Strain identifier

BacDive ID: 1239

Type strain: Yes

Species: Bacillus carboniphilus

Strain history: CIP <- 2007, DSMZ <- JCM <- T. Fujita <- M. Matsuhashi, Tokai Univ., Shizuoka, Japan: strain Kasumi 6

NCBI tax ID(s): 86663 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7086

BacDive-ID: 1239

DSM-Number: 17613

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

description: Bacillus carboniphilus DSM 17613 is an obligate aerobe, spore-forming, mesophilic bacterium that forms circular colonies and has a brown red pigmentation.

NCBI tax id

  • NCBI tax id: 86663
  • Matching level: species

strain history

@refhistory
7086<- JCM <- T. Fujita <- M. Matsuhashi, Kasumi-6
67771<- JCM <- T. Fujita <- M. Matsuhashi strain Kasumi-6
67770T. Fujita <-- M. Matsuhashi strain Kasumi-6.
117178CIP <- 2007, DSMZ <- JCM <- T. Fujita <- M. Matsuhashi, Tokai Univ., Shizuoka, Japan: strain Kasumi 6

doi: 10.13145/bacdive1239.20230509.8.1

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 carboniphilus
  • full scientific name: Bacillus carboniphilus Fujita et al. 1996

@ref: 7086

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus carboniphilus

full scientific name: Bacillus carboniphilus Fujita et al. 1996

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23316positive3.0-5.0 µm0.5-0.9 µmrod-shapedyesperitrichous
67771rod-shapedyesperitrichous
67771positive
117178positiverod-shapedno

colony morphology

  • @ref: 23316
  • colony color: grayish yellow
  • colony shape: circular
  • medium used: Nutrient agar

pigmentation

  • @ref: 23316
  • production: yes
  • color: brown red

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7086CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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
23316Nutrient agar (NA)yes
36103MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117178CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7086positivegrowth30mesophilic
23316positivemaximum47thermophilic
23316positiveminimum17psychrophilic
36103positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23316obligate aerobe
67771aerobe
117178obligate aerobe

spore formation

  • @ref: 23316
  • spore description: ellipsoidal, central or terminal, unswollen sporangia
  • type of spore: endospore
  • spore formation: yes

halophily

  • @ref: 23316
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 7 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2331615963ribitol-builds acid from
2331617057cellobiose-builds acid from
2331615824D-fructose-builds acid from
2331612936D-galactose-builds acid from
2331617634D-glucose-builds acid from
2331616899D-mannitol-builds acid from
2331616024D-mannose-builds acid from
2331616988D-ribose-builds acid from
2331617317D-sorbose-builds acid from
2331665327D-xylose-builds acid from
2331617113erythritol-builds acid from
2331617754glycerol-builds acid from
2331630849L-arabinose-builds acid from
2331662345L-rhamnose-builds acid from
2331617716lactose-builds acid from
2331617306maltose-builds acid from
2331628053melibiose-builds acid from
2331617268myo-inositol-builds acid from
2331616634raffinose-builds acid from
2331617814salicin-builds acid from
2331628017starch-builds acid from
2331617992sucrose-builds acid from
2331627082trehalose-builds acid from
2331617634D-glucose-builds gas from
2331616899D-mannitol-builds gas from
2331665327D-xylose-builds gas from
2331630849L-arabinose-builds gas from
23316309162-oxoglutarate-carbon source
2331630089acetate-carbon source
2331658187alginate-carbon source
2331616947citrate-carbon source
233168391D-gluconate-carbon source
2331629806fumarate-carbon source
2331629991L-aspartate-carbon source
2331629985L-glutamate-carbon source
2331615589L-malate-carbon source
2331624996lactate-carbon source
2331615792malonate-carbon source
2331617272propionate-carbon source
2331615361pyruvate-carbon source
2331630031succinate-carbon source
23316132950tartrate-carbon source
2331629016arginine-degradation
2331625094lysine-degradation
2331618257ornithine-degradation
233164853esculin-hydrolysis
2331616199urea-hydrolysis
2331617632nitrate-reduction
23316casein+hydrolysis
233165291gelatin+hydrolysis
23316606565hippurate+hydrolysis
2331628017starch+hydrolysis
2331653426tween 80+hydrolysis
11717817632nitrate+reduction
11717816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2331615688acetoinno
11717835581indoleno

metabolite tests

  • @ref: 23316
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
23316beta-galactosidase-3.2.1.23
23316catalase+1.11.1.6
23316cytochrome oxidase+1.9.3.1
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
117178oxidase-
117178catalase+1.11.1.6
117178urease-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
117178-+++-+++++++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7086AirTokai University, NumazuJapanJPNAsia
67770AirTokai University, Numazu, Shizuoka Pref.JapanJPNAsia
67771From airTokai University, Numazu, Shizuoka Pref.JapanJPNAsia
117178Environment, AirJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_160672.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_15913;97_19507;98_24371;99_160672&stattab=map
  • Last taxonomy: Bacillus carboniphilus
  • 16S sequence: AB021182
  • Sequence Identity:
  • Total samples: 47
  • soil counts: 23
  • aquatic counts: 9
  • animal counts: 13
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70861Risk group (German classification)
1171781Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7086
  • description: Bacillus carboniphilus gene for 16S ribosomal RNA
  • accession: AB021182
  • length: 1504
  • database: ena
  • NCBI tax ID: 86663

GC content

@refGC-contentmethod
708637.9
2331637.9high performance liquid chromatography (HPLC)

External links

@ref: 7086

culture collection no.: DSM 17613, ATCC 700100, CIP 109750, JCM 9731, kASUMI 6t, KCTC 3837, LMG 18001, CGMCC 1.3652, NCIMB 13460, Kasumi 6

straininfo link

  • @ref: 70895
  • straininfo: 10705

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23934481Bacillus oceani sp. nov., a new slightly halophilic bacterium, isolated from a deep sea sediment environment.Liu YJ, Long LJ, Huang XF, You ZQ, Wang FZ, Li J, Kim CJ, Tian XP, Zhang SAntonie Van Leeuwenhoek10.1007/s10482-013-9995-02013Aerobiosis, Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Molecular Sequence Data, Nitrogen/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureMetabolism
Phylogeny25667390Bacillus oleivorans sp. nov., a diesel oil-degrading and solvent-tolerant bacterium.Azmatunnisa M, Rahul K, Subhash Y, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.0001032015Bacillus/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Gasoline, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SolventsGenetics
Phylogeny34057547Bacillus fonticola sp. nov., isolated from deep sea cold seep sediment.Sun YY, Zhou HZ, Sun QLArch Microbiol10.1007/s00203-021-02401-82021*Bacillus/classification/genetics, Fatty Acids/analysis, *Geologic Sediments/microbiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity

Reference

@idauthorscataloguedoi/urltitlejournal
7086Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17613)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17613
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
23316TAKASHI FUJITA, OSAMU SHIDA, HIROAKI TAKAGI, KIYOHIKO KUNUGITA, A. N. PANKRUSHINA, MICHIO MATSUHASHI10.1099/00207713-46-1-116Description of Bacillus carboniphilus sp. nov.IJSEM 46: 116-118 1996
36103Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7528
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
70895Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10705.1StrainInfo: A central database for resolving microbial strain identifiers
117178Curators of the CIPCollection of Institut Pasteur (CIP 109750)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109750