Strain identifier

BacDive ID: 132443

Type strain: Yes

Species: Virgibacillus flavescens

Strain Designation: S1-20

Strain history: <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; S1-20 <- D.-C. Zhang, Chinese Acad. Sci. (CAS), Inst. of Oceanology, Beijing

NCBI tax ID(s): 1611422 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 24232

BacDive-ID: 132443

DSM-Number: 29015

keywords: 16S sequence, Bacteria, aerobe, Gram-variable, motile, rod-shaped, colony-forming

description: Virgibacillus flavescens S1-20 is an aerobe, Gram-variable, motile bacterium that forms circular colonies and was isolated from marine sediment .

NCBI tax id

  • NCBI tax id: 1611422
  • Matching level: species

strain history

  • @ref: 24232
  • history: <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; S1-20 <- D.-C. Zhang, Chinese Acad. Sci. (CAS), Inst. of Oceanology, Beijing

doi: 10.13145/bacdive132443.20230509.8.1

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 flavescens
  • full scientific name: Virgibacillus flavescens Zhang et al. 2016

@ref: 24232

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus flavescens

full scientific name: Virgibacillus flavescens Zhang et al. 2016

strain designation: S1-20

type strain: yes

Morphology

cell morphology

  • @ref: 43747
  • gram stain: variable
  • cell length: 1.9-2.2 µm
  • cell width: 0.6-0.7 nm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43747
  • colony color: Yellow
  • colony shape: circular
  • medium used: MA agar

pigmentation

@refproductionname
43747noCarotenoid
43747noFlexirubin-type

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43747Marine agar (MA)yes
43747Trypticase Soy Agar (TSA)no
24232BACTO 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

culture temp

@refgrowthtypetemperaturerange
43747positivegrowth1-30
24232positivegrowth25mesophilic

culture pH

  • @ref: 43747
  • ability: positive
  • type: growth
  • pH: 7-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43747
  • oxygen tolerance: aerobe

murein

  • @ref: 24232
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4374717128adipate-assimilation
4374727689decanoate-assimilation
4374716947citrate-assimilation
4374717634D-glucose-assimilation
4374716899D-mannitol-assimilation
4374716024D-mannose-assimilation
4374730849L-arabinose-assimilation
4374725115malate-assimilation
4374717306maltose-assimilation
43747506227N-acetylglucosamine-assimilation
4374718401phenylacetate-assimilation
4374732032potassium gluconate-assimilation
4374753258sodium citrate-assimilation
4374729016arginine-carbon source
4374717057cellobiose-carbon source
4374715824D-fructose-carbon source
4374717634D-glucose-carbon source
4374716024D-mannose-carbon source
4374765327D-xylose-carbon source
4374724996lactate-carbon source
4374729806fumarate-carbon source
4374728260galactose-carbon source
4374717754glycerol-carbon source
4374715428glycine-carbon source
4374730849L-arabinose-carbon source
4374717716lactose-carbon source
4374717306maltose-carbon source
43747506227N-acetylglucosamine-carbon source
4374728044phenylalanine-carbon source
4374715361pyruvate-carbon source
4374730031succinate-carbon source
4374717992sucrose-carbon source
4374727082trehalose-carbon source
437472509agar-degradation
4374758187alginate-degradation
4374785146carboxymethylcellulose-degradation
4374717309pectin-degradation
4374762969polygalacturonic acid-degradation
4374728017starch-degradation
4374717234glucose-fermentation
437474853esculin-hydrolysis
4374717632nitrate-reduction
43747casein+hydrolysis
437475291gelatin+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4374716136hydrogen sulfideno
4374735581indoleno

enzymes

@refvalueactivityec
43747cytochrome oxidase+1.9.3.1
43747catalase+1.11.1.6
43747alkaline phosphatase+3.1.3.1
43747esterase (C 4)+
43747leucine arylamidase+3.4.11.1
43747chymotrypsin+3.4.4.5
43747naphthol-AS-BI-phosphohydrolase+
43747alpha-glucosidase+3.2.1.20
43747urease-3.5.1.5
43747esterase Lipase (C 8)-
43747lipase (C 14)-
43747valine arylamidase-
43747cystine arylamidase-3.4.11.3
43747trypsin-3.4.21.4
43747acid phosphatase-3.1.3.2
43747alpha-galactosidase-3.2.1.22
43747beta-galactosidase-3.2.1.23
43747beta-glucuronidase-3.2.1.31
43747beta-glucosidase-3.2.1.21
43747N-acetyl-beta-glucosaminidase-3.2.1.52
43747alpha-mannosidase-3.2.1.24
43747alpha-fucosidase-3.2.1.51
43747arginine dihydrolase-3.5.3.6
43747lysine decarboxylase-4.1.1.18
43747ornithine decarboxylase-4.1.1.17
43747tryptophan deaminase-4.1.99.1
43747gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24232marine sediment (38° 45' N 123° 00' E)Southern Yellow SeaChinaCHNAsia38.75123
43747Marine sediment of the Yellow SeaYellow Sea, ChinaChinaCHNAsia38.751232012-10-25 -

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_121799.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_10900;97_13207;98_16259;99_121799&stattab=map
  • Last taxonomy: Virgibacillus flavescens
  • 16S sequence: KP197672
  • Sequence Identity:
  • Total samples: 144
  • soil counts: 131
  • aquatic counts: 3
  • animal counts: 10

Safety information

risk assessment

  • @ref: 24232
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24232
  • description: Virgibacillus flavescens strain S1-20 16S ribosomal RNA gene, partial sequence
  • accession: KP197672
  • length: 1558
  • database: ena
  • NCBI tax ID: 1611422

GC content

  • @ref: 24232
  • GC-content: 38.3
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 24232

culture collection no.: DSM 29015, LMG 28381

straininfo link

  • @ref: 90781
  • straininfo: 403941

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26674201Virgibacillus flavescens sp. nov., isolated from marine sediment.Zhang DC, Schumann P, Wu J, Franca L, Neuner K, Margesin RInt J Syst Evol Microbiol10.1099/ijsem.0.0008462015
Phylogeny29465338Virgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii.Tak EJ, Kim HS, Lee JY, Kang W, Sung H, Kim PS, Hyun DW, Shin NR, Roh JR, Park SD, Shim HE, Bae JWInt J Syst Evol Microbiol10.1099/ijsem.0.0026502018Animals, 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/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24232Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29015Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29015)
43747De-Chao Zhang, Peter Schumann, Jiang Wu, Luís Franca, Kathrin Neuner, Rosa MargesinVirgibacillus flavescens sp. nov., isolated from marine sediment10.1099/ijsem.0.000846IJSEM 66: 1138-1143 201626674201
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90781Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403941.1