Strain identifier

BacDive ID: 1482

Type strain: Yes

Species: Virgibacillus carmonensis

Strain Designation: mccs2332

Strain history: CIP <- 2004, DSMZ <- LMG: strain mccs2332 <- J. Heyrman, Univ. Ghent, Belgium

NCBI tax ID(s): 171692 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5587

BacDive-ID: 1482

DSM-Number: 14868

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

description: Virgibacillus carmonensis mccs2332 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from mural painting.

NCBI tax id

  • NCBI tax id: 171692
  • Matching level: species

strain history

@refhistory
5587<- D. Janssens, LMG; mccs2332 <- J. Heyrman, Univ. Ghent, Belgium
67770DSM 14868 <-- D. Janssens mccs2332 <-- J. Heyrman R-5521.
117185CIP <- 2004, DSMZ <- LMG: strain mccs2332 <- J. Heyrman, Univ. Ghent, Belgium

doi: 10.13145/bacdive1482.20230509.8.1

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 carmonensis
  • full scientific name: Virgibacillus carmonensis Heyrman et al. 2003

@ref: 5587

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus carmonensis

full scientific name: Virgibacillus carmonensis Heyrman et al. 2003

strain designation: mccs2332

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23062positive2.0-7.0 µm0.5-0.7 µmrod-shapedyes
117185positiverod-shapedyes

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
230620.5-1.0 mmpink tint (larger colonies)circular1 dayMA medium
117185

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5587BACTO 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
23062MA mediumyes
33930Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
117185CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5587positivegrowth28mesophilic
23062positivegrowth10.0-40.0
23062positiveoptimum25.0-30.0mesophilic
33930positivegrowth30mesophilic
67770positivegrowth30mesophilic
117185positivegrowth10-30
117185nogrowth37mesophilic
117185nogrowth45thermophilic
117185nogrowth55thermophilic

culture pH

  • @ref: 117185
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23062aerobe
117185obligate aerobe

spore formation

  • @ref: 23062
  • spore description: ellipsoidal, sometimes nearly spherical,subterminal,in swollen sporangia
  • type of spore: endospore
  • spore formation: yes

halophily

@refsalttested relationconcentrationgrowth
23062NaCloptimum5.0 %
23062NaCloptimum10.0 %
23062NaClgrowth0.0 %no
117185NaClgrowth0-10 %positive

murein

  • @ref: 23062
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23062168082-dehydro-D-gluconate-builds acid from
2306227613amygdalin-builds acid from
2306218305arbutin-builds acid from
2306215963ribitol-builds acid from
2306217108D-arabinose-builds acid from
2306218333D-arabitol-builds acid from
2306217057cellobiose-builds acid from
2306215824D-fructose-builds acid from
2306228847D-fucose-builds acid from
2306212936D-galactose-builds acid from
2306217634D-glucose-builds acid from
2306217716lactose-builds acid from
2306262318D-lyxose-builds acid from
2306217306maltose-builds acid from
2306216899D-mannitol-builds acid from
2306216024D-mannose-builds acid from
230626731melezitose-builds acid from
2306228053melibiose-builds acid from
2306216634raffinose-builds acid from
2306216988D-ribose-builds acid from
2306217992sucrose-builds acid from
2306217924D-sorbitol-builds acid from
2306216443D-tagatose-builds acid from
2306216551D-trehalose-builds acid from
2306232528turanose-builds acid from
2306265327D-xylose-builds acid from
2306216813galactitol-builds acid from
2306217113erythritol-builds acid from
230624853esculin-builds acid from
2306228066gentiobiose-builds acid from
2306224265gluconate-builds acid from
2306217754glycerol-builds acid from
2306228087glycogen-builds acid from
2306217268myo-inositol-builds acid from
2306215443inulin-builds acid from
2306230849L-arabinose-builds acid from
2306218403L-arabitol-builds acid from
2306218287L-fucose-builds acid from
2306262345L-rhamnose-builds acid from
2306217266L-sorbose-builds acid from
2306265328L-xylose-builds acid from
23062320061methyl alpha-D-glucopyranoside-builds acid from
2306243943methyl alpha-D-mannoside-builds acid from
2306274863methyl beta-D-xylopyranoside-builds acid from
23062506227N-acetylglucosamine-builds acid from
2306217814salicin-builds acid from
2306228017starch-builds acid from
2306217151xylitol-builds acid from
2306217108D-arabinose-carbon source
2306215824D-fructose-carbon source
2306217634D-glucose-carbon source
2306265327D-xylose-carbon source
2306217716lactose-carbon source
2306227897tryptophan-energy source
23062174265-dehydro-D-gluconate+builds acid from
2306217057cellobiose+carbon source
2306228053melibiose+carbon source
2306216551D-trehalose+carbon source
2306216634raffinose+carbon source
2306217992sucrose+carbon source
23062casein+hydrolysis
230624853esculin+hydrolysis
2306217632nitrate+reduction
11718516947citrate-carbon source
1171854853esculin-hydrolysis
117185606565hippurate-hydrolysis
11718517632nitrate+reduction
11718516301nitrite-reduction
11718517632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2306235581indoleno
2306216136hydrogen sulfideno
2306215688acetoinno
11718535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
2306215688acetoin-
2306235581indole-
11718515688acetoin-
11718517234glucose-

enzymes

@refvalueactivityec
23062arginine dihydrolase-3.5.3.6
23062beta-galactosidase-3.2.1.23
23062catalase+1.11.1.6
23062gelatinase-
23062lysine decarboxylase-4.1.1.18
23062ornithine decarboxylase-4.1.1.17
23062tryptophan deaminase-4.1.99.1
23062urease-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
117185oxidase-
117185beta-galactosidase-3.2.1.23
117185alcohol dehydrogenase-1.1.1.1
117185gelatinase+
117185amylase-
117185DNase-
117185caseinase+3.4.21.50
117185catalase+1.11.1.6
117185tween esterase-
117185gamma-glutamyltransferase-2.3.2.2
117185lecithinase-
117185lipase-
117185lysine decarboxylase-4.1.1.18
117185ornithine decarboxylase-4.1.1.17
117185urease-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
117185-+++-+---+++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5587mural paintingSeville, CarmonaSpainESPEurope
23062Servilia tomb of Roman necropolis of Carmona (Seville)
67770Biofilm formation on the mural paintings of the Servilia tombnecropolis of CarmonaSpainESPEurope
117185Mural paintingSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Other#Painting

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55871Risk group (German classification)
1171851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Virgibacillus carmonensis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 588AB367174588ena171692
20218Virgibacillus carmonensis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 505AB367175505ena171692
23062Virgibacillus carmonensis partial 16S rRNA gene, type strain LMG 20964TAJ3163021518nuccore171692

GC content

  • @ref: 23062
  • GC-content: 38.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 5587

culture collection no.: DSM 14868, JCM 16508, LMG 20964, KCTC 3819, CIP 108266

straininfo link

  • @ref: 71128
  • straininfo: 85322

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710619Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus.Heyrman J, Logan NA, Busse HJ, Balcaen A, Lebbe L, Rodriguez-Diaz M, Swings J, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.02371-02003Bacillus/*classification/genetics/isolation & purification/metabolism, Base Composition, Biodegradation, Environmental, Biofilms, DNA, Bacterial/analysis/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Paintings, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Sequence Analysis, DNAGenetics
Phylogeny19643886Virgibacillus salinus sp. nov., a moderately halophilic bacterium from sediment of a saline lake.Carrasco IJ, Marquez MC, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.009530-02009Bacillaceae/*classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolismMetabolism
Phylogeny19651717Virgibacillus byunsanensis sp. nov., isolated from a marine solar saltern.Yoon JH, Kang SJ, Jung YT, Lee KC, Oh HW, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.009837-02009Bacillaceae/*classification/genetics/physiology, Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, Korea, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salts/chemistry, Seawater/*microbiology, Sequence Homology, Nucleic Acid, *Water MicrobiologyGenetics
Phylogeny21239563Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food.Kim J, Jung MJ, Roh SW, Nam YD, Shin KS, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.028191-02011Animals, 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/metabolismMetabolism
Phylogeny24801155Pseudogracilibacillus auburnensis gen. nov., sp. nov., isolated from the rhizosphere of Zea mays.Glaeser SP, McInroy JA, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.064584-02014Alabama, Bacillaceae/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyGenetics
Phylogeny25062698Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.Amoozegar MA, Bagheri M, Didari M, Mehrshad M, Schumann P, Sproer C, Sanchez-Porro C, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.065375-02014Bacillaceae/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Spores, Bacterial/genetics, Virgibacillus/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
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
Phylogeny32997153Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea.Wang Y, Jiang GQ, Lin HP, Sun P, Zhang HY, Lu DM, Wang LY, Kim CJ, Tang SKArch Microbiol10.1007/s00203-020-02043-22020Bacillaceae/*classification/*drug effects/genetics/isolation & purification, Base Composition, Fatty Acids/analysis, Genome, Bacterial/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sodium Chloride/*pharmacology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5587Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14868)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14868
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
23062Jeroen Heyrman,Niall A. Logan,Hans-Jürgen Busse,An Balcaen,Liesbeth Lebbe,Marina Rodriguez-Diaz,Jean Swings,Paul De Vos10.1099/ijs.0.02371-0Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus VirgibacillusIJSEM 53: 501-511 200312710619
33930Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5869
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
71128Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85322.1StrainInfo: A central database for resolving microbial strain identifiers
117185Curators of the CIPCollection of Institut Pasteur (CIP 108266)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108266