Strain identifier

BacDive ID: 1481

Type strain: Yes

Species: Virgibacillus necropolis

Strain Designation: mccs2660

Strain history: CIP <- 2010, DSMZ <- LMG: strain mccs2660 <- J. Heyrman, Univ. Ghent, Belgium

NCBI tax ID(s): 163877 (species)

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General

@ref: 5585

BacDive-ID: 1481

DSM-Number: 14866

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

description: Virgibacillus necropolis mccs2660 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from mural painting.

NCBI tax id

  • NCBI tax id: 163877
  • Matching level: species

strain history

@refhistory
5585<- D. Janssens, LMG; mccs2660 <- J. Heyrman, Univ. Ghent
67770DSM 14866 <-- D. Janssens mccs2660 <-- J. Heyrman R-5449.
121254CIP <- 2010, DSMZ <- LMG: strain mccs2660 <- J. Heyrman, Univ. Ghent, Belgium

doi: 10.13145/bacdive1481.20230509.8.1

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

@ref: 5585

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus necropolis

full scientific name: Virgibacillus necropolis Heyrman et al. 2003

strain designation: mccs2660

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23062positive2.0-5.0 µm0.5-0.7 µmrod-shapedyes
69480yes96.365
69480positive100
121254positiverod-shapedyes

colony morphology

  • @ref: 23062
  • colony size: 0.2-0.5 mm
  • colony color: cream-coloured
  • colony shape: circular
  • incubation period: 1 day
  • medium used: MA medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5585BACTO 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
40485Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121254CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5585positivegrowth28mesophilic
23062positivegrowth10.0-40.0
23062positiveoptimum25.0-35.0mesophilic
40485positivegrowth30mesophilic
67770positivegrowth30mesophilic
121254positivegrowth10-37
121254nogrowth45thermophilic
121254nogrowth55thermophilic

culture pH

  • @ref: 121254
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 23062
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23062ellipsoidal,terminal or subterminal or central,in swollen sporangiaendosporeyes
69481yes100
69480yes100

halophily

@refsalttested relationconcentrationgrowth
23062NaCloptimum5.0 %
23062NaCloptimum10.0 %
23062NaClgrowth0.0 %no
121254NaClgrowth0-2 %positive
121254NaClgrowth4 %no
121254NaClgrowth6 %no
121254NaClgrowth8 %no
121254NaClgrowth10 %no

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
23062174265-dehydro-D-gluconate-builds acid from
2306227613amygdalin-builds acid from
2306217108D-arabinose-builds acid from
2306215824D-fructose-builds acid from
2306217634D-glucose-builds acid from
2306216024D-mannose-builds acid from
2306228053melibiose-builds acid from
2306216443D-tagatose-builds acid from
2306216551D-trehalose-builds acid from
2306228260galactose-builds acid from
2306217754glycerol-builds acid from
2306228087glycogen-builds acid from
2306218287L-fucose-builds acid from
2306262345L-rhamnose-builds acid from
2306229864mannitol-builds acid from
2306217268myo-inositol-builds acid from
23062506227N-acetylglucosamine-builds acid from
2306233942ribose-builds acid from
2306227897tryptophan-energy source
2306217108D-arabinose-growth
2306215824D-fructose-growth
2306265327D-xylose-growth
2306217057cellobiose+carbon source
2306217634D-glucose+carbon source
2306228053melibiose+carbon source
2306216551D-trehalose+carbon source
2306217716lactose+carbon source
2306216634raffinose+carbon source
2306217992sucrose+carbon source
23062casein+hydrolysis
2306217632nitrate+reduction
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-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
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
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
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12125416947citrate-carbon source
1212544853esculin-hydrolysis
12125417632nitrate+reduction
12125416301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
2306235581indoleno
2306216136hydrogen sulfideno
2306215688acetoinno
12125435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
2306215688acetoin-
2306235581indole-
12125415688acetoin-
12125417234glucose-

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
121254oxidase-
121254beta-galactosidase+3.2.1.23
121254alcohol dehydrogenase-1.1.1.1
121254gelatinase-
121254amylase-
121254caseinase-3.4.21.50
121254catalase+1.11.1.6
121254tween esterase-
121254lecithinase-
121254lipase-
121254lysine decarboxylase-4.1.1.18
121254ornithine decarboxylase-4.1.1.17
121254protease-
121254urease-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
121254-+++-++-++++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121254-----+/---------------------------------+---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121254+------+-+----++-----++---------------------------+----------------------+-+-----+-+-------+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5585mural paintingSeville, CarmonaSpainESPEurope
67770Biofilm formation on the mural paintings of the Servilia tombnecropolis of CarmonaSpainESPEurope
121254Mural paintingSpainESPEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_21561.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_10900;97_13207;98_16259;99_21561&stattab=map
  • Last taxonomy: Virgibacillus
  • 16S sequence: AJ315056
  • Sequence Identity:
  • Total samples: 48
  • soil counts: 6
  • aquatic counts: 9
  • animal counts: 28
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55851Risk group (German classification)
1212541Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Virgibacillus necropolis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 505AB367186505ena163877
20218Virgibacillus necropolis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 589AB367187589ena163877
5585Virgibacillus necropolis 16S rRNA gene, type strain LMG 19488TAJ3150561522ena163877

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Virgibacillus necropolis LMG 19488GCA_002224365completencbi163877
66792Virgibacillus necropolis strain LMG 19488163877.4completepatric163877

GC content

  • @ref: 67770
  • GC-content: 37.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes66.6no
gram-positiveyes91.378yes
anaerobicno99.272yes
aerobicyes93.494yes
halophileyes83.897no
spore-formingyes92.14yes
thermophileno97.963yes
glucose-utilyes88.257yes
motileyes83.408no
glucose-fermentno88.246no

External links

@ref: 5585

culture collection no.: DSM 14866, JCM 16509, LMG 19488, KCTC 3820, CIP 108265

straininfo link

  • @ref: 71127
  • straininfo: 13178

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
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

@idauthorscataloguedoi/urltitlejournalpubmed
5585Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14866)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14866
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
40485Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5868
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)
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
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
71127Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13178.1StrainInfo: A central database for resolving microbial strain identifiers
121254Curators of the CIPCollection of Institut Pasteur (CIP 108265)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108265