Strain identifier

BacDive ID: 158787

Type strain: Yes

Species: Virgibacillus phasianinus

Strain Designation: LM2416

Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; LM2416.

NCBI tax ID(s): 2017483 (species)

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General

@ref: 65542

BacDive-ID: 158787

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

description: Virgibacillus phasianinus LM2416 is an aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from faecal sample of Swinhoe's pheasant.

NCBI tax id

  • NCBI tax id: 2017483
  • Matching level: species

strain history

  • @ref: 67770
  • history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; LM2416.

doi: 10.13145/bacdive158787.20230509.8.1

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 phasianinus
  • full scientific name: Virgibacillus phasianinus Tak et al. 2018

@ref: 65542

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus phasianinus

strain designation: LM2416

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65542positive1.2-1.9 µm0.3-0.4 µmrod-shapedyes
69480positive100

colony morphology

  • @ref: 65542
  • colony size: 0.5-1 mm
  • colony color: beige
  • colony shape: circular
  • incubation period: 2 days
  • medium used: MA

Culture and growth conditions

culture medium

  • @ref: 65542
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65542positivegrowth10-30
65542positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
65542positivegrowth6-7
65542positiveoptimum6-7

Physiology and metabolism

oxygen tolerance

  • @ref: 65542
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480yes100
69481yes100

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65542NaClpositivegrowth0-20 %(w/v)
65542NaClpositiveoptimum10 %(w/v)moderately halophilic

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6554218333D-arabitol+builds acid from
6554215824D-fructose+builds acid from
6554212936D-galactose+builds acid from
6554217634D-glucose+builds acid from
6554262318D-lyxose-builds acid from
6554216899D-mannitol+assimilation
6554216899D-mannitol+builds acid from
6554216024D-mannose+assimilation
6554216024D-mannose+builds acid from
6554216988D-ribose+builds acid from
6554216443D-tagatose+builds acid from
6554265327D-xylose-builds acid from
655424853esculin+builds acid from
6554217754glycerol+builds acid from
6554218287L-fucose+builds acid from
6554217266L-sorbose-builds acid from
6554217306maltose+assimilation
6554217306maltose+builds acid from
655426731melezitose+builds acid from
65542320061methyl alpha-D-glucopyranoside+builds acid from
65542506227N-acetylglucosamine+assimilation
65542506227N-acetylglucosamine+builds acid from
6554217632nitrate+reduction
65542potassium 5-dehydro-D-gluconate+builds acid from
6554232032potassium gluconate+assimilation
6554232032potassium gluconate+builds acid from
6554217992sucrose+builds acid from
6554227082trehalose+builds acid from
6554232528turanose+builds acid from

enzymes

@refvalueactivityec
65542catalase+1.11.1.6
65542cytochrome oxidase-1.9.3.1
65542alkaline phosphatase+3.1.3.1
65542esterase (C 4)+
65542esterase Lipase (C 8)+
65542leucine arylamidase+3.4.11.1
65542alpha-chymotrypsin+3.4.21.1
65542acid phosphatase+3.1.3.2
65542naphthol-AS-BI-phosphohydrolase+
65542beta-galactosidase+3.2.1.23
65542alpha-glucosidase+3.2.1.20
65542N-acetyl-beta-glucosaminidase+3.2.1.52
65542protease+
65542beta-glucuronidase-3.2.1.31
65542urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation procedure
65542faecal sample of Swinhoe's pheasantSeoul Grand Park, Makgye-dong, Gwacheon-si, GyeonggidoRepublic of KoreaKORAsiaMA2010000 times diluted sample
67770Faecal sample of Swinhoe's pheasant in Seoul Grand ParkMakgye-dong, Gwacheon-si, Gyeonggi-doRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Birds

Sequence information

16S sequences

  • @ref: 65542
  • description: 16S rRNA gene sequence
  • accession: KY785406
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Virgibacillus phasianinus LM2416
  • accession: GCA_002216775
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2017483

GC content

  • @ref: 65542
  • GC-content: 39.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno79.854no
gram-positiveyes93.138yes
anaerobicno99.623no
aerobicyes95.721yes
halophileyes91.935yes
spore-formingyes88.855no
thermophileno96.68yes
glucose-utilyes88.875no
motileno62.316yes
glucose-fermentno87.399no

External links

@ref: 65542

culture collection no.: KCTC 33927, JCM 32144

literature

  • topic: Phylogeny
  • Pubmed-ID: 29465338
  • title: Virgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii.
  • authors: Tak EJ, Kim HS, Lee JY, Kang W, Sung H, Kim PS, Hyun DW, Shin NR, Roh JR, Park SD, Shim HE, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002650
  • year: 2018
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Feces/*microbiology, Galliformes/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Virgibacillus/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65542Euon Jung Tak, Hyun Sik Kim, June-Young Lee, Woorim Kang, Hojun Sung, Pil Soo Kim, Dong-Wook Hyun, Na-Ri Shin, Jeong Rae Roh, Sun Duk Park, Hyung Eun Shim and Jin-Woo BaeVirgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii10.1099/ijsem.0.002650IJSEM 68: 1190-1196 201829465338
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1