Strain identifier

BacDive ID: 1217

Type strain: Yes

Species: Neobacillus soli

Strain Designation: IDA 0086, R-16300, ISA0086

Strain history: CIP <- 2005, DSMZ <- J Heyman: strain R-16300 <- A. Felske: strain ISA0086

NCBI tax ID(s): 1348630 (strain), 220688 (species)

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General

@ref: 5924

BacDive-ID: 1217

DSM-Number: 15604

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

description: Neobacillus soli IDA 0086 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from soil, Drentse A agricultural research area.

NCBI tax id

NCBI tax idMatching level
220688species
1348630strain

strain history

@refhistory
5924<- J. Heyrman; R-16300 <- A. Felske; IDA 0086
67770IAM 15259 <-- LMG 21838 <-- J. Heyrman <-- A. Felske.
122659CIP <- 2005, DSMZ <- J Heyman: strain R-16300 <- A. Felske: strain ISA0086

doi: 10.13145/bacdive1217.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Neobacillus
  • species: Neobacillus soli
  • full scientific name: Neobacillus soli (Heyrman et al. 2004) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus soli

@ref: 5924

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Neobacillus

species: Neobacillus soli

full scientific name: Neobacillus soli (Heyrman et al. 2004) Patel and Gupta 2020

strain designation: IDA 0086, R-16300, ISA0086

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
23312positive
23312variable0.6-1.2 µmrod-shapedyes
69480yes97.84
69480positive100
122659positiverod-shapedyes

colony morphology

@refcolony colorcolony shapemedium used
23312creamcircularTSA
122659

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5924NUTRIENT 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
38316MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122659CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
122659CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5924positivegrowth30mesophilic
23312positivemaximum40-45thermophilic
23312positiveoptimum30mesophilic
38316positivegrowth30mesophilic
67770positivegrowth28mesophilic
122659positivegrowth10-45
122659nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
23312positiveminimum4.0-5.0acidophile
23312positiveoptimum7.0-8.0
23312positivemaximum9.0-9.5alkaliphile
122659positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23312facultative anaerobe
122659obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23312ellispoidal, paracentral, may swell the sporangiaendosporeyes
69481yes100
69480yes100
122659yes

halophily

  • @ref: 122659
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2331216947citrate-assimilation
23312168082-dehydro-D-gluconate-builds acid from
23312174265-dehydro-D-gluconate-builds acid from
2331227613amygdalin-builds acid from
2331218305arbutin-builds acid from
2331215963ribitol-builds acid from
2331217108D-arabinose-builds acid from
2331218333D-arabitol-builds acid from
2331217057cellobiose-builds acid from
2331228847D-fucose-builds acid from
2331217716lactose-builds acid from
2331262318D-lyxose-builds acid from
2331216899D-mannitol-builds acid from
233126731melezitose-builds acid from
2331228053melibiose-builds acid from
2331216634raffinose-builds acid from
2331217992sucrose-builds acid from
2331217924D-sorbitol-builds acid from
2331216443D-tagatose-builds acid from
2331232528turanose-builds acid from
2331265327D-xylose-builds acid from
2331216813galactitol-builds acid from
2331217113erythritol-builds acid from
2331228066gentiobiose-builds acid from
2331224265gluconate-builds acid from
2331217754glycerol-builds acid from
2331217268myo-inositol-builds acid from
2331215443inulin-builds acid from
2331230849L-arabinose-builds acid from
2331218403L-arabitol-builds acid from
2331218287L-fucose-builds acid from
2331262345L-rhamnose-builds acid from
2331217266L-sorbose-builds acid from
2331265328L-xylose-builds acid from
23312320061methyl alpha-D-glucopyranoside-builds acid from
2331243943methyl alpha-D-mannoside-builds acid from
2331274863methyl beta-D-xylopyranoside-builds acid from
2331217814salicin-builds acid from
2331217151xylitol-builds acid from
2331215824D-fructose+builds acid from
2331217634D-glucose+builds acid from
2331216024D-mannose+builds acid from
2331228087glycogen+builds acid from
23312506227N-acetylglucosamine+builds acid from
2331228017starch+builds acid from
23312casein+hydrolysis
233124853esculin+hydrolysis
233125291gelatin+hydrolysis
2331217632nitrate+reduction
2331212936D-galactose+/-builds acid from
2331217306maltose+/-builds acid from
2331216988D-ribose+/-builds acid from
2331216551D-trehalose+/-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-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
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
12265916947citrate-carbon source
1226594853esculin+hydrolysis
122659606565hippurate+hydrolysis
12265917632nitrate+reduction
12265916301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
2331235581indoleno
2331216136hydrogen sulfideno
2331215688acetoinno
12265935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2331215688acetoin-
12265915688acetoin-
12265917234glucose-

enzymes

@refvalueactivityec
23312arginine dihydrolase-3.5.3.6
23312beta-galactosidase-3.2.1.23
23312lysine decarboxylase-4.1.1.18
23312ornithine decarboxylase-4.1.1.17
23312tryptophan deaminase-4.1.99.1
23312urease-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
122659oxidase+
122659beta-galactosidase+3.2.1.23
122659alcohol dehydrogenase-1.1.1.1
122659gelatinase+
122659amylase+
122659DNase+
122659caseinase+3.4.21.50
122659catalase+1.11.1.6
122659tween esterase-
122659gamma-glutamyltransferase+2.3.2.2
122659lecithinase-
122659lipase-
122659lysine decarboxylase-4.1.1.18
122659ornithine decarboxylase-4.1.1.17
122659protease+
122659urease-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
122659-+++-+---+++--++-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122659----+----+/-+++----+---+--+/---+/----+/----++---------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122659-------------------+-------------+-----------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
23312soil, Drentse A agricultural research areaAnlooer Diepje brookNetherlandsNLDEurope53.03336.68333
5924soilnear AnlooNetherlandsNLDEurope
67770Soil in the Drentse A agricultural research area along the Anlooër Diepje brookNetherlandsNLDEurope
122659Environment, SoilNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4427.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_292;97_323;98_360;99_4427&stattab=map
  • Last taxonomy: Neobacillus
  • 16S sequence: AJ542513
  • Sequence Identity:
  • Total samples: 214
  • soil counts: 146
  • aquatic counts: 15
  • animal counts: 17
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59241Risk group (German classification)
1226591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus soli gene for 16S rRNA, partial sequence, strain: NBRC 102451AB6817931454ena220688
23312Bacillus soli partial 16S rRNA gene, strain LMG 21838AJ5425131441nuccore220688

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus soli NBRC 1024511348630.3wgspatric1348630
66792Bacillus soli strain DSM 15604220688.4wgspatric220688
66792Bacillus soli NBRC 1024512731957661draftimg1348630
67770Neobacillus soli NBRC 102451GCA_001591665contigncbi1348630
67770Neobacillus soli DSM 15604GCA_002335815scaffoldncbi220688

GC content

  • @ref: 23312
  • GC-content: 40.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes83.63no
gram-positiveyes84.983no
anaerobicno99.268yes
halophileno82.694no
spore-formingyes91.542no
thermophileno98.765no
glucose-utilyes85.197no
aerobicyes76.329no
glucose-fermentno89.58no
flagellatedyes67.215no

External links

@ref: 5924

culture collection no.: DSM 15604, CIP 108804, LMG 21838, JCM 21710, IAM 15259, KCTC 13572, NBRC 102451

straininfo link

  • @ref: 70873
  • straininfo: 85442

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14742458Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands.Heyrman J, Vanparys B, Logan NA, Balcaen A, Rodriguez-Diaz M, Felske A, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.02723-02004Bacillus/*classification/genetics/isolation & purification, Climate, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Poaceae, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny16166719Bacillus herbersteinensis sp. nov.Wieser M, Worliczek H, Kampfer P, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.63660-02005Austria, Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, *Paintings, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPathogenicity
Phylogeny22611202Bacillus ginsengisoli sp. nov., isolated from soil of a ginseng field.Nguyen NL, Kim YJ, Hoang VA, Min JW, Liang ZQ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.031740-02012Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26654465Bacillus cucumis sp. nov. isolated from the rhizosphere of cucumber (Cucumis sativus).Kampfer P, Busse HJ, Glaeser SP, Kloepper JW, Hu CH, McInroy JAInt J Syst Evol Microbiol10.1099/ijsem.0.0008312015
Phylogeny27265352Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.Zhang XX, Gao JS, Zhang L, Zhang CW, Ma XT, Zhang JInt J Syst Evol Microbiol10.1099/ijsem.0.0012152016Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5924Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15604)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15604
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
23312Jeroen Heyrman, Bram Vanparys, Niall A. Logan, An Balcaen, Marina Rodríguez-Díaz, Andreas Felske, Paul De Vos10.1099/ijs.0.02723-0Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslandsIJSEM 54: 47-57 200414742458
38316Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6474
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
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
70873Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85442.1StrainInfo: A central database for resolving microbial strain identifiers
122659Curators of the CIPCollection of Institut Pasteur (CIP 108804)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108804