Strain identifier

BacDive ID: 1476

Type strain: Yes

Species: Virgibacillus salexigens

Strain Designation: C-20Mo

Strain history: CIP <- 1998, A. Ventosa, Fac. Pharm., Univ. Sevilla, Spain: strain C-20Mo

NCBI tax ID(s): 61016 (species)

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General

@ref: 4383

BacDive-ID: 1476

DSM-Number: 11483

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

description: Virgibacillus salexigens C-20Mo is an obligate aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from saltern in Huelva.

NCBI tax id

  • NCBI tax id: 61016
  • Matching level: species

strain history

@refhistory
4383<- M.J. Garabito, C-20Mo
67770DSM 11483 <-- M. J. Garabito; Univ. of Seville, Spain; C-20Mo.
122371CIP <- 1998, A. Ventosa, Fac. Pharm., Univ. Sevilla, Spain: strain C-20Mo

doi: 10.13145/bacdive1476.20230509.8.1

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 salexigens
  • full scientific name: Virgibacillus salexigens (Garabito et al. 1997) Heyrman et al. 2003

  • synonyms

    @refsynonym
    20215Salibacillus salexigens
    20215Bacillus salexigens

@ref: 4383

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus salexigens

full scientific name: Virgibacillus salexigens (Garabito et al. 1997) Heyrman et al. 2003

strain designation: C-20Mo

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23060positive1.5-3.5 µm0.3-0.6 µmrod-shapedyes
69480yes97.458
69480positive100
122371positiverod-shapedyes

colony morphology

@refcolony shapemedium used
23060circular10% (wt/vol) total salts complex medium
122371

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4383CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: NaCl 100.0 g/l Agar 15.0 g/l Casein peptone 15.0 g/l Soy peptone 5.0 g/l Distilled water
2306010% (wt/vol) total salts complex mediumyes
39328Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122371CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
4383positivegrowth30mesophilic
23060positivegrowth15.0-45.0
23060positivegrowth45.0thermophilic
23060nogrowth50.0thermophilic
23060positiveoptimum37.0mesophilic
39328positivegrowth37mesophilic
67770positivegrowth37mesophilic
122371positivegrowth30-45
122371nogrowth10psychrophilic
122371nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
23060positivegrowth6.0-11.0alkaliphile
23060positiveoptimum7.5
23060positivegrowth6.0
23060positivegrowth11.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23060obligate aerobe
122371obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23060oval,subterminal or central,in swollen sporangiaendosporeyes
69481yes100
69480yes99.734
122371yes

halophily

@refsaltgrowthtested relationconcentration
122371NaClpositivegrowth2-10 %
122371NaClnogrowth0 %

murein

  • @ref: 23060
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2306012936D-galactose-builds acid from
2306016899D-mannitol-builds acid from
2306028053melibiose-builds acid from
2306016551D-trehalose-builds acid from
2306065327D-xylose-builds acid from
2306016813galactitol-builds acid from
2306062345L-rhamnose-builds acid from
2306017716lactose-builds acid from
2306016947citrate-carbon source
2306027897tryptophan-energy source
2306028017starch-hydrolysis
2306053426tween 80-hydrolysis
2306018186tyrosine-hydrolysis
2306017632nitrate-reduction
2306015824D-fructose+builds acid from
2306017634D-glucose+builds acid from
2306016024D-mannose+builds acid from
2306017754glycerol+builds acid from
2306017306maltose+builds acid from
23060casein+hydrolysis
2306016991dna+hydrolysis
230604853esculin+hydrolysis
230605291gelatin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+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
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+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
6837115824D-fructose+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
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12237116947citrate-carbon source
1223714853esculin+hydrolysis
12237117632nitrate-reduction
12237116301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2306048923erythromycinyesyes
23060100147nalidixic acidyesyes
2306059062polymyxinyesyes
2306028971ampicillinyesyes
2306028669bacitracinyesyes
230603393carbenicillinyesyes
230603542cephalothinyesyes
2306017698chloramphenicolyesyes
2306028368novobiocinyesyes
2306018208penicillin gyesyes
2306028077rifampicinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2306035581indoleno
2306015688acetoinno
2306016136hydrogen sulfideyes
12237135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testcitrate testmethylred-test
2306015688acetoin-
2306035581indole-
2306016947citrate-
12237115688acetoin-
12237117234glucose-

enzymes

@refvalueactivityec
23060arginine dihydrolase-3.5.3.6
23060catalase+1.11.1.6
23060cytochrome oxidase+1.9.3.1
23060lysine decarboxylase-4.1.1.18
23060ornithine decarboxylase-4.1.1.17
23060phenylalanine deaminase-4.3.1.5
23060phosphatase-
23060tryptophan deaminase-4.1.99.1
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
122371oxidase+
122371beta-galactosidase+3.2.1.23
122371alcohol dehydrogenase-1.1.1.1
122371gelatinase+
122371amylase-
122371caseinase+3.4.21.50
122371catalase+1.11.1.6
122371tween esterase+
122371gamma-glutamyltransferase-2.3.2.2
122371lecithinase-
122371lipase-
122371lysine decarboxylase-4.1.1.18
122371ornithine decarboxylase-4.1.1.17
122371protease-
122371tryptophan deaminase-
122371urease-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
122371-+-+-----+++-+---+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122371+/----+-----+++--------++/-++++/-+---+---+/-+--+------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122371+++++--+-+++---++++-++++-------+-+++--------+----++-++--+--++-----------+--+--+---------+-++++--+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
4383saltern in HuelvaSpainESPEurope
59520SalternSpainESPEuropeHuelva
67770SalternSpainESPEuropeHuelva
122371Environment, Salterns waterSpainESPEuropeHuelva1991

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_4297.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1861;97_2610;98_3234;99_4297&stattab=map
  • Last taxonomy: Virgibacillus
  • 16S sequence: LC016572
  • Sequence Identity:
  • Total samples: 11
  • soil counts: 3
  • aquatic counts: 2
  • animal counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43831Risk group (German classification)
1223711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218B.salexigens 16S rRNA geneY116031533ena61016
20218Virgibacillus salexigens isolate Ss1 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723666427ena61016
67770Virgibacillus salexigens gene for 16S ribosomal RNA, partial sequence, strain: JCM 30552LC0165721521ena61016

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Virgibacillus salexigens DSM 11483GCA_014905415scaffoldncbi61016
66792Virgibacillus massiliensis strain Vm-51462526.12wgspatric1462526
66792Virgibacillus salexigens strain DSM 1148361016.3wgspatric61016
66792Virgibacillus salexigens strain NT N5361016.4wgspatric61016
66792Virgibacillus salexigens strain P261016.5wgspatric61016

GC content

@refGC-contentmethod
438336.3-39.5
2306039.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.939no
flagellatedyes87.484no
gram-positiveyes91.905yes
anaerobicno99.359yes
aerobicyes94.224no
halophileyes93.609no
spore-formingyes95.847no
glucose-utilyes87.79no
glucose-fermentno87.881no
thermophileno97.692no

External links

@ref: 4383

culture collection no.: DSM 11483, ATCC 700290, CCM 4646, JCM 30552, CCUG 52350, CIP 105608, KACC 10867, KACC 14582, KCTC 3704, KCTC 3844, LMG 21520

straininfo link

  • @ref: 71122
  • straininfo: 12431

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9226905Bacillus salexigens sp. nov., a new moderately halophilic Bacillus species.Garabito MJ, Arahal DR, Mellado E, Marquez MC, Ventosa AInt J Syst Bacteriol10.1099/00207713-47-3-7351997Bacillus/chemistry/*classification/genetics, Carbohydrate Metabolism, Cell Wall/chemistry, DNA, Bacterial/analysis, Diaminopimelic Acid/analysis, Gram-Positive Endospore-Forming Bacteria/chemistry/*classification/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Salts/metabolism, *Soil MicrobiologyMetabolism
Metabolism34143291Distribution of class IId bacteriocin-producing Virgibacillus salexigens in various environments.Omachi H, Terahara T, Futami K, Kawato S, Imada C, Kamei K, Waku T, Kondo A, Naganuma T, Agustini TW, Kobayashi TWorld J Microbiol Biotechnol10.1007/s11274-021-03085-42021Amino Acid Sequence, Anti-Bacterial Agents/metabolism, Bacterial Proteins/genetics/metabolism, Bacteriocins/*genetics/metabolism, Environmental Microbiology, Humans, RNA, Ribosomal, 16S, Seawater/microbiology, Sequence Analysis, DNA, Virgibacillus/*classification/*genetics/metabolism, Whole Genome SequencingPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4383Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11483)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11483
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
23060Maria J. Garabito,David R. Arahal,Encarnación Mellado,M. Carmen Márquez,Antonio Ventosa10.1099/00207713-47-3-735Bacillus salexigens sp. nov., a New Moderately Halophilic Bacillus SpeciesIJSEM 47: 735-741 19979226905
39328Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17647
59520Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52350)https://www.ccug.se/strain?id=52350
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71122Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12431.1StrainInfo: A central database for resolving microbial strain identifiers
122371Curators of the CIPCollection of Institut Pasteur (CIP 105608)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105608