Strain identifier

BacDive ID: 815

Type strain: Yes

Species: Bacillus smithii

Strain Designation: NRS-173

Strain history: CIP <- 1993, L.K. Nakamura, NRRL, Bacillus coagulans <- N.R. Smith: strain NRS-173 <- R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA

NCBI tax ID(s): 1220590 (strain), 1479 (species)

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General

@ref: 1617

BacDive-ID: 815

DSM-Number: 4216

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

description: Bacillus smithii NRS-173 is an aerobe, spore-forming, thermophilic bacterium that was isolated from cheese.

NCBI tax id

NCBI tax idMatching level
1220590strain
1479species

strain history

@refhistory
1617<- NRRL <- N.R. Smith (Bacillus coagulans)
67770NRRL NRS-173 <-- N. R. Smith NRS-173.
122645CIP <- 1993, L.K. Nakamura, NRRL, Bacillus coagulans <- N.R. Smith: strain NRS-173 <- R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA

doi: 10.13145/bacdive815.20230509.8.1

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 smithii
  • full scientific name: Bacillus smithii Nakamura et al. 1988

@ref: 1617

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus smithii

full scientific name: Bacillus smithii Nakamura et al. 1988

strain designation: NRS-173

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.378
69480100positive
122645yespositiverod-shaped

colony morphology

  • @ref: 48769
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1617NUTRIENT 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
40787MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122645CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122645CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1617positivegrowth55thermophilic
40787positivegrowth55thermophilic
48769positivegrowth56thermophilic
67770positivegrowth55thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 48769
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

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
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368L-arabinose-fermentation30849
68368amygdalin-fermentation27613
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol-fermentation16899
68368D-glucose-fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
48769----------+----------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
48769-+--++++---++--+--+---------+---+-------+++----+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
1617cheese
48769Cheese
67770Cheese
122645Food, CheeseUnited States of AmericaUSANorth America1947

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_3451.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1802;97_2160;98_2650;99_3451&stattab=map
  • Last taxonomy: Bacillus smithii subclade
  • 16S sequence: Z26935
  • Sequence Identity:
  • Total samples: 4607
  • soil counts: 1519
  • aquatic counts: 542
  • animal counts: 1984
  • plant counts: 562

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
16171Risk group (German classification)
1226451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218B.smithii 16S ribosomal RNAX606431429ena1479
20218B.smithii gene for 16S ribosomal RNAZ269351524ena1479
20218Bacillus smithii gene for 16S rRNA, partial sequenceAB006935277ena1479
20218Bacillus smithii strain JCM9076 DNA for 16S ribosomal RNA, partial sequenceD783161437ena1479
20218Bacillus smithii gene for 16S rRNA, partial sequenceAB2717491480ena1479
67770Bacillus smithii gene for 16S rRNA, partial sequence, strain: JCM 9076LC3790731477ena1479

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus smithii DSM 4216GCA_001050115completencbi1479
66792Bacillus smithii NBRC 153111220590.3wgspatric1220590
66792Bacillus smithii strain DSM 42161479.9plasmidpatric1479
66792Bacillus smithii strain DSM 42161479.5completepatric1479
66792Bacillus smithii NBRC 153112681812984draftimg1220590
66792Bacillus smithii DSM 42162654588021completeimg1479
67770Bacillus smithii NBRC 15311GCA_001591985contigncbi1220590

GC content

@refGC-contentmethod
161740.2
6777038.7-39.7Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes85.927no
flagellatedyes81.394no
gram-positiveyes93.427no
anaerobicno97.94no
aerobicyes74.924no
halophileno75.074no
spore-formingyes96.111no
thermophileyes80.428yes
glucose-utilyes88.702no
glucose-fermentno92.152yes

External links

@ref: 1617

culture collection no.: DSM 4216, IFO 15311, NBRC 15311, NRRL NRS-173, CCUG 27413, LMG 12526, JCM 9076, CGMCC 1.3752, CIP 103790

straininfo link

  • @ref: 70489
  • straininfo: 7196

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879257Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough.Bae SS, Lee JH, Kim SJInt J Syst Evol Microbiol10.1099/ijs.0.63424-02005Bacillus/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Geologic Sediments/*microbiology, Growth Inhibitors/pharmacology, Hot Temperature, Molecular Sequence Data, Movement, Pacific Ocean, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Spores, Bacterial/cytology, Water MicrobiologyEnzymology
Phylogeny16738094Caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in China.Xue Y, Zhang X, Zhou C, Zhao Y, Cowan DA, Heaphy S, Grant WD, Jones BE, Ventosa A, Ma YInt J Syst Evol Microbiol10.1099/ijs.0.64105-02006China, Fatty Acids, Nonesterified/analysis, Gram-Positive Rods/*classification/*isolation & purification/physiology/ultrastructure, Hot Springs/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, Spores, Bacterial, *Water MicrobiologyGenetics
Metabolism25556192Isolation and screening of thermophilic bacilli from compost for electrotransformation and fermentation: characterization of Bacillus smithii ET 138 as a new biocatalyst.Bosma EF, van de Weijer AH, Daas MJ, van der Oost J, de Vos WM, van Kranenburg RAppl Environ Microbiol10.1128/AEM.03640-142015Bacillus/genetics/*isolation & purification/metabolism/*radiation effects, Carboxylic Acids/metabolism, Electroporation, Fermentation, Glucose/metabolism, Hot Temperature, Hydrogen-Ion Concentration, Plasmids, *Soil, *Soil Microbiology, *Transformation, Bacterial, Xylose/metabolismPhylogeny
Metabolism26148486Establishment of markerless gene deletion tools in thermophilic Bacillus smithii and construction of multiple mutant strains.Bosma EF, van de Weijer AH, van der Vlist L, de Vos WM, van der Oost J, van Kranenburg RMicrob Cell Fact10.1186/s12934-015-0286-52015Bacillus/*metabolism, Fermentation, Gene Deletion, Ketone Oxidoreductases/*metabolism, Metabolic Engineering/*methods, MutagenesisEnzymology
Genetics27559429Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).Bosma EF, Koehorst JJ, van Hijum SA, Renckens B, Vriesendorp B, van de Weijer AH, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg RStand Genomic Sci10.1186/s40793-016-0172-82016
Pathogenicity34975786A Rapid Screening Method of Candidate Probiotics for Inflammatory Bowel Diseases and the Anti-inflammatory Effect of the Selected Strain Bacillus smithii XY1.Huang X, Ai F, Ji C, Tu P, Gao Y, Wu Y, Yan F, Yu TFront Microbiol10.3389/fmicb.2021.7603852021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1617Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4216)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4216
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
40787Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15626
48769Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27413)https://www.ccug.se/strain?id=27413
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
70489Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7196.1StrainInfo: A central database for resolving microbial strain identifiers
122645Curators of the CIPCollection of Institut Pasteur (CIP 103790)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103790