Strain identifier

BacDive ID: 1214

Type strain: Yes

Species: Neobacillus bataviensis

Strain Designation: IDA 1115, R-16315

Strain history: CIP <- 2005, DSMZ <- J. Heyrman: strain R-16315 <- A. Felske: strain IDA 1115

NCBI tax ID(s): 1117379 (strain), 220685 (species)

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General

@ref: 5901

BacDive-ID: 1214

DSM-Number: 15601

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

description: Neobacillus bataviensis IDA 1115 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and has a light brown pigmentation.

NCBI tax id

NCBI tax idMatching level
220685species
1117379strain

strain history

@refhistory
5901<- J. Heyrman; R-16315 <- A. Felske; IDA 1115
67770IAM 15255 <-- LMG 21833 <-- J. Heyrman <-- A. Felske.
116739CIP <- 2005, DSMZ <- J. Heyrman: strain R-16315 <- A. Felske: strain IDA 1115

doi: 10.13145/bacdive1214.20250331.9.3

Name and taxonomic classification

LPSN

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

  • synonyms

    • @ref: 20215
    • synonym: Bacillus bataviensis

@ref: 5901

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Neobacillus

species: Neobacillus bataviensis

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

strain designation: IDA 1115, R-16315

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
23312positive
23312variable0.7-1.2 µmrod-shapedyes
116739positiverod-shapedyes

colony morphology

@refcolony colorcolony shapemedium used
23312creamcircularTSA
116739

pigmentation

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5901NUTRIENT 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
38241MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116739CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116739CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
5901positivegrowth30
23312positivemaximum50-55
23312positiveoptimum30
38241positivegrowth30
67770positivegrowth28
116739positivegrowth10-45
116739nogrowth55

culture pH

@refabilitytypepHPH range
23312positiveminimum4.0-6.0acidophile
23312positiveoptimum7.0-8.0
23312positivemaximum9.5-10.0alkaliphile
116739positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
23312facultative anaerobe
116739obligate aerobe
125439obligate aerobe95.2

spore formation

@refspore descriptiontype of sporespore formationconfidence
23312ellispoidal, may be spherical, central, paracentral, occasionally subterminal, slightly swollen sporangiaendosporeyes
116739yes
125438yes90.098

halophily

  • @ref: 116739
  • 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
2331215963ribitol-builds acid from
2331217108D-arabinose-builds acid from
2331218333D-arabitol-builds acid from
2331228847D-fucose-builds acid from
2331262318D-lyxose-builds acid from
2331217924D-sorbitol-builds acid from
2331216443D-tagatose-builds acid from
2331265327D-xylose-builds acid from
2331216813galactitol-builds acid from
2331217113erythritol-builds acid from
2331224265gluconate-builds acid from
2331228087glycogen-builds acid from
2331217268myo-inositol-builds acid from
2331230849L-arabinose-builds acid from
2331218403L-arabitol-builds acid from
2331262345L-rhamnose-builds acid from
2331217266L-sorbose-builds acid from
2331265328L-xylose-builds acid from
2331274863methyl beta-D-xylopyranoside-builds acid from
2331228017starch-builds acid from
2331217151xylitol-builds acid from
23312casein-hydrolysis
2331217057cellobiose+builds acid from
2331215824D-fructose+builds acid from
2331212936D-galactose+builds acid from
2331217634D-glucose+builds acid from
2331217716lactose+builds acid from
2331217306maltose+builds acid from
2331216899D-mannitol+builds acid from
2331216024D-mannose+builds acid from
233126731melezitose+builds acid from
2331216634raffinose+builds acid from
2331216551D-trehalose+builds acid from
2331232528turanose+builds acid from
2331228066gentiobiose+builds acid from
23312506227N-acetylglucosamine+builds acid from
233124853esculin+hydrolysis
233125291gelatin+hydrolysis
2331217632nitrate+reduction
2331218305arbutin+/-builds acid from
2331228053melibiose+/-builds acid from
2331216988D-ribose+/-builds acid from
2331217992sucrose+/-builds acid from
2331217754glycerol+/-builds acid from
2331215443inulin+/-builds acid from
2331218287L-fucose+/-builds acid from
23312320061methyl alpha-D-glucopyranoside+/-builds acid from
2331243943methyl alpha-D-mannoside+/-builds acid from
2331217814salicin+/-builds acid from
11673916947citrate-carbon source
1167394853esculin+hydrolysis
116739606565hippurate+hydrolysis
11673917632nitrate+reduction
11673916301nitrite+reduction
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837112936D-galactose+builds acid from
6837117754glycerol+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
683716731melezitose+builds acid from
6837115443inulin+builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-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

metabolite production

@refChebi-IDmetaboliteproduction
2331235581indoleno
2331216136hydrogen sulfideno
2331215688acetoinno
11673935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2331215688acetoin-
11673915688acetoin-
11673917234glucose-

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
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116739oxidase+
116739beta-galactosidase+3.2.1.23
116739alcohol dehydrogenase-1.1.1.1
116739gelatinase+/-
116739amylase+
116739DNase+
116739caseinase-3.4.21.50
116739catalase+1.11.1.6
116739tween esterase-
116739gamma-glutamyltransferase+2.3.2.2
116739lecithinase-
116739lipase-
116739lysine decarboxylase-4.1.1.18
116739ornithine decarboxylase-4.1.1.17
116739tryptophan deaminase-
116739urease+3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382lipase (C 14)-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116739-+++-+---+++-+++---+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116739+---+----++++----+--+/-+--+-+++/-+/-+++++/-+/---++---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116739+--------++--------------+-------+---------------+--------+----------+--+-----+--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
23312soil, Drentse A agricultural research areaAnlooer Diepje brookNetherlandsNLDEurope53.03336.68333
5901soilnear AnlooNetherlandsNLDEurope
67770Soil in the Drentse A agricultural research area along the Anlooër Diepje brookNetherlandsNLDEurope
116739Environment, SoilNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_433.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_292;97_323;98_360;99_433&stattab=map
  • Last taxonomy: Neobacillus
  • 16S sequence: AJ542508
  • Sequence Identity:
  • Total samples: 5867
  • soil counts: 3750
  • aquatic counts: 634
  • animal counts: 1294
  • plant counts: 189

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59011Risk group (German classification)
1167391Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus bataviensis partial 16S rRNA gene, isolate OS-225AM2373991399nuccore220685
20218Bacillus bataviensis gene for 16S rRNA, partial sequence, strain: NBRC 102449AB6817911475nuccore220685
23312Bacillus bataviensis partial 16S rRNA gene, strain LMG 21833AJ5425081502nuccore1117379

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus bataviensis LMG 218331117379.3wgspatric1117379
66792Bacillus bataviensis LMG 218332537561923draftimg1117379
67770Neobacillus bataviensis LMG 21833GCA_000307875contigncbi1117379

GC content

  • @ref: 67770
  • GC-content: 40.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.2
125439BacteriaNetgram_stainReaction to gram-stainingvariable84.2
125439BacteriaNetmotilityAbility to perform movementyes80.8
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes88.6
125438gram-positivegram-positivePositive reaction to Gram-stainingyes65.758no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.039no
125438spore-formingspore-formingAbility to form endo- or exosporesyes90.098no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes57.294no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno87.911no
125438motile2+flagellatedAbility to perform flagellated movementyes60.627no

External links

@ref: 5901

culture collection no.: DSM 15601, CIP 108807, LMG 21833, JCM 21706, IAM 15255

straininfo link

  • @ref: 70870
  • straininfo: 85426

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
Phylogeny26559004Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments.Zhu D, Zhang P, Niu L, Xie C, Li P, Sun J, Hang FInt J Syst Evol Microbiol10.1099/ijsem.0.0007632015
Phylogeny29465340Bacillus alkalitolerans sp. nov., isolated from marine sediment near a hydrothermal vent.Liu Y, Yu M, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0026482018Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Hydrothermal Vents/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33625539Bacillus salipaludis sp. nov., isolated from saline-alkaline soil.Xue L, Tang L, Zhao J, Fang Z, Liu H, Qiao J, Zhang GArch Microbiol10.1007/s00203-021-02239-02021Bacillus/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, Soil Microbiology, WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5901Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15601)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15601
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
38241Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6477
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
70870Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85426.1StrainInfo: A central database for resolving microbial strain identifiers
116739Curators of the CIPCollection of Institut Pasteur (CIP 108807)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108807
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