Strain identifier

BacDive ID: 18124

Type strain: Yes

Species: Solibacillus silvestris

Strain Designation: HR3-23

Strain history: CIP <- 1999, DSMZ: strain HR3-23

NCBI tax ID(s): 76853 (species)

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General

@ref: 4648

BacDive-ID: 18124

DSM-Number: 12223

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, motile

description: Solibacillus silvestris HR3-23 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 76853
  • Matching level: species

strain history

@refhistory
4648<- H. Rheims; HR3-23
122611CIP <- 1999, DSMZ: strain HR3-23

doi: 10.13145/bacdive18124.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Solibacillus
  • species: Solibacillus silvestris
  • full scientific name: Solibacillus silvestris (Rheims et al. 1999) Krishnamurthi et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Bacillus silvestris

@ref: 4648

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Solibacillus

species: Solibacillus silvestris

full scientific name: Solibacillus silvestris (Rheims et al. 1999) Krishnamurthi et al. 2009

strain designation: HR3-23

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.797
69480100positive
122611yespositiverod-shaped

colony morphology

  • @ref: 122611

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4648NUTRIENT 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
40277MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122611CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4648positivegrowth30mesophilic
40277positivegrowth30mesophilic
122611positivegrowth10-45
122611nogrowth55thermophilic

culture pH

  • @ref: 122611
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 122611
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.999
122611yes

halophily

@refsaltgrowthtested relationconcentration
122611NaClpositivegrowth0-4 %
122611NaClnogrowth6 %
122611NaClnogrowth8 %
122611NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122611citrate-carbon source16947
122611esculin-hydrolysis4853
122611hippurate+hydrolysis606565
122611nitrate-reduction17632
122611nitrite-reduction16301

metabolite production

  • @ref: 122611
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12261115688acetoin-
12261117234glucose-

enzymes

@refvalueactivityec
122611oxidase-
122611beta-galactosidase-3.2.1.23
122611alcohol dehydrogenase-1.1.1.1
122611gelatinase-
122611amylase-
122611DNase+
122611caseinase-3.4.21.50
122611catalase+1.11.1.6
122611tween esterase+
122611gamma-glutamyltransferase+2.3.2.2
122611lecithinase-
122611lipase-
122611lysine decarboxylase-4.1.1.18
122611ornithine decarboxylase-4.1.1.17
122611protease-
122611urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122611--++-----+++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122611-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122611---------------------+--------------------------------------------+--------+-----+------+------+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4648forest soilnear Braunschweig, Lower SaxonyGermanyDEUEurope
122611Environment, Forest soilGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1045.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_600;97_703;98_819;99_1045&stattab=map
  • Last taxonomy: Solibacillus
  • 16S sequence: AJ006086
  • Sequence Identity:
  • Total samples: 48013
  • soil counts: 9955
  • aquatic counts: 4001
  • animal counts: 31464
  • plant counts: 2593

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46481Risk group (German classification)
1226111Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4648
  • description: Bacillus silvestris 16S rRNA gene
  • accession: AJ006086
  • length: 1528
  • database: ena
  • NCBI tax ID: 76853

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solibacillus silvestris strain DSM 1222376853.3completepatric76853
66792Solibacillus silvestris DSM 122232684623075completeimg76853

GC content

  • @ref: 4648
  • GC-content: 39.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.338no
flagellatedyes79.544no
gram-positiveyes89.432no
anaerobicno98.152no
halophileno80.919no
spore-formingyes94.656no
glucose-utilyes83.177no
aerobicyes90.765no
thermophileno99.379yes
glucose-fermentno88.419no

External links

@ref: 4648

culture collection no.: DSM 12223, MTCC 10789, ATCC BAA 269, CIP 106059

straininfo link

  • @ref: 87112
  • straininfo: 14082

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319505Bacillus silvestris sp. nov., a new member of the genus Bacillus that contains lysine in its cell wall.Rheims H, Fruhling A, Schumann P, Rohde M, Stackebrandt EInt J Syst Bacteriol10.1099/00207713-49-2-7951999Bacillus/*chemistry/*classification/genetics/physiology, Base Composition, Cell Wall/*chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Germany, Lipids/analysis, Lysine/*analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, TreesGenetics
Phylogeny18842851Bacillus cecembensis sp. nov., isolated from the Pindari glacier of the Indian Himalayas.Reddy GS, Uttam A, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.65515-02008Bacillus/chemistry/*classification/*genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Ice Cover/*microbiology, India, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny19406792Re-examination of the taxonomic position of Bacillus silvestris Rheims et al. 1999 and proposal to transfer it to Solibacillus gen. nov. as Solibacillus silvestris comb. nov.Krishnamurthi S, Chakrabarti T, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.65742-02009Bacillus/*classification/genetics/isolation & purification/physiology, *Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Lipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Spores, BacterialTranscriptome
Phylogeny20222449[Isolation and identification of a bacterial strain KHg2 with high resistance to mercury and cloning and expression of its merA gene].Zeng Y, Chen Q, Wang M, Sun J, Gao JWei Sheng Wu Xue Bao2009Bacillus/classification/genetics/*isolation & purification/*metabolism, Bacterial Proteins/*genetics/metabolism, *Cloning, Molecular, Mercury/*metabolism, Molecular Sequence Data, *Soil MicrobiologyEnzymology
Phylogeny26907585Reclassification of Bacillus isronensisShivaji et al. 2009 as Solibacillus isronensis comb. nov. and emended description of genus Solibacillus Krishnamurthi et al. 2009.Mual P, Singh NK, Verma A, Schumann P, Krishnamurthi S, Dastager S, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0009822016Bacillus/*classification, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, Lipids/chemistry, Peptidoglycan/chemistry, *Phylogeny, Planococcaceae/*classification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial, Vitamin K 2/chemistryTranscriptome
Phylogeny28475026Solibacillus kalamii sp. nov., isolated from a high-efficiency particulate arrestance filter system used in the International Space Station.Checinska Sielaff A, Kumar RM, Pal D, Mayilraj S, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijsem.0.0017062017*Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Spacecraft, Vitamin K 2/chemistryTranscriptome
Phylogeny29694672Characterization of Solibacillus silvestris strain AM1 that produces amyloid bioemulsifier.Markande AR, Vemuluri VR, Shouche YS, Nerurkar ASJ Basic Microbiol10.1002/jobm.2017006852018Amyloid/*metabolism, Carbon/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Emulsifying Agents/metabolism, Fatty Acids/analysis, Hydrogen-Ion Concentration, India, Nucleic Acid Hybridization, Phylogeny, Planococcaceae/*classification/*genetics/isolation & purification/*metabolism, RNA, Ribosomal, 16S/genetics, Sodium Chloride, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitle
4648Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12223)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12223
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
40277Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18147
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)
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
87112Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14082.1StrainInfo: A central database for resolving microbial strain identifiers
122611Curators of the CIPCollection of Institut Pasteur (CIP 106059)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106059