Strain identifier

BacDive ID: 570

Type strain: Yes

Species: Viridibacillus arvi

Strain Designation: R-16993

Strain history: <- J. Heyrman; R-16993 <- A. Felske

NCBI tax ID(s): 263475 (species)

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General

@ref: 6363

BacDive-ID: 570

DSM-Number: 16317

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

description: Viridibacillus arvi R-16993 is an anaerobe, spore-forming, mesophilic bacterium that forms irregular colonies and was isolated from soil.

NCBI tax id

  • NCBI tax id: 263475
  • Matching level: species

strain history

  • @ref: 6363
  • history: <- J. Heyrman; R-16993 <- A. Felske

doi: 10.13145/bacdive570.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Viridibacillus
  • species: Viridibacillus arvi
  • full scientific name: Viridibacillus arvi (Heyrman et al. 2005) Albert et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Bacillus arvi

@ref: 6363

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Viridibacillus

species: Viridibacillus arvi

full scientific name: Viridibacillus arvi (Heyrman et al. 2005) Albert et al. 2007

strain designation: R-16993

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23359variable3.0-8.0 µm0.8-1.0 µmrod-shapedyes
69480yes91.173
69480positive100

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
233591.0-3.0 mmcreamirregular1 dayNA
23358PCA, TSA and R2A

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6363CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23359BFA, NAyes
23358PCA, TSA and R2Ayes

culture temp

@refgrowthtypetemperaturerange
6363positivegrowth30mesophilic
23359positivegrowth20-30
23359nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
23359nogrowth5.0
23359positivegrowth7-9alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 23359
  • oxygen tolerance: anaerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23359abundantly,spherical and appear in terminal positions, swelling the sporangia slightlyendosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
23359NaClpositivegrowth5 %(w/v)
23359NaClnogrowth7 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335817057cellobiose-builds acid from
2335812936D-galactose-builds acid from
2335817634D-glucose-builds acid from
2335817716lactose-builds acid from
2335816899D-mannitol-builds acid from
2335816024D-mannose-builds acid from
2335816988D-ribose-builds acid from
2335865327D-xylose-builds acid from
2335817754glycerol-builds acid from
2335830849L-arabinose-builds acid from
2335817992sucrose-builds acid from
2335927897tryptophan-energy source
233594853esculin-hydrolysis
233595291gelatin-hydrolysis
2335928017starch-hydrolysis
2335916947citrate-other
2335916136hydrogen sulfide-other
2335917632nitrate-reduction
2335915824D-fructose+builds acid from
23359506227N-acetylglucosamine+/-builds acid from
23359casein+/-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2335935581indoleno
2335915688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2335915688acetoin-
2335935581indole-

enzymes

@refvalueactivityec
23359arginine dihydrolase-3.5.3.6
23359beta-galactosidase+/-3.2.1.23
23359catalase+1.11.1.6
23359cytochrome oxidase-1.9.3.1
23359lysine decarboxylase-4.1.1.18
23359ornithine decarboxylase-4.1.1.17
23359tryptophan deaminase-4.1.99.1
23359urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 6363
  • sample type: soil
  • geographic location: Drentse A research area
  • country: Netherlands
  • origin.country: NLD
  • continent: Europe

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1713.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_974;97_1134;98_1352;99_1713&stattab=map
  • Last taxonomy: Viridibacillus arvi
  • 16S sequence: AJ627211
  • Sequence Identity:
  • Total samples: 4566
  • soil counts: 2124
  • aquatic counts: 689
  • animal counts: 1411
  • plant counts: 342

Safety information

risk assessment

  • @ref: 6363
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23359
  • description: Bacillus arvi partial 16S rRNA gene, type strain LMG 22165
  • accession: AJ627211
  • length: 1505
  • database: nuccore
  • NCBI tax ID: 263475

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Viridibacillus arvi DSM 16317GCA_001274945scaffoldncbi263475
66792Viridibacillus arvi strain DSM 16317263475.9wgspatric263475
66792Viridibacillus arvi DSM 163172651869790draftimg263475

GC content

  • @ref: 23359
  • GC-content: 35.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.41yes
flagellatedyes81.785no
gram-positiveyes75.655yes
anaerobicno98.291no
halophileno87.103no
spore-formingyes95.246yes
thermophileno99.867no
glucose-utilyes90.036no
aerobicyes83.577yes
glucose-fermentno85.901no

External links

@ref: 6363

culture collection no.: DSM 16317, LMG 22165

straininfo link

  • @ref: 70247
  • straininfo: 128652

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653863Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil.Heyrman J, Rodriguez-Diaz M, Devos J, Felske A, Logan NA, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.63240-02005Bacillus/chemistry/*classification/genetics/isolation & purification, DNA Fingerprinting/methods, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genome, Bacterial, Molecular Sequence Data, Netherlands, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny18048716Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.Albert RA, Archambault J, Lempa M, Hurst B, Richardson C, Gruenloh S, Duran M, Worliczek HL, Huber BE, Rossello-Mora R, Schumann P, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.65256-02007Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria/chemistry/*classification/*genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny34940943Viridibacillus soli sp. nov., isolated from forest soil in Ailaoshan National Nature Reserve.Xu Y, Zhao JY, Geng Y, Yuan HR, Li LL, Wen ML, Li MG, Tang SKArch Microbiol10.1007/s00203-021-02676-x2021China, DNA, Bacterial/genetics, Fatty Acids, *Forests, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SoilTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6363Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16317)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16317
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
23358Richard A. Albert, Julieta Archambault, Melissa Lempa, Beth Hurst, Christine Richardson, Stephanie Gruenloh, Metin Duran, Hanna Lucia Worliczek, Birgit E. Huber, Ramon Rosselló-Mora, Peter Schumann, Hans-Jürgen Busse10.1099/ijs.0.65256-0Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.IJSEM 57: 2729-2737 200718048716
23359Jeroen Heyrman, Marina Rodríguez-Díaz, Joke Devos, Andreas Felske, Niall A. Logan, Paul De Vos10.1099/ijs.0.63240-0Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soilIJSEM 55: 111-117 200515653863
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)
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
70247Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128652.1StrainInfo: A central database for resolving microbial strain identifiers