17984
  • sample type: digestive tract of healthy Chinese prawns Penaeus chinensis O'sbeck
  • host species: Penaeus chinensis
  • geographic location: Qingdao
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Crustacea
#Host Body-Site#Gastrointestinal tract

Safety information

risk assessment

  • @ref: 17984
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17984
  • description: Vibrio atypicus strain HHS02 16S ribosomal RNA gene, partial sequence
  • accession: FJ009624
  • length: 1401
  • database: nuccore
  • NCBI tax ID: 558271

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio atypicus DSM 25292GCA_009811315scaffoldncbi558271
66792Vibrio atypicus strain DSM 25292558271.4wgspatric558271
66792Vibrio atypicus strain TUMSAT1558271.3wgspatric558271

GC content

@refGC-contentmethod
1798444.4high performance liquid chromatography (HPLC)
2960944.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.917no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.588yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no68.633no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.706yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.875yes
125438motile2+flagellatedAbility to perform flagellated movementyes91.216no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.8
125439BacteriaNetmotilityAbility to perform movementyes86.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98

External links

@ref: 17984

culture collection no.: DSM 25292, CGMCC 1.8461, LMG 24781, HHS 02

straininfo link

  • @ref: 86356
  • straininfo: 359269

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19965995Vibrio atypicus sp. nov., isolated from the digestive tract of the Chinese prawn (Penaeus chinensis O'sbeck).Wang Y, Zhang XH, Yu M, Wang H, Austin BInt J Syst Evol Microbiol10.1099/ijs.0.016915-02009Animals, Bacterial Proteins/genetics, DNA, Bacterial/genetics, Fatty Acids/metabolism, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Penaeidae/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Vibrio/*classification/genetics/*isolation & purification/metabolismMetabolism
Genetics32029560Draft Genome Sequences of Vibrio atypicus Strains DSM 25292(T) and TUMSAT1.Kawato S, Nozaki R, Kondo H, Hirono IMicrobiol Resour Announc10.1128/MRA.01526-192020

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25292)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25292
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
29609Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2599928776041
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)
68369Automatically annotated from API 20NE
86356Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359269.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1