Strain identifier

BacDive ID: 1474

Type strain: Yes

Species: Virgibacillus pantothenticus

Strain Designation: B 21, 3028

Strain history: CIP <- 1951, H. Proom, Wellcome Res. Lab., Beckenham, UK: strain 3028

NCBI tax ID(s): 1473 (species)

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General

@ref: 2027

BacDive-ID: 1474

DSM-Number: 26

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

description: Virgibacillus pantothenticus B 21 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1473
  • Matching level: species

strain history

@refhistory
384351951, H. Proom, Wellcome Res. Lab., Beckenham, UK: strain 3028
2027<- ATCC <- R.E. Gordon <- N.R. Smith, B 21 <- H. Proom, CN 3028
67770IAM 11061 <-- ATCC 14576 <-- R. E. Gordon <-- N. R. Smith NRS 1321 <-- H. Proom CN 3028.
121534CIP <- 1951, H. Proom, Wellcome Res. Lab., Beckenham, UK: strain 3028

doi: 10.13145/bacdive1474.20230509.8.1

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 pantothenticus
  • full scientific name: Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998

  • synonyms

    • @ref: 20215
    • synonym: Bacillus pantothenticus

@ref: 2027

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus pantothenticus

full scientific name: Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998 emend. Heyndrickx et al. 1999

strain designation: B 21, 3028

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23061positive2.0-8.0 mm0.5-0.7 mmrod-shapedyes
121534positiverod-shapedyes

colony morphology

  • @ref: 23061
  • colony size: 1.0-4.0 mm
  • colony color: creamy-grey
  • colony shape: circular
  • incubation period: 2 days
  • medium used: trypticase soy agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23061trypticase soy agaryes
2027NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38435MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121534CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121534CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
23061positivegrowth15.0-50.0
23061positiveoptimum37.0mesophilic
2027positivegrowth30mesophilic
38435positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23061facultative anaerobe
121534facultative anaerobe

spore formation

  • @ref: 23061
  • spore description: spherical to ellipsoidal,terminal or sometimes subterminal, in swollen sporangia
  • type of spore: endospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
23061NaClpositivegrowth4.0 %
23061NaClpositivegrowth10.0 %

murein

  • @ref: 23061
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23061168082-dehydro-D-gluconate-builds acid from
23061174265-dehydro-D-gluconate-builds acid from
2306115963ribitol-builds acid from
2306118333D-arabitol-builds acid from
2306128847D-fucose-builds acid from
2306162318D-lyxose-builds acid from
230616731melezitose-builds acid from
2306116634raffinose-builds acid from
2306165327D-xylose-builds acid from
2306116813galactitol-builds acid from
2306117113erythritol-builds acid from
2306128066gentiobiose-builds acid from
2306124265gluconate-builds acid from
2306128087glycogen-builds acid from
2306117268myo-inositol-builds acid from
2306115443inulin-builds acid from
2306130849L-arabinose-builds acid from
2306118403L-arabitol-builds acid from
2306118287L-fucose-builds acid from
2306117266L-sorbose-builds acid from
2306165328L-xylose-builds acid from
2306117716lactose-builds acid from
2306129864mannitol-builds acid from
2306128053melibiose-builds acid from
2306130911sorbitol-builds acid from
2306117151xylitol-builds acid from
2306127613amygdalin-builds gas from
2306118305arbutin-builds gas from
2306117057cellobiose-builds gas from
2306117108D-arabinose-builds gas from
2306115824D-fructose-builds gas from
2306117634D-glucose-builds gas from
2306116024D-mannose-builds gas from
2306116443D-tagatose-builds gas from
2306132528turanose-builds gas from
2306128260galactose-builds gas from
2306117754glycerol-builds gas from
2306117306maltose-builds gas from
23061320061methyl alpha-D-glucopyranoside-builds gas from
2306143943methyl alpha-D-mannoside-builds gas from
23061506227N-acetylglucosamine-builds gas from
2306126546rhamnose-builds gas from
2306133942ribose-builds gas from
2306117814salicin-builds gas from
2306128017starch-builds gas from
2306117992sucrose-builds gas from
2306127082trehalose-builds gas from
2306117632nitrate-reduction
2306127613amygdalin+builds acid from
2306118305arbutin+builds acid from
2306117057cellobiose+builds acid from
2306117108D-arabinose+builds acid from
2306115824D-fructose+builds acid from
2306117634D-glucose+builds acid from
2306116024D-mannose+builds acid from
2306116443D-tagatose+builds acid from
2306132528turanose+builds acid from
2306128260galactose+builds acid from
2306117754glycerol+builds acid from
2306117306maltose+builds acid from
23061320061methyl alpha-D-glucopyranoside+builds acid from
2306143943methyl alpha-D-mannoside+builds acid from
23061506227N-acetylglucosamine+builds acid from
2306126546rhamnose+builds acid from
2306133942ribose+builds acid from
2306117814salicin+builds acid from
2306128017starch+builds acid from
2306117992sucrose+builds acid from
2306127082trehalose+builds acid from
23061casein+hydrolysis
230614853esculin+hydrolysis
230615291gelatin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117113erythritol-builds acid from
12153417632nitrate+reduction
12153416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2306115688acetoinno
2306116136hydrogen sulfideyes
12153435581indoleno

metabolite tests

  • @ref: 23061
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
23061arginine dihydrolase-3.5.3.6
23061beta-galactosidase-3.2.1.23
23061catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
121534oxidase+
121534catalase+1.11.1.6
121534urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121534--++-+-----+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121534+/--+/--+----+++/-+-+-----++++++-+--++---+---+/--+-+/---+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2027soilSouthern EnglandUnited KingdomGBREurope
44993Soil,garden
67770SoilUnited KingdomGBREurope
121534Environment, Soil, gardenUnited KingdomGBREurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20271Risk group (German classification)
1215341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Virgibacillus pantothenticus clone BPANTO-1R 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478073651ena1473
20218Virgibacillus pantothenticus isolate Vpa1 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723672651ena1473
67770Virgibacillus pantothenticus gene for 16S rRNA, partial sequence, strain: NBRC 102447AB6817891490ena1473
67770Virgibacillus pantothenticus gene for 16S rRNA, partial sequence, strain: IAM 11061D162751491ena1473
67770Bacillus pantothenticus DNA for 16S ribosomal RNA, partial sequenceD784771448ena1473

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Virgibacillus pantothenticus DSM 26GCA_900156795scaffoldncbi1473
67770Virgibacillus pantothenticus DSM 26GCA_001189575scaffoldncbi1473

GC content

@refGC-contentmethod
2306136.9
202736.9thermal denaturation, midpoint method (Tm)
202736.8Buoyant density centrifugation (BD)
6777038.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.453yes
flagellatedyes80.336no
gram-positiveyes90.193yes
anaerobicno98.684yes
aerobicyes73.744yes
halophileyes92.379yes
spore-formingyes97.117no
thermophileno91.738yes
glucose-utilyes91.218no
glucose-fermentno78.042no

External links

@ref: 2027

culture collection no.: DSM 26, ATCC 14576, CCM 2049, LMG 7129, NCIB 8775, NCTC 8162, CCUG 7424, CIP 51.24, IAM 11061, CN 3028, NRS B21, JCM 20334, BCRC 14681, CCEB 635, CECT 42, NBRC 102447, NCAIM B.01092, NCFB 1765, NCIMB 8775, NRRL NRS-1321, OUT 8418, PCM 454, VKM B-1244, VKM B-507, NCDO 1765, NRRL: NRS-1321

straininfo link

  • @ref: 71120
  • straininfo: 13587

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842865Virgibacillus salarius sp. nov., a halophilic bacterium isolated from a Saharan salt lake.Hua NP, Hamza-Chaffai A, Vreeland RH, Isoda H, Naganuma TInt J Syst Evol Microbiol10.1099/ijs.0.65693-02008Bacillaceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Genotype, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Tunisia, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Genetics26383648Genome Sequence of Virgibacillus pantothenticus DSM 26T (ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil.Wang JP, Liu B, Liu GH, Chen DJ, Zhu YJ, Chen Z, Che JMGenome Announc10.1128/genomeA.01064-152015Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2027Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23061M. Heyndrickx,L. Lebbe,K. Kersters,B. Hoste,R. De Wachter,P. De Vos,G. Forsyth,N. A. Logan10.1099/00207713-49-3-1083Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998IJSEM 49: 1083-1090 199910425765
38435Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11979
44993Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7424)https://www.ccug.se/strain?id=7424
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
71120Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13587.1StrainInfo: A central database for resolving microbial strain identifiers
121534Curators of the CIPCollection of Institut Pasteur (CIP 51.24)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2051.24