Strain identifier

BacDive ID: 1318

Type strain: Yes

Species: Cytobacillus kochii

Strain Designation: do080905 5-1, G 5819

Strain history: <- H. Seiler, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC 4582

NCBI tax ID(s): 859143 (species)

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General

@ref: 17333

BacDive-ID: 1318

DSM-Number: 23667

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

description: Cytobacillus kochii do080905 5-1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from dairy product.

NCBI tax id

  • NCBI tax id: 859143
  • Matching level: species

strain history

  • @ref: 17333
  • history: <- H. Seiler, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC 4582

doi: 10.13145/bacdive1318.20230509.8.1

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 kochii
  • full scientific name: Cytobacillus kochii (Seiler et al. 2012) Patel and Gupta 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus kochii

@ref: 17333

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Cytobacillus

species: Cytobacillus kochii

full scientific name: Cytobacillus kochii (Seiler et al. 2012) Patel and Gupta 2020

strain designation: do080905 5-1, G 5819

type strain: yes

Morphology

cell morphology

  • @ref: 29978
  • gram stain: positive
  • cell length: 3-13 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 29978
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17333
  • name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220
  • composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17333positivegrowth30mesophilic
29978positivegrowth10-40
29978positiveoptimum30mesophilic
62149positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29978positivegrowth6-10.5alkaliphile
29978positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29978aerobe
62149aerobe

spore formation

  • @ref: 29978
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
29978NaClpositivegrowth0-10 %
29978NaClpositiveoptimum0.50 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29978161933-hydroxybenzoate+carbon source
29978370543-hydroxybutyrate+carbon source
2997830089acetate+carbon source
2997816449alanine+carbon source
2997816947citrate+carbon source
2997824265gluconate+carbon source
2997817240itaconate+carbon source
2997825115malate+carbon source
2997818401phenylacetate+carbon source
2997826271proline+carbon source
2997817272propionate+carbon source
2997833942ribose+carbon source
2997817822serine+carbon source
2997853424tween 20+carbon source
2997853423tween 40+carbon source
2997853425tween 60+carbon source
2997853426tween 80+carbon source
2997831011valerate+carbon source

enzymes

@refvalueactivityec
29978acid phosphatase+3.1.3.2
29978alkaline phosphatase+3.1.3.1
29978catalase+1.11.1.6
29978gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17333dairy productOchsenfurt, BavariaGermanyDEUEurope
62149Dairy productBavaria,OchsenfurtGermanyDEUEurope2008

isolation source categories

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

Safety information

risk assessment

  • @ref: 17333
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17333
  • description: Bacillus kochii partial 16S rRNA gene, type strain WCC 4582T
  • accession: FN995265
  • length: 1511
  • database: ena
  • NCBI tax ID: 859143

Genome sequences

  • @ref: 66792
  • description: Cytobacillus kochii DSM 23667
  • accession: 2926483779
  • assembly level: draft
  • database: img
  • NCBI tax ID: 859143

GC content

@refGC-contentmethod
1733336.4high performance liquid chromatography (HPLC)
2997836.4

External links

@ref: 17333

culture collection no.: DSM 23667, CCUG 59877, LMG 25855, WCC 4582

straininfo link

  • @ref: 70968
  • straininfo: 402969

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21705449Bacillus kochii sp. nov., isolated from foods and a pharmaceuticals manufacturing site.Seiler H, Schmidt V, Wenning M, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.027771-02011Aerobiosis, Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, *Food Microbiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spores, Bacterial/cytology, TemperatureBiotechnology
Phylogeny24488932Bacillus solimangrovi sp. nov., isolated from mangrove soil.Lee GH, Rhee MS, Chang DH, Kwon KK, Bae KS, Yang SH, Kim BCInt J Syst Evol Microbiol10.1099/ijs.0.058230-02014Avicennia/*microbiology, Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Micronesia, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28820088Bacillus praedii sp. nov., isolated from purplish paddy soil.Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Liu QY, Wang MKInt J Syst Evol Microbiol10.1099/ijsem.0.0020302017Bacillus/*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, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny28984568Bacillus ciccensis sp. nov., isolated from maize (Zea mays L.) seeds.Liu Y, Li N, Eom MK, Schumann P, Zhang X, Cao Y, Ge Y, Xiao M, Zhao J, Cheng C, Kim SGInt J Syst Evol Microbiol10.1099/ijsem.0.0023412017Bacillus/*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, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17333Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23667)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23667
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
29978Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2634628776041
62149Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59877)https://www.ccug.se/strain?id=59877
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
70968Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402969.1StrainInfo: A central database for resolving microbial strain identifiers