Strain identifier

BacDive ID: 602

Type strain: Yes

Species: Bacillus badius

Strain Designation: 663, Henry 110, 110, NRS-663

Strain history: CIP <- 1958, R.E. Gordon, New Jersey Agri. Stat., New Brunswick, USA <- N.R. Smith: strain NRS-663 <- B.S. Henry: strain 110 <- 1919, M. Batchelor

NCBI tax ID(s): 1348627 (strain), 1455 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2024

BacDive-ID: 602

DSM-Number: 23

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

description: Bacillus badius 663 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Human, Intestinal tract of a child, Bacteriological Laboratory and the Harriet Lane Home, Johns Hopkins University.

NCBI tax id

NCBI tax idMatching level
1455species
1348627strain

strain history

@refhistory
2024<- ATCC <- R.E. Gordon <- N.R. Smith, 663 <- B.S. Henry, 110 <- M. Batchelor
67770NRRL NRS-663 <-- N. R. Smith NRS-663 <-- B. S. Henry 110 <-- M. Batchelor.
116701CIP <- 1958, R.E. Gordon, New Jersey Agri. Stat., New Brunswick, USA <- N.R. Smith: strain NRS-663 <- B.S. Henry: strain 110 <- 1919, M. Batchelor

doi: 10.13145/bacdive602.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus badius
  • full scientific name: Bacillus badius Batchelor 1919 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Pseudobacillus badius
    20215Bacillus encimensis

@ref: 2024

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus badius

full scientific name: Bacillus badius Batchelor 1919

strain designation: 663, Henry 110, 110, NRS-663

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.284
69480100positive
116701yespositiverod-shaped

colony morphology

  • @ref: 116701

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41065MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2024NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
116701CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
116701CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2024positivegrowth30mesophilic
41065positivegrowth30mesophilic
44982positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
116701positivegrowth22-45
116701nogrowth10psychrophilic
116701nogrowth55thermophilic

culture pH

  • @ref: 116701
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44982aerobe
116701obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
116701yes

halophily

  • @ref: 116701
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
116701citrate-carbon source16947
116701esculin-hydrolysis4853
116701hippurate-hydrolysis606565
116701nitrate-reduction17632
116701nitrite-reduction16301
116701nitrate-respiration17632

metabolite production

  • @ref: 116701
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11670115688acetoin-
11670117234glucose-

enzymes

@refvalueactivityec
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
116701oxidase-
116701beta-galactosidase-3.2.1.23
116701alcohol dehydrogenase-1.1.1.1
116701gelatinase+/-
116701amylase-
116701DNase-
116701caseinase+3.4.21.50
116701catalase+1.11.1.6
116701tween esterase-
116701gamma-glutamyltransferase-2.3.2.2
116701lecithinase-
116701lipase-
116701lysine decarboxylase-4.1.1.18
116701ornithine decarboxylase-4.1.1.17
116701urease-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
116701--++-------+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116701+/----+/---------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116701-------------------+-----------+-----------------+-----------+----------++-+---+++-+------+++++---+

Isolation, sampling and environmental information

isolation

  • @ref: 116701
  • sample type: Human, Intestinal tract of a child, Bacteriological Laboratory and the Harriet Lane Home, Johns Hopkins University
  • geographic location: Baltimore, Maryland
  • country: United States of America
  • origin.country: USA
  • continent: North America

taxonmaps

  • @ref: 69479
  • File name: preview.99_4961.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1133;97_1329;98_3709;99_4961&stattab=map
  • Last taxonomy: Bacillus badius subclade
  • 16S sequence: X77790
  • Sequence Identity:
  • Total samples: 2217
  • soil counts: 680
  • aquatic counts: 379
  • animal counts: 1037
  • plant counts: 121

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20241Risk group (German classification)
1167011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus badius clone BBAD-1R 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478074439ena1455
20218Bacillus badius strain ATCC14574 DNA for 16S ribosomal RNA, partial sequenceD783101435ena1455
20218B.badius (ATCC 14574) 16S rRNA geneX777901442ena1455
20218Bacillus badius gene for 16S rRNA, partial sequenceAB006921279ena1455
20218Bacillus badius gene for 16S rRNA, partial sequenceAB2717481481ena1455
20218B.badius 16S ribosomal RNAX606101433ena1455

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus badius MTCC 14581455.5wgspatric1455
66792Bacillus badius NBRC 157131348627.3wgspatric1348627
66792Bacillus badius MTCC 14582636415587draftimg1455
66792Bacillus badius NBRC 157132731957658draftimg1348627
67770Bacillus badius NBRC 15713GCA_001591605contigncbi1348627
67770Bacillus badius MTCC 1458GCA_000829535contigncbi1455

GC content

@refGC-contentmethod
202443.8thermal denaturation, midpoint method (Tm)
202443.5Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.491no
gram-positiveyes89.976no
anaerobicno96.873yes
halophileno89.488no
spore-formingyes96.038no
thermophileno99.302yes
glucose-utilyes76.182no
aerobicyes88.979yes
flagellatedyes77.088no
glucose-fermentno94.441no

External links

@ref: 2024

culture collection no.: DSM 23, ATCC 14574, CCM 2113, NCIB 9364, NCTC 10333, CCUG 7412, CIP 58.52, IAM 11059, NRS 663, JCM 12228, BCRC 11699, CECT 17, HAMBI 1885, IFO 15713, KCTC 3739, LMG 7122, MTCC 1458, NBIMCC 2210, NBRC 15713, NCFB 1760, NCIMB 9364, NRRL NRS-663, VKM B-496, NCDO 1760

straininfo link

  • @ref: 70279
  • straininfo: 36979

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology3311741Phenylalanine dehydrogenase of Bacillus badius. Purification, characterization and gene cloning.Asano Y, Nakazawa A, Endo K, Hibino Y, Ohmori M, Numao N, Kondo KEur J Biochem10.1111/j.1432-1033.1987.tb13399.x1987Amino Acid Oxidoreductases/genetics/*isolation & purification, Amino Acids/isolation & purification, Bacillus/*enzymology/genetics, Biological Evolution, Chromosomes, Bacterial, *Cloning, Molecular, DNA, Bacterial/genetics/isolation & purification, Electrophoresis, Polyacrylamide Gel, Escherichia coli/enzymology/genetics, *Genetic Vectors, Isoelectric Point, Plasmids, Substrate SpecificityPhylogeny
Phylogeny6508070[Description of the type strain of Bacillus badius].Pichinoty FAnn Microbiol (Paris)1984Bacillus/classification/growth & development/*physiology
Enzymology8535000Nucleotide sequencing of phenylalanine dehydrogenase gene from Bacillus badius IAM 11059.Yamada A, Dairi T, Ohno Y, Huang XL, Asano YBiosci Biotechnol Biochem10.1271/bbb.59.19941995Amino Acid Oxidoreductases/*genetics, Amino Acid Sequence, Bacillus/*enzymology/genetics, Base Sequence, DNA, Bacterial, Genes, Bacterial, Molecular Sequence Data, Open Reading Frames, Sequence Homology, Amino AcidGenetics
Phylogeny19605722Bacillus acidiproducens sp. nov., vineyard soil isolates that produce lactic acid.Jung MY, Kim JS, Chang YHInt J Syst Evol Microbiol10.1099/ijs.0.003913-02009Aerobiosis, Anaerobiosis, Bacillus/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Flagella/physiology, Galactose/analysis, Glucose/analysis, Korea, Lactic Acid/*metabolism, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytologyMetabolism
Phylogeny23064349Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room.Seiler H, Wenning M, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.044396-02012Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Environment, Controlled, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny23625259Bacillus thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus.Yang G, Zhou X, Zhou S, Yang D, Wang Y, Wang DInt J Syst Evol Microbiol10.1099/ijs.0.048942-02013Anthraquinones/metabolism, Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Fumarates/metabolism, Genes, Bacterial, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivativesMetabolism
Phylogeny28820124Bacillus wudalianchiensis sp. nov., isolated from grass soils of the Wudalianchi scenic area.Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Zhang HFInt J Syst Evol Microbiol10.1099/ijsem.0.0020422017Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivativesTranscriptome
Phylogeny28947104Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius.Verma A, Pal Y, Khatri I, Ojha AK, Gruber-Vodicka H, Schumann P, Dastager S, Subramanian S, Mayilraj S, Krishnamurthi SSyst Appl Microbiol10.1016/j.syapm.2017.07.0102017Bacillus/*classification/*genetics, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Phylogeny30982666Taxonomic insights into the phylogeny of Bacillus badius and proposal for its reclassification to the genus Pseudobacillus as Pseudobacillus badius comb. nov. and reclassification of Bacillus wudalianchiensis Liu et al., 2017 as Pseudobacillus wudalianchiensis comb. nov.Verma A, Pal Y, Ojha AK, Kumari M, Khatri I, Rameshkumar N, Schumann P, Dastager SG, Mayilraj S, Subramanian S, Krishnamurthi SSyst Appl Microbiol10.1016/j.syapm.2019.03.0032019Bacillaceae/chemistry/*classification/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Bacterial/genetics, Lipids/analysis, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2024Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23
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
41065Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9712
44982Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7412)https://www.ccug.se/strain?id=7412
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
70279Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36979.1StrainInfo: A central database for resolving microbial strain identifiers
116701Curators of the CIPCollection of Institut Pasteur (CIP 58.52)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2058.52