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, Gram-positive, motile, rod-shaped

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/bacdive18124.20250331.9.3

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

  • @ref: 122611
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

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

@refgrowthtypetemperature
4648positivegrowth30
40277positivegrowth30
122611positivegrowth10-45
122611nogrowth55

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
122611obligate aerobe
125439obligate aerobe94.2

spore formation

@refspore formationconfidence
125438yes90.908
125439yes94
122611yes

halophily

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12261116947citrate-carbon source
1226114853esculin-hydrolysis
122611606565hippurate+hydrolysis
12261117632nitrate-reduction
12261116301nitrite-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
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
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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382leucine arylamidase-3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382valine arylamidase-

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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4648Bacillus silvestris 16S rRNA geneAJ0060861528nuccore76853
124043Solibacillus silvestris genomic DNA containing 16S-23S intergenic spacer region, strain MTCC 10789, DSM 12223TLN681356451nuccore76853

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes74.143no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.137yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.575yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes90.908no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.414no
125438motile2+flagellatedAbility to perform flagellated movementyes82.67no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes94
125439BacteriaNetmotilityAbility to perform movementyes87.4
125439BacteriaNetgram_stainReaction to gram-stainingvariable77.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe94.2

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1