Strain identifier

BacDive ID: 1216

Type strain: Yes

Species: Neobacillus novalis

Strain Designation: IDA 3307, R-15439

Strain history: CIP <- 2005, DSMZ <- J. Heyrman: strain R-15439 <- A. Felske: strain IDA 3307

NCBI tax ID(s): 1349756 (strain), 220687 (species)

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General

@ref: 5923

BacDive-ID: 1216

DSM-Number: 15603

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

description: Neobacillus novalis IDA 3307 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms irregular colonies and has a light brown pigmentation.

NCBI tax id

NCBI tax idMatching level
220687species
1349756strain

strain history

@refhistory
5923<- J. Heyrman; R-15439 <- A. Felske; IDA 3307
67770IAM 15258 <-- LMG 21837 <-- J. Heyrman <-- A. Felske.
121363CIP <- 2005, DSMZ <- J. Heyrman: strain R-15439 <- A. Felske: strain IDA 3307

doi: 10.13145/bacdive1216.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Bacillus novalis

@ref: 5923

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Neobacillus

species: Neobacillus novalis

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

strain designation: IDA 3307, R-15439

type strain: yes

Morphology

cell morphology

@refgram staincell lengthmotilitycell shape
23312positive0.6-1.2 µmyes
121363positiveyesrod-shaped

colony morphology

@refcolony colorcolony shapemedium used
23312creamirregularTSA
121363

pigmentation

  • @ref: 23312
  • production: yes
  • color: light brown

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5923NUTRIENT 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
23312Trypticase Soy Agar (TSA)yes
38317MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121363CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121363CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
5923positivegrowth30mesophilic
23312positivemaximum50-55thermophilic
23312positiveoptimum30-40
38317positivegrowth30mesophilic
67770positivegrowth28mesophilic
121363positivegrowth22-45
121363nogrowth10psychrophilic
121363nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
23312positiveminimum4.0-5.0acidophile
23312positiveoptimum7.0-9.0alkaliphile
23312positivemaximum9.5-10.0
121363positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23312facultative anaerobe
121363facultative anaerobe

spore formation

@refspore descriptiontype of sporespore formation
23312ellispoidal, subterminal, occasionally paracentral, slightly swollen sporangiaendosporeyes
121363yes

halophily

  • @ref: 121363
  • 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
2331218305arbutin-builds acid from
2331215963ribitol-builds acid from
2331217108D-arabinose-builds acid from
2331218333D-arabitol-builds acid from
2331228847D-fucose-builds acid from
2331217716lactose-builds acid from
2331262318D-lyxose-builds acid from
233126731melezitose-builds acid from
2331228053melibiose-builds acid from
2331216634raffinose-builds acid from
2331216988D-ribose-builds acid from
2331217992sucrose-builds acid from
2331216443D-tagatose-builds acid from
2331232528turanose-builds acid from
2331216813galactitol-builds acid from
2331217113erythritol-builds acid from
2331224265gluconate-builds acid from
2331217754glycerol-builds acid from
2331228087glycogen-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
2331228017starch-builds acid from
2331217151xylitol-builds acid from
2331215824D-fructose+builds acid from
2331217634D-glucose+builds acid from
2331217306maltose+builds acid from
2331216024D-mannose+builds acid from
2331217924D-sorbitol+builds acid from
2331216551D-trehalose+builds acid from
2331265327D-xylose+builds acid from
23312506227N-acetylglucosamine+builds acid from
23312casein+hydrolysis
233124853esculin+hydrolysis
233125291gelatin+hydrolysis
2331217632nitrate+reduction
2331227613amygdalin+/-builds acid from
2331217057cellobiose+/-builds acid from
2331212936D-galactose+/-builds acid from
2331216899D-mannitol+/-builds acid from
2331228066gentiobiose+/-builds acid from
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
683714853esculin+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
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12136316947citrate-carbon source
1213634853esculin+hydrolysis
121363606565hippurate+hydrolysis
12136317632nitrate+reduction
12136316301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
2331235581indoleno
2331216136hydrogen sulfideno
2331215688acetoinno
12136335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2331215688acetoin-
12136315688acetoin-
12136317234glucose+

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
121363oxidase+
121363beta-galactosidase-3.2.1.23
121363alcohol dehydrogenase-1.1.1.1
121363gelatinase+
121363amylase-
121363DNase+
121363caseinase+3.4.21.50
121363catalase+1.11.1.6
121363tween esterase+
121363gamma-glutamyltransferase+2.3.2.2
121363lecithinase+
121363lipase+
121363lysine decarboxylase-4.1.1.18
121363ornithine decarboxylase-4.1.1.17
121363urease+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
121363-+++-++--++++--+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121363+---+/-+----+++----++--+++/-++/-++---+------+-------+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
23312soil, Drentse A agricultural research areaAnlooer Diepje brookNetherlandsNLDEurope53.03336.68333
5923soilnear AnlooNetherlandsNLDEurope
67770Soil in the Drentse A agricultural research area along the Anlooër Diepje brookNetherlandsNLDEurope
121363Environment, SoilNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2048.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_292;97_323;98_360;99_2048&stattab=map
  • Last taxonomy: Neobacillus
  • 16S sequence: AJ542512
  • Sequence Identity:
  • Total samples: 85
  • soil counts: 72
  • aquatic counts: 4
  • animal counts: 4
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59231Risk group (German classification)
1213631Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus novalis gene for 16S rRNA, partial sequence, strain: NBRC 102450AB6817921475ena220687
23312Bacillus novalis partial 16S rRNA gene, strain LMG 21837AJ5425121503nuccore220687

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus novalis NBRC 1024501349756.3wgspatric1349756
66792Bacillus novalis NBRC 1024502681812999draftimg1349756
67770Neobacillus novalis NBRC 102450GCA_001591805contigncbi1349756

GC content

  • @ref: 23312
  • GC-content: 40.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.114yes
gram-positiveyes77.804no
anaerobicno96.668yes
halophileno80.172no
spore-formingyes94.516yes
glucose-utilyes89.586no
aerobicno56.419yes
flagellatedyes74.095no
thermophileno98.62no
glucose-fermentno87.025no

External links

@ref: 5923

culture collection no.: DSM 15603, CIP 108805, LMG 21837, JCM 21709, IAM 15258, NBRC 102450

straininfo link

  • @ref: 70872
  • straininfo: 85521

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
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
Phylogeny23314911Bacillus abyssalis sp. nov., isolated from a sediment of the South China Sea.You ZQ, Li J, Qin S, Tian XP, Wang FZ, Zhang S, Li WJAntonie Van Leeuwenhoek10.1007/s10482-013-9875-72013Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Phylogeny25013229Bacillus mesonae sp. nov., isolated from the root of Mesona chinensis.Liu B, Liu GH, Hu GH, Chen MCInt J Syst Evol Microbiol10.1099/ijs.0.059485-02014Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genotype, Lamiaceae/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25813363Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust.Sylvan JB, Hoffman CL, Momper LM, Toner BM, Amend JP, Edwards KJInt J Syst Evol Microbiol10.1099/ijs.0.0002112015Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Manganese/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Spores, Bacterial/genetics, *Water MicrobiologyGenetics
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
Genetics27979958Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T.Liu B, Liu GH, Zhu YJ, Wang JP, Che JM, Chen QQ, Chen ZGenome Announc10.1128/genomeA.01423-162016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5923Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15603)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15603
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
38317Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6475
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
70872Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85521.1StrainInfo: A central database for resolving microbial strain identifiers
121363Curators of the CIPCollection of Institut Pasteur (CIP 108805)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108805