Strain identifier

BacDive ID: 675

Type strain: Yes

Species: Cytobacillus firmus

Strain Designation: 613, original

Strain history: CIP <- 1952, R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA: strain 613 <- N.R. Smith: strain 613 <- 1937, J. Porter G. Bredemann: strain original <- W. Werner

NCBI tax ID(s): 1314753 (strain), 1399 (species)

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General

@ref: 2019

BacDive-ID: 675

DSM-Number: 12

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Cytobacillus firmus 613 is an aerobe, spore-forming, mesophilic bacterium of the family Bacillaceae.

NCBI tax id

NCBI tax idMatching level
1399species
1314753strain

strain history

@refhistory
2019<- ATCC <- R.E. Gordon <- N.R. Smith, 613 <- J.R. Porter <- G. Bredemann <- W. Werner
67770CCM 2213 <-- NCIB 9366 <-- R. E. Gordon <-- N. R. Smith <-- J. R. Porter <-- G. Bredemann <-- W. Werner.
119356CIP <- 1952, R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA: strain 613 <- N.R. Smith: strain 613 <- 1937, J. Porter G. Bredemann: strain original <- W. Werner

doi: 10.13145/bacdive675.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Cytobacillus
  • species: Cytobacillus firmus
  • full scientific name: Cytobacillus firmus (Bredemann and Werner 1933) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus firmus

@ref: 2019

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Cytobacillus

species: Cytobacillus firmus

full scientific name: Cytobacillus firmus (Bredemann and Werner 1933) Patel and Gupta 2020

strain designation: 613, original

type strain: yes

Morphology

cell morphology

  • @ref: 119356
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refincubation periodhemolysis ability
449871 day
1193561

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37349MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2019NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Soil extract 500.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
119356CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2019positivegrowth30mesophilic
37349positivegrowth30mesophilic
44987positivegrowth37mesophilic
67770positivegrowth30mesophilic
119356positivegrowth10-37
119356nogrowth45thermophilic
119356nogrowth55thermophilic

culture pH

  • @ref: 119356
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44987aerobe
119356obligate aerobe

spore formation

  • @ref: 119356
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
119356NaClpositivegrowth2-6 %
119356NaClnogrowth0 %
119356NaClnogrowth8 %
119356NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11935616947citrate-carbon source
1193564853esculin-hydrolysis
119356606565hippurate+hydrolysis
11935617632nitrate+reduction
11935616301nitrite-reduction
11935617632nitrate-respiration
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 119356
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11935615688acetoin-
11935617234glucose-

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
68379catalase-1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
119356oxidase-
119356beta-galactosidase+3.2.1.23
119356alcohol dehydrogenase-1.1.1.1
119356gelatinase+
119356amylase-
119356DNase-
119356caseinase+3.4.21.50
119356catalase+1.11.1.6
119356tween esterase-
119356gamma-glutamyltransferase+2.3.2.2
119356lysine decarboxylase-4.1.1.18
119356ornithine decarboxylase-4.1.1.17
119356urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlRIBXYLMANMALLACSACGLYGCAT
44987++++----------++-+--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119356-+++-+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119356+--+---+-++--------------------+-+---------------+---------+---------------+---++-----+---+++++---+

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_2539.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_264;97_962;98_1233;99_2539&stattab=map
  • Last taxonomy: Bacillales
  • 16S sequence: X60616
  • Sequence Identity:
  • Total samples: 1952
  • soil counts: 985
  • aquatic counts: 304
  • animal counts: 441
  • plant counts: 222

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20191Risk group (German classification)
1193561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus firmus gene for 16S rRNA, partial sequenceAB006925276ena1399
20218Bacillus firmus gene for 16S rRNA, partial sequence, strain: IAM 12464D162681483ena1399
20218Bacillus firmus strain JCM2512 DNA for 16S ribosomal RNA, partial sequenceD783141434ena1399
20218Bacillus firmus gene for 16S rRNA, partial sequenceAB2717501477ena1399
20218B.firmus 16S ribosomal RNAX606161431ena1399
20218Paenibacillus turicensis strain BNRS613 16S ribosomal RNA gene, partial sequenceHM133983353ena160487
20218Paenibacillus turicensis strain BNRS614 16S ribosomal RNA gene, partial sequenceHM133987452ena160487

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cytobacillus firmus NCTC10335GCA_900445365contigncbi1399
66792Bacillus firmus NBRC 153061314753.7wgspatric1314753
66792Bacillus firmus strain NCTC103351399.16wgspatric1399
66792Bacillus firmus NBRC 153062731957652draftimg1314753
66792Bacillus firmus NCTC 103352814123191draftimg1399
67770Cytobacillus firmus NBRC 15306GCA_001591465contigncbi1314753

GC content

@refGC-contentmethod
201941.4thermal denaturation, midpoint method (Tm)
201940.7Buoyant density centrifugation (BD)
6777043.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.866no
gram-positiveyes91.216no
anaerobicno97.762no
halophileno78.486no
spore-formingyes95.343no
glucose-utilyes88.008no
flagellatedyes79.658no
thermophileno93.961yes
aerobicyes88.98yes
glucose-fermentno93.487no

External links

@ref: 2019

culture collection no.: DSM 12, ATCC 14575, CCM 2213, JCM 2512, NCIB 9366, NCTC 10335, CCUG 7418, NRS 613, BCRC 11730, CECT 14, CIP 52.70, IAM 12464, IAM 14179, IFO 15306, KCTC 3626, LMG 7125, NBRC 15306, NCIMB 9366, NRRL B-14307, NRRL NRS-613, VKM B-498, VTT E-97061, NCDO 1762

straininfo link

  • @ref: 70350
  • straininfo: 92139

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738118Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov.Mayr R, Busse HJ, Worliczek HL, Ehling-Schulz M, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.64038-02006Catalase/metabolism, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/*genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Species SpecificityMetabolism
Phylogeny17082387Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis.Ko KS, Oh WS, Lee MY, Lee JH, Lee H, Peck KR, Lee NY, Song JHInt J Syst Evol Microbiol10.1099/ijs.0.64213-02006Bacillus/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Female, Genes, rRNA, Humans, Infant, Newborn, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sepsis/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidPathogenicity
Phylogeny20118297Bacillus oceanisediminis sp. nov., isolated from marine sediment.Zhang J, Wang J, Fang C, Song F, Xin Y, Qu L, Ding KInt J Syst Evol Microbiol10.1099/ijs.0.019851-02010Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny21335493Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant.Vaz-Moreira I, Figueira V, Lopes AR, Lobo-da-Cunha A, Sproer C, Schumann P, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.028605-02011Aerobiosis, Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Drinking Water/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature, *Water PurificationEnzymology
Phylogeny22634699Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site.Seiler H, Wenning M, Schmidt V, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.036277-02012Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Drug Industry, *Environment, Controlled, Fatty Acids/analysis, Germany, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25944807Bacillus crescens sp. nov., isolated from soil.Shivani Y, Subhash Y, Dave Bharti P, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.0002962015Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny36478127Cytobacillus pseudoceanisediminis sp. nov., A Novel Facultative Methylotrophic Bacterium with High Heavy Metal Resistance Isolated from the Deep Underground Saline Spring.Tarasov K, Yakhnenko A, Zarubin M, Gangapshev A, Potekhina NV, Avtukh AN, Kravchenko ECurr Microbiol10.1007/s00284-022-03141-82022RNA, Ribosomal, 16S/genetics, Phylogeny, *Metals, Heavy, DNA

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2019Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12
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
37349Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13323
44987Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7418)https://www.ccug.se/strain?id=7418
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/
68379Automatically annotated from API Coryne
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
70350Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92139.1StrainInfo: A central database for resolving microbial strain identifiers
119356Curators of the CIPCollection of Institut Pasteur (CIP 52.70)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2052.70