Strain identifier

BacDive ID: 23737

Type strain: Yes

Species: Oceanobacillus indicireducens

Strain Designation: A21

Strain history: I. Yumoto A21.

NCBI tax ID(s): 1004261 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20697

BacDive-ID: 23737

DSM-Number: 28042

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

description: Oceanobacillus indicireducens A21 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from fermented Polygonum indigo liquor sample aged for 4 days prepared in a laboratory.

NCBI tax id

  • NCBI tax id: 1004261
  • Matching level: species

strain history

@refhistory
20697<- JCM <- I. Yumoto; A21
67770I. Yumoto A21.

doi: 10.13145/bacdive23737.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Oceanobacillus
  • species: Oceanobacillus indicireducens
  • full scientific name: Oceanobacillus indicireducens Hirota et al. 2013

@ref: 20697

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Oceanobacillus

species: Oceanobacillus indicireducens

full scientific name: Oceanobacillus indicireducens Hirota et al. 2013

strain designation: A21

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30373positive6.5 µm2.15 µmrod-shapedyes
69480yes90.518

pigmentation

  • @ref: 30373
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20697
  • name: HORIKOSHI-1 MEDIUM (DSMZ Medium 1081)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1081
  • composition: Name: HORIKOSHI-1 MEDIUM (DSMZ Medium 1081) Composition: Agar 15.0 g/l Glucose 10.0 g/l Na2CO3 10.0 g/l Yeast extract 5.0 g/l Polypeptone 5.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperature
20697positivegrowth37
30373positivegrowth18-48
30373positiveoptimum39
67770positivegrowth30

culture pH

@refabilitytypepHPH range
30373positivegrowth07-12alkaliphile
30373positiveoptimum10

Physiology and metabolism

oxygen tolerance

  • @ref: 30373
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30373yes
69481yes100
69480yes92.974

halophily

@refsaltgrowthtested relationconcentration
30373NaClpositivegrowth0-10 %
30373NaClpositiveoptimum5 %

observation

  • @ref: 30373
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3037317057cellobiose+carbon source
3037328757fructose+carbon source
3037317234glucose+carbon source
3037328087glycogen+carbon source
3037317306maltose+carbon source
3037329864mannitol+carbon source
3037337684mannose+carbon source
30373506227N-acetylglucosamine+carbon source
3037316634raffinose+carbon source
3037317814salicin+carbon source
3037317992sucrose+carbon source
3037327082trehalose+carbon source

enzymes

@refvalueactivityec
30373catalase+1.11.1.6
30373gelatinase+
30373cytochrome oxidase+1.9.3.1
30373urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
20697fermented Polygonum indigo ( Polygonum tinctorium Lour.) liquor sample aged for 4 days prepared in a laboratoryPolygonum tinctoriumHokkaidoJapanJPNAsia
67770Fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample aged for 4 days prepared in a laboratoryPolygonum tinctorium

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Engineered#Laboratory
#Host#Plants#Shrub (Scrub)
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_11801.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_5972;97_7183;98_8864;99_11801&stattab=map
  • Last taxonomy: Oceanobacillus indicireducens subclade
  • 16S sequence: AB623011
  • Sequence Identity:
  • Total samples: 346
  • soil counts: 73
  • aquatic counts: 55
  • animal counts: 211
  • plant counts: 7

Safety information

risk assessment

  • @ref: 20697
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20697
  • description: Oceanobacillus indicireducens gene for 16S ribosomal RNA, partial sequence
  • accession: AB623011
  • length: 1516
  • database: nuccore
  • NCBI tax ID: 1004261

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oceanobacillus indicireducens JCM 17251GCA_014647195scaffoldncbi1004261
66792Oceanobacillus indicireducens strain JCM 172511004261.3wgspatric1004261

GC content

@refGC-contentmethod
2069739.7high performance liquid chromatography (HPLC)
3037339.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes82.248no
gram-positiveyes88.442yes
anaerobicno98.623no
aerobicyes82.962no
halophileyes85.882no
spore-formingyes92.974yes
glucose-utilyes84.039yes
thermophileno98.577yes
motileyes90.518yes
glucose-fermentno86.754no

External links

@ref: 20697

culture collection no.: DSM 28042, JCM 17251, NCIMB 14685, BCRC 80660

straininfo link

  • @ref: 87774
  • straininfo: 398524

literature

  • topic: Phylogeny
  • Pubmed-ID: 22843722
  • title: Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye.
  • authors: Hirota K, Aino K, Nodasaka Y, Yumoto I
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.034579-0
  • year: 2012
  • mesh: Bacillaceae/*classification/genetics/isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Coloring Agents/*metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Indigo Carmine, Indoles/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polygonum, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20697Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28042Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28042)
30373Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172671328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87774Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID398524.1