Strain identifier

BacDive ID: 1494

Type strain: Yes

Species: Virgibacillus soli

Strain Designation: CC-YMP-6

Strain history: CIP <- 2011, P. Kämpfer, J. Liebig Giessen Univ., Giessen, Germany <- A.B. Arun, Yenepoya Univ., Mangalore, Karnataka State, India: strain CC-YMP-6

NCBI tax ID(s): 480284 (species)

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General

@ref: 16630

BacDive-ID: 1494

DSM-Number: 22952

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

description: Virgibacillus soli CC-YMP-6 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 480284
  • Matching level: species

strain history

@refhistory
16630<- P. Kämpfer, Univ. Giessen, Germany; CC-YMP-6 <- A. B. Arun, Yenepoya Univ., Mangalore, India
122670CIP <- 2011, P. Kämpfer, J. Liebig Giessen Univ., Giessen, Germany <- A.B. Arun, Yenepoya Univ., Mangalore, Karnataka State, India: strain CC-YMP-6

doi: 10.13145/bacdive1494.20230509.8.1

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 soli
  • full scientific name: Virgibacillus soli Kämpfer et al. 2011

@ref: 16630

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus soli

full scientific name: Virgibacillus soli Kämpfer et al. 2011

strain designation: CC-YMP-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23064variable5.0 µm0.5 µmrod-shapedyes
122670positiverod-shapedyes

colony morphology

@refcolony sizecolony colorincubation periodmedium used
230642.0-4.0 mmorange to brownish3 daysCaso agar (Merck 105458)
617201-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16630CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water
23064Caso agar (Merck 105458)yes
23064Nutrient agar (NA)yes
23064tryptone soy agaryes
40337MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122670CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16630positivegrowth28mesophilic
23064positivegrowth15.0-40.0
23064nogrowth5.0psychrophilic
23064nogrowth45.0thermophilic
23064positiveoptimum25.0-30.0mesophilic
40337positivegrowth30mesophilic
61720positivegrowth30-37mesophilic

culture pH

@refabilitytypepHPH range
23064positiveoptimum7.5-8.5alkaliphile
23064positivegrowth7.0-10.0
23064positivegrowth10.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61720aerobe
122670facultative anaerobe

spore formation

  • @ref: 23064
  • spore description: spherical to ellipsoidal,terminal
  • type of spore: endospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
23064NaClnogrowth>6.0 %(w/v)
23064NaClpositivegrowth0.0 %(w/v)
23064NaClnogrowth20.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2306415824D-fructose-builds acid from
2306412936D-galactose-builds acid from
2306416899D-mannitol-builds acid from
2306416024D-mannose-builds acid from
23064506227N-acetylglucosamine-builds acid from
2306427082trehalose-builds acid from
23064casein-hydrolysis
230644853esculin-hydrolysis
2306417634D-glucose+builds acid from
2306417234glucose+carbon source
2306417992sucrose+carbon source
230645291gelatin+hydrolysis
2306428017starch+hydrolysis
2306417632nitrate+reduction
12267017632nitrate+reduction
12267016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2306435581indoleno
2306416136hydrogen sulfideno
2306415688acetoinno
12267035581indoleno

enzymes

@refvalueactivityec
23064arginine dihydrolase-3.5.3.6
23064beta-galactosidase-3.2.1.23
23064catalase+1.11.1.6
23064cytochrome oxidase+1.9.3.1
23064gelatinase+
23064lysine decarboxylase-4.1.1.18
23064ornithine decarboxylase-4.1.1.17
23064tryptophan deaminase-4.1.99.1
23064urease-3.5.1.5
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
122670oxidase+
122670catalase+1.11.1.6
122670urease-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
122670-+---+---+++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperaturesampling dateisolation date
16630soilYang-Ming MountainTaiwanTWNAsia
23064nutrient agar2 days30.0
61720Soil,mountainTaiwanTWNAsia2007
122670Environment, Soil samplesYang Ming mountainTaiwanTWNAsia2007

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166301Risk group (German classification)
1226701Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16630
  • description: Virgibacillus soli strain CC-YMP-6 16S ribosomal RNA gene, partial sequence
  • accession: EU213011
  • length: 1526
  • database: ena
  • NCBI tax ID: 480284

External links

@ref: 16630

culture collection no.: DSM 22952, CCM 7714, CCUG 58580, CIP 110293

straininfo link

  • @ref: 71140
  • straininfo: 363868

literature

  • topic: Phylogeny
  • Pubmed-ID: 20228217
  • title: Virgibacillus soli sp. nov., isolated from mountain soil.
  • authors: Kampfer P, Arun AB, Busse HJ, Langer S, Young CC, Chen WM, Syed AA, Rekha PD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.020974-0
  • year: 2010
  • mesh: DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Taiwan, Virgibacillus/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16630Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22952)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22952
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
23064P. Kämpfer,A. B. Arun,H.-J. Busse,S. Langer,C.-C. Young,W.-M. Chen,A. A. Syed,P. D. Rekha10.1099/ijs.0.020974-0Virgibacillus soli sp. nov., isolated from mountain soilIJSEM 61: 275-280 201120228217
40337Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8137
61720Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58580)https://www.ccug.se/strain?id=58580
68382Automatically annotated from API zym
71140Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363868.1StrainInfo: A central database for resolving microbial strain identifiers
122670Curators of the CIPCollection of Institut Pasteur (CIP 110293)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110293