Strain identifier

BacDive ID: 22931

Type strain: Yes

Species: Virgibacillus alimentarius

Strain Designation: J18

Strain history: J.-W. Bae J18.

NCBI tax ID(s): 698769 (species)

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

@ref: 19130

BacDive-ID: 22931

DSM-Number: 26676

keywords: genome sequence, 16S sequence, Bacteria, aerobe, halophilic, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Virgibacillus alimentarius J18 is an aerobe, halophilic, spore-forming bacterium that forms circular colonies and was isolated from Jeotgal, traditional salt-fermented seafood made of gizzard shad.

NCBI tax id

  • NCBI tax id: 698769
  • Matching level: species

strain history

@refhistory
19130<- JCM <- J.-W. Bae; J18
67770J.-W. Bae J18.

doi: 10.13145/bacdive22931.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Virgibacillus
  • species: Virgibacillus alimentarius
  • full scientific name: Virgibacillus alimentarius Kim et al. 2011
  • synonyms

    • @ref: 20215
    • synonym: Virgibacillus campisalis

@ref: 19130

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus alimentarius

full scientific name: Virgibacillus alimentarius Kim et al. 2011

strain designation: J18

type strain: yes

Morphology

cell morphology

  • @ref: 23056
  • gram stain: positive
  • cell length: 1.2 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 23056
  • colony size: 1.0-2.0 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: marine agar

pigmentation

  • @ref: 23056
  • production: yes
  • color: cream

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19130MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)yeshttps://mediadive.dsmz.de/medium/514dName: MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d) Composition: Difco marine broth 37.4 g/l Agar 15.0 g/l Malt extract 1.0 g/l Soy peptone 1.0 g/l Pancreatic digest of casein 1.0 g/l Distilled water
23056Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
19130positivegrowth28mesophilic
23056positivegrowth4.0-40.0
23056positiveoptimum37.0mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
23056positivegrowth7.0-11.0alkaliphile
23056positiveoptimum10.0

Physiology and metabolism

oxygen tolerance

  • @ref: 23056
  • oxygen tolerance: aerobe

spore formation

  • @ref: 23056
  • spore description: ellipsoidal,terminal or subterminal
  • type of spore: endospore
  • spore formation: yes

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23056halophilicNaClpositivegrowth0.0-30.0 %
23056NaCloptimum9.0-10.0 %

murein

  • @ref: 23056
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2305627613amygdalin-builds acid from
2305618305arbutin-builds acid from
2305617057cellobiose-builds acid from
2305617108D-arabinose-builds acid from
2305618333D-arabitol-builds acid from
2305615824D-fructose-builds acid from
2305628847D-fucose-builds acid from
2305612936D-galactose-builds acid from
2305662318D-lyxose-builds acid from
2305616899D-mannitol-builds acid from
2305616024D-mannose-builds acid from
2305617924D-sorbitol-builds acid from
2305665327D-xylose-builds acid from
2305616813galactitol-builds acid from
2305617113erythritol-builds acid from
2305624265gluconate-builds acid from
2305628087glycogen-builds acid from
2305617268myo-inositol-builds acid from
2305615443inulin-builds acid from
2305630849L-arabinose-builds acid from
2305618403L-arabitol-builds acid from
2305618287L-fucose-builds acid from
2305662345L-rhamnose-builds acid from
2305617266L-sorbose-builds acid from
2305665328L-xylose-builds acid from
2305617716lactose-builds acid from
2305617306maltose-builds acid from
230566731melezitose-builds acid from
2305628053melibiose-builds acid from
23056320061methyl alpha-D-glucopyranoside-builds acid from
2305643943methyl alpha-D-mannoside-builds acid from
2305674863methyl beta-D-xylopyranoside-builds acid from
2305616634raffinose-builds acid from
2305617814salicin-builds acid from
2305628017starch-builds acid from
2305617992sucrose-builds acid from
2305627082trehalose-builds acid from
2305632528turanose-builds acid from
2305617151xylitol-builds acid from
2305616947citrate-carbon source
2305627897tryptophan-energy source
23056O-nitrophenyl-beta-D-galactopyranosid-hydrolysis
23056168082-dehydro-D-gluconate+builds acid from
23056174265-dehydro-D-gluconate+builds acid from
2305615963ribitol+builds acid from
2305617634D-glucose+builds acid from
2305616988D-ribose+builds acid from
2305616443D-tagatose+builds acid from
230564853esculin+builds acid from
2305617754glycerol+builds acid from
23056506227N-acetylglucosamine+builds acid from
2305653424tween 20+hydrolysis
2305653423tween 40+hydrolysis
2305653425tween 60+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2305635581indoleno
2305616136hydrogen sulfideno
2305615688acetoinyes

metabolite tests

@refChebi-IDmetaboliteindole testcitrate test
2305635581indole-
2305616947citrate-

enzymes

@refvalueactivityec
23056arginine dihydrolase-3.5.3.6
23056beta-galactosidase-3.2.1.23
23056catalase-1.11.1.6
23056cytochrome oxidase+1.9.3.1
23056gelatinase-
23056lysine decarboxylase-4.1.1.18
23056ornithine decarboxylase-4.1.1.17
23056tryptophan deaminase-4.1.99.1
23056urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation procedure
19130Jeotgal, traditional salt-fermented seafood made of gizzard shadRepublic of KoreaKORAsia
23056marine agar (MA; BBL)25.0dilution-plating method
67770Jeotgal, traditional salt-fermented seafood made of gizzard shadRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_3806.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1954;97_2350;98_2899;99_3806&stattab=map
  • Last taxonomy: Virgibacillus
  • 16S sequence: GU202420
  • Sequence Identity:
  • Total samples: 64
  • soil counts: 22
  • aquatic counts: 6
  • animal counts: 34
  • plant counts: 2

Safety information

risk assessment

  • @ref: 19130
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19130
  • description: Virgibacillus alimentarius strain J18 16S ribosomal RNA gene, partial sequence
  • accession: GU202420
  • length: 1458
  • database: ena
  • NCBI tax ID: 698769

Genome sequences

  • @ref: 67770
  • description: Virgibacillus alimentarius J18
  • accession: GCA_000709085
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 698769

GC content

@refGC-contentmethod
1913037.0
2305637.0fluorimetric
6777037thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.822yes
flagellatedyes67.253no
gram-positiveyes92.839yes
anaerobicno99.632no
halophileyes95.619yes
spore-formingyes94.501yes
thermophileno97.312yes
glucose-utilyes86.961no
aerobicyes94.521no
glucose-fermentno92.973no

External links

@ref: 19130

culture collection no.: DSM 26676, JCM 16994, KACC 14624

straininfo link

  • @ref: 87179
  • straininfo: 397593

literature

  • topic: Phylogeny
  • Pubmed-ID: 21239563
  • title: Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food.
  • authors: Kim J, Jung MJ, Roh SW, Nam YD, Shin KS, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.028191-0
  • year: 2011
  • mesh: Animals, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fishes, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sodium Chloride/metabolism, Virgibacillus/*classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
19130Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26676)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26676
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
23056Jandi Kim,Mi-Ja Jung,Seong Woon Roh,Young-Do Nam,Kee-Sun Shin,Jin-Woo Bae10.1099/ijs.0.028191-0Virgibacillus alimentarius sp. nov., isolated from a traditional Korean foodIJSEM 61: 2851-2855 201121239563
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
87179Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397593.1StrainInfo: A central database for resolving microbial strain identifiers