Strain identifier
BacDive ID: 22931
Type strain:
Species: Virgibacillus alimentarius
Strain Designation: J18
Strain history: J.-W. Bae J18.
NCBI tax ID(s): 698769 (species)
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
@ref | history |
---|---|
19130 | <- JCM <- J.-W. Bae; J18 |
67770 | J.-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
@ref | name | growth | link | composition |
---|---|---|---|---|
19130 | MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d) | yes | https://mediadive.dsmz.de/medium/514d | Name: 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 |
23056 | Marine agar (MA) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19130 | positive | growth | 28 | mesophilic |
23056 | positive | growth | 4.0-40.0 | |
23056 | positive | optimum | 37.0 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
23056 | positive | growth | 7.0-11.0 | alkaliphile |
23056 | positive | optimum | 10.0 |
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
@ref | halophily level | salt | growth | tested relation | concentration |
---|---|---|---|---|---|
23056 | halophilic | NaCl | positive | growth | 0.0-30.0 % |
23056 | NaCl | optimum | 9.0-10.0 % |
murein
- @ref: 23056
- murein short key: A31
- type: A1gamma m-Dpm-direct
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23056 | 27613 | amygdalin | - | builds acid from |
23056 | 18305 | arbutin | - | builds acid from |
23056 | 17057 | cellobiose | - | builds acid from |
23056 | 17108 | D-arabinose | - | builds acid from |
23056 | 18333 | D-arabitol | - | builds acid from |
23056 | 15824 | D-fructose | - | builds acid from |
23056 | 28847 | D-fucose | - | builds acid from |
23056 | 12936 | D-galactose | - | builds acid from |
23056 | 62318 | D-lyxose | - | builds acid from |
23056 | 16899 | D-mannitol | - | builds acid from |
23056 | 16024 | D-mannose | - | builds acid from |
23056 | 17924 | D-sorbitol | - | builds acid from |
23056 | 65327 | D-xylose | - | builds acid from |
23056 | 16813 | galactitol | - | builds acid from |
23056 | 17113 | erythritol | - | builds acid from |
23056 | 24265 | gluconate | - | builds acid from |
23056 | 28087 | glycogen | - | builds acid from |
23056 | 17268 | myo-inositol | - | builds acid from |
23056 | 15443 | inulin | - | builds acid from |
23056 | 30849 | L-arabinose | - | builds acid from |
23056 | 18403 | L-arabitol | - | builds acid from |
23056 | 18287 | L-fucose | - | builds acid from |
23056 | 62345 | L-rhamnose | - | builds acid from |
23056 | 17266 | L-sorbose | - | builds acid from |
23056 | 65328 | L-xylose | - | builds acid from |
23056 | 17716 | lactose | - | builds acid from |
23056 | 17306 | maltose | - | builds acid from |
23056 | 6731 | melezitose | - | builds acid from |
23056 | 28053 | melibiose | - | builds acid from |
23056 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
23056 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
23056 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
23056 | 16634 | raffinose | - | builds acid from |
23056 | 17814 | salicin | - | builds acid from |
23056 | 28017 | starch | - | builds acid from |
23056 | 17992 | sucrose | - | builds acid from |
23056 | 27082 | trehalose | - | builds acid from |
23056 | 32528 | turanose | - | builds acid from |
23056 | 17151 | xylitol | - | builds acid from |
23056 | 16947 | citrate | - | carbon source |
23056 | 27897 | tryptophan | - | energy source |
23056 | O-nitrophenyl-beta-D-galactopyranosid | - | hydrolysis | |
23056 | 16808 | 2-dehydro-D-gluconate | + | builds acid from |
23056 | 17426 | 5-dehydro-D-gluconate | + | builds acid from |
23056 | 15963 | ribitol | + | builds acid from |
23056 | 17634 | D-glucose | + | builds acid from |
23056 | 16988 | D-ribose | + | builds acid from |
23056 | 16443 | D-tagatose | + | builds acid from |
23056 | 4853 | esculin | + | builds acid from |
23056 | 17754 | glycerol | + | builds acid from |
23056 | 506227 | N-acetylglucosamine | + | builds acid from |
23056 | 53424 | tween 20 | + | hydrolysis |
23056 | 53423 | tween 40 | + | hydrolysis |
23056 | 53425 | tween 60 | + | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
23056 | 35581 | indole | no |
23056 | 16136 | hydrogen sulfide | no |
23056 | 15688 | acetoin | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | citrate test |
---|---|---|---|---|
23056 | 35581 | indole | - | |
23056 | 16947 | citrate | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23056 | arginine dihydrolase | - | 3.5.3.6 |
23056 | beta-galactosidase | - | 3.2.1.23 |
23056 | catalase | - | 1.11.1.6 |
23056 | cytochrome oxidase | + | 1.9.3.1 |
23056 | gelatinase | - | |
23056 | lysine decarboxylase | - | 4.1.1.18 |
23056 | ornithine decarboxylase | - | 4.1.1.17 |
23056 | tryptophan deaminase | - | 4.1.99.1 |
23056 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | enrichment culture | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|
19130 | Jeotgal, traditional salt-fermented seafood made of gizzard shad | Republic of Korea | KOR | Asia | |||
23056 | marine agar (MA; BBL) | 25.0 | dilution-plating method | ||||
67770 | Jeotgal, traditional salt-fermented seafood made of gizzard shad | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
19130 | 37.0 | |
23056 | 37.0 | fluorimetric |
67770 | 37 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 86.822 | yes |
flagellated | yes | 67.253 | no |
gram-positive | yes | 92.839 | yes |
anaerobic | no | 99.632 | no |
halophile | yes | 95.619 | yes |
spore-forming | yes | 94.501 | yes |
thermophile | no | 97.312 | yes |
glucose-util | yes | 86.961 | no |
aerobic | yes | 94.521 | no |
glucose-ferment | no | 92.973 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
19130 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26676) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26676 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
23056 | Jandi Kim,Mi-Ja Jung,Seong Woon Roh,Young-Do Nam,Kee-Sun Shin,Jin-Woo Bae | 10.1099/ijs.0.028191-0 | Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food | IJSEM 61: 2851-2855 2011 | 21239563 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
87179 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397593.1 | StrainInfo: A central database for resolving microbial strain identifiers |