Strain identifier

BacDive ID: 1150

Type strain: Yes

Species: Bacillus vallismortis

Strain Designation: DV1-F-3, DV-1-F3

Strain history: CIP <- 1996, M. Roberts, Cent. Microb. Ecol., East Lansing, MI, USA: strain DV-1-F3

NCBI tax ID(s): 564287 (strain), 72361 (species)

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

@ref: 4164

BacDive-ID: 1150

DSM-Number: 11031

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

description: Bacillus vallismortis DV1-F-3 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from sand dune with mesquite tree.

NCBI tax id

NCBI tax idMatching level
72361species
564287strain

strain history

@refhistory
4164<- NRRL
67770NRRL B-14890 <-- F. M. Cohan DV-1-F3.
123790CIP <- 1996, M. Roberts, Cent. Microb. Ecol., East Lansing, MI, USA: strain DV-1-F3

doi: 10.13145/bacdive1150.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus vallismortis
  • full scientific name: Bacillus vallismortis Roberts et al. 1996

@ref: 4164

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus vallismortis

full scientific name: Bacillus vallismortis Roberts et al. 1996

strain designation: DV1-F-3, DV-1-F3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilitycell shape
23302positive2.0-4.0 µm0.8-1.0 µmyes
123790positiveyesrod-shaped

colony morphology

@refcolony sizecolony colorcolony shapeincubation period
233022.0 mmopaquecircular2 days
123790

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4164NUTRIENT 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
35170MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123790CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4164positivegrowth30mesophilic
23302positivemaximum50thermophilic
23302positiveminimum5-10psychrophilic
23302positiveoptimum28-30mesophilic
35170positivegrowth30mesophilic
67770positivegrowth30mesophilic
123790positivegrowth30-45
123790nogrowth10psychrophilic
123790nogrowth22psychrophilic
123790nogrowth55thermophilic

culture pH

@refabilitytypepH
23302positivegrowth5.7
123790positivegrowth6

Physiology and metabolism

oxygen tolerance

  • @ref: 123790
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore descriptiontype of sporespore formation
23302ellipsoidal spores centrally and paracentrally in unswollen sporangiaendosporeyes
123790yes

halophily

@refsaltgrowthtested relationconcentration
23302NaClpositivegrowth3 %
23302NaClpositivegrowth5 %
23302NaClpositivegrowth7 %
23302NaClpositivegrowth10 %
123790NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2330217272propionate-assimilation
2330217716lactose-builds acid from
2330217057cellobiose-builds gas from
2330228757fructose-builds gas from
2330228260galactose-builds gas from
2330217234glucose-builds gas from
2330230849L-arabinose-builds gas from
2330262345L-rhamnose-builds gas from
2330217306maltose-builds gas from
2330229864mannitol-builds gas from
2330237684mannose-builds gas from
2330233942ribose-builds gas from
2330217814salicin-builds gas from
2330230911sorbitol-builds gas from
2330217992sucrose-builds gas from
2330227082trehalose-builds gas from
2330218222xylose-builds gas from
23302egg yolk-degradation
2330261995lecithin-degradation
2330228044phenylalanine-degradation
2330218186tyrosine-degradation
2330216199urea-degradation
2330217716lactose-fermentation
2330228053melibiose-fermentation
2330216947citrate+assimilation
2330217057cellobiose+builds acid from
2330228757fructose+builds acid from
2330228260galactose+builds acid from
2330217234glucose+builds acid from
2330230849L-arabinose+builds acid from
2330262345L-rhamnose+builds acid from
2330217306maltose+builds acid from
2330229864mannitol+builds acid from
2330237684mannose+builds acid from
2330233942ribose+builds acid from
2330217814salicin+builds acid from
2330230911sorbitol+builds acid from
2330217992sucrose+builds acid from
2330227082trehalose+builds acid from
2330218222xylose+builds acid from
2330253426tween 80+degradation
23302casein+hydrolysis
2330228017starch+hydrolysis
2330217632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
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
6837116634raffinose-builds acid from
683716731melezitose-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
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+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
6837117754glycerol+builds acid from
12379016947citrate-carbon source
1237904853esculin+hydrolysis
123790606565hippurate+hydrolysis
12379017632nitrate+reduction
12379016301nitrite-reduction
12379017632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
2330235581indoleno
2330216136hydrogen sulfideno
2330216016dihydroxyacetoneno
2330215688acetoinyes
12379035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2330215688acetoin+
12379015688acetoin+
12379017234glucose-

enzymes

@refvalueactivityec
23302catalase+1.11.1.6
23302cytochrome oxidase+1.9.3.1
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
123790oxidase-
123790beta-galactosidase+3.2.1.23
123790alcohol dehydrogenase-1.1.1.1
123790gelatinase+
123790amylase+
123790DNase+
123790caseinase+3.4.21.50
123790catalase+1.11.1.6
123790tween esterase-
123790gamma-glutamyltransferase+2.3.2.2
123790lecithinase-
123790lipase-
123790lysine decarboxylase-4.1.1.18
123790ornithine decarboxylase-4.1.1.17
123790protease+
123790urease-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
123790-+++-+----++-+-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123790+--+------+++---+/-+--+/--+/-++++---+-+/---+/-+/--+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123790+++-+-+++++-+--++++++++----+---+++++-----+-++----++--+-+---++--------------+---++-----+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
23302sand dune with mesquite treeDeath Valley, CaliforniaUSAUSANorth America36.65-117.083
4164soilDeath ValleyUSAUSANorth America
67770Desert soil in Death ValleyCAUSAUSANorth America
123790Environment, Soil, sand duneDeath Valley, CaliforniaUnited States of AmericaUSANorth America1990

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_21.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_17;97_17;98_20;99_21&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: AB681417
  • Sequence Identity:
  • Total samples: 18201
  • soil counts: 3768
  • aquatic counts: 2854
  • animal counts: 9674
  • plant counts: 1905

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41641Risk group (German classification)
1237901Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus vallismortis strain BCRC 17183 16S ribosomal RNA gene, partial sequenceEF4334041468ena72361
20218Bacillus vallismortis gene for 16S ribosomal RNAAB0211981530ena72361
20218Bacillus vallismortis gene for 16S rRNA, partial sequence, strain: NBRC 101236AB6814171475ena72361
20218Bacillus vallismortis strain NRRL B-14890 16S ribosomal RNA gene, partial sequenceEU1384631168ena72361

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus vallismortis DSM 11031GCA_004116955completencbi72361
66792Bacillus vallismortis DV1-F-31051502.3wgspatric1051502
66792Bacillus vallismortis strain DSM 1103172361.11completepatric72361
66792Bacillus vallismortis DV1-F-32547132131draftimg1051502
66792Bacillus vallismortis DSM 110312880152234completeimg72361
67770Bacillus vallismortis DV1-F-3GCA_000245315scaffoldncbi1051502

GC content

@refGC-contentmethod
416443thermal denaturation, midpoint method (Tm)
2330243.00thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.425yes
flagellatedyes84.908no
gram-positiveyes89.348no
anaerobicno99.422no
aerobicyes92.463no
halophileyes87.277yes
spore-formingyes97.046yes
thermophileno97.223no
glucose-utilyes89.521no
glucose-fermentno89.641no

External links

@ref: 4164

culture collection no.: DSM 11031, NRRL B-14890, JCM 12234, ATCC 700092, BCRC 17183, CIP 104792, KCTC 3707, LMG 18725, NBRC 101236

straininfo link

  • @ref: 70821
  • straininfo: 13133

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8934905Bacillus vallismortis sp. nov., a close relative of Bacillus subtilis, isolated from soil in Death Valley, California.Roberts MS, Nakamura LK, Cohan FMInt J Syst Bacteriol10.1099/00207713-46-2-4701996Bacillus subtilis/*classification/enzymology/genetics, Bacterial Proteins/genetics, California, DNA Gyrase, DNA Polymerase III/genetics, DNA Topoisomerases, Type II/genetics, DNA, Bacterial/analysis, DNA-Directed RNA Polymerases/genetics, F Factor, Phenotype, Phylogeny, Restriction Mapping, *Soil MicrobiologyPhenotype
Phylogeny19933584Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand.Sumpavapol P, Tongyonk L, Tanasupawat S, Chokesajjawatee N, Luxananil P, Visessanguan WInt J Syst Evol Microbiol10.1099/ijs.0.018879-02009Bacillus/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Food Microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature, ThailandBiotechnology
Genetics22493193Whole-genome sequences of Bacillus subtilis and close relatives.Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel JJ Bacteriol10.1128/JB.05675-112012Bacillus/classification/*genetics, Chromosomes, Bacterial, DNA, Bacterial/genetics, Gene Expression Regulation, Bacterial, *Genome, Bacterial, Molecular Sequence DataPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4164Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11031)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11031
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
23302MICHAEL S. ROBERTS, L. K. NAKAMURA, FREDERICK M. COHAN10.1099/00207713-46-2-470Bacillus vallismortis sp. nov., a Close Relative of Bacillus subtilis, Isolated from Soil in Death Valley, CaliforniaIJSEM 46: 470-475 19968934905
35170Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16739
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
70821Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13133.1StrainInfo: A central database for resolving microbial strain identifiers
123790Curators of the CIPCollection of Institut Pasteur (CIP 104792)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104792