Strain identifier

BacDive ID: 1223

Type strain: No

Species: Metabacillus indicus

Strain Designation: JG-30

Strain history: CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain JG-30

NCBI tax ID(s): 246786 (species)

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General

@ref: 6316

BacDive-ID: 1223

DSM-Number: 16189

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

description: Metabacillus indicus JG-30 is an aerobe, spore-forming, mesophilic bacterium that was isolated from jeotgal, a traditional Korean fermented seafood.

NCBI tax id

  • NCBI tax id: 246786
  • Matching level: species

strain history

@refhistory
6316<- J.-H. Yoon; JG-30
67771<- Jung-Hoon Yoon, KRIBB, Korea
118274CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain JG-30

doi: 10.13145/bacdive1223.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Metabacillus
  • species: Metabacillus indicus
  • full scientific name: Metabacillus indicus (Suresh et al. 2004) Patel and Gupta 2020

  • synonyms

    @refsynonym
    20215Bacillus indicus
    20215Bacillus cibi

@ref: 6316

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Metabacillus

species: Metabacillus indicus

full scientific name: Metabacillus indicus (Suresh et al. 2004) Patel and Gupta 2020

strain designation: JG-30

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31283variable2.5 µm0.7 µmrod-shapedyes
67771rod-shapedyes
67771variable
69480yes96.436
69480positive100
118274positiverod-shapedyes

colony morphology

  • @ref: 118274
  • hemolysis ability: 1

pigmentation

  • @ref: 31283
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6316BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l MnSO4 0.01 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
38307Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118274CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6316positivegrowth30mesophilic
31283positivegrowth04-50
31283positiveoptimum37mesophilic
38307positivegrowth37mesophilic
67771positivegrowth37mesophilic
118274positivegrowth10-45
118274nogrowth55thermophilic

culture pH

@refabilitytypepH
31283positivegrowth5.5-7.5
31283positiveoptimum7
118274positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31283aerobe
67771aerobe
118274obligate aerobe

spore formation

@refspore formationtype of sporeconfidence
31283yes
67771yesendospore
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31283NaClpositivegrowth0-12 %
31283NaClpositiveoptimum0.5 %
118274NaClpositivegrowth2-4 %
118274NaClnogrowth0 %
118274NaClnogrowth6 %
118274NaClnogrowth8 %
118274NaClnogrowth10 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3128330089acetate+carbon source
3128317057cellobiose+carbon source
3128328757fructose+carbon source
3128328260galactose+carbon source
3128317234glucose+carbon source
3128325115malate+carbon source
3128317306maltose+carbon source
3128337684mannose+carbon source
3128328053melibiose+carbon source
3128315361pyruvate+carbon source
3128316634raffinose+carbon source
3128330031succinate+carbon source
3128317992sucrose+carbon source
3128327082trehalose+carbon source
3128353426tween 80+carbon source
312834853esculin+hydrolysis
3128317632nitrate+reduction
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
11827416947citrate-carbon source
1182744853esculin+hydrolysis
118274606565hippurate-hydrolysis
11827417632nitrate-reduction
11827416301nitrite-reduction
11827417632nitrate-respiration

metabolite production

  • @ref: 118274
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11827415688acetoin-
11827417234glucose-

enzymes

@refvalueactivityec
31283alkaline phosphatase+3.1.3.1
31283cytochrome 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
118274oxidase+
118274beta-galactosidase+3.2.1.23
118274alcohol dehydrogenase-1.1.1.1
118274gelatinase+
118274amylase-
118274caseinase+3.4.21.50
118274catalase+1.11.1.6
118274tween esterase+
118274gamma-glutamyltransferase-2.3.2.2
118274lecithinase+
118274lipase-
118274lysine decarboxylase-4.1.1.18
118274ornithine decarboxylase-4.1.1.17
118274protease+
118274urease-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
118274-+++-+---++-++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118274+--------+++--------+/-++/-+/-++/--++/-+++--+++-+/--------+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118274++++--+++++++---+++---+-----------++-----+-------+------++-+----------------------+---+-+++-+++---+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6316jeotgal, a traditional Korean fermented seafoodRepublic of KoreaKORAsia
67771From Jeotgal, a traditional Korean fermented seafoodRepublic of KoreaKORAsia
118274Food, Jeotgal, a traditional Korean fermented seafoodRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_6832.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3218;97_3948;98_5033;99_6832&stattab=map
  • Last taxonomy: Metabacillus indicus
  • 16S sequence: AY550276
  • Sequence Identity:
  • Total samples: 508
  • soil counts: 169
  • aquatic counts: 149
  • animal counts: 128
  • plant counts: 62

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63161Risk group (German classification)
1182741Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6316
  • description: Bacillus cibi strain JG-30 16S ribosomal RNA gene, partial sequence
  • accession: AY550276
  • length: 1493
  • database: ena
  • NCBI tax ID: 246786

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus cibi strain DSM 16189265729.29wgspatric246786
66792Bacillus indicus DSM 161892619619115draftimg246786
67771Metabacillus indicus DSM 16189GCA_000709935contigncbi246786

GC content

@refGC-contentmethod
631645high performance liquid chromatography (HPLC)
3128345
6777145.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.785yes
gram-positiveyes89.921yes
anaerobicno97.657yes
aerobicyes92.098yes
halophileyes61.034no
spore-formingyes96.53yes
glucose-utilyes88.99yes
flagellatedyes81.366no
thermophileno97.745yes
glucose-fermentno94.188no

External links

@ref: 6316

culture collection no.: DSM 16189, KCTC 3880, BCRC 80033, CIP 108730

straininfo link

  • @ref: 70879
  • straininfo: 137997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774653Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.Yoon JH, Lee CH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63208-02005Bacillus/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny16166719Bacillus herbersteinensis sp. nov.Wieser M, Worliczek H, Kampfer P, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.63660-02005Austria, Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, *Paintings, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPathogenicity
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
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
Phylogeny25142211Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus.Stropko SJ, Pipes SE, Newman JDInt J Syst Evol Microbiol10.1099/ijs.0.068205-02014Bacillus/*classification, Base Composition, DNA, Bacterial/genetics, Genome, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28714845Bacillus mangrovi sp. nov., isolated from a sediment sample from a mangrove forest.Gupta V, Singh PK, Korpole S, Tanuku NRS, Pinnaka AKInt J Syst Evol Microbiol10.1099/ijsem.0.0019282017Avicennia/*microbiology, Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6316Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16189)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16189
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
31283Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2760228776041
38307Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6391
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
70879Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137997.1StrainInfo: A central database for resolving microbial strain identifiers
118274Curators of the CIPCollection of Institut Pasteur (CIP 108730)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108730