Strain identifier

BacDive ID: 23741

Type strain: Yes

Species: Amphibacillus indicireducens

Strain Designation: C40

Strain history: I. Yumoto C40.

NCBI tax ID(s): 1076330 (species)

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General

@ref: 20923

BacDive-ID: 23741

DSM-Number: 27992

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

description: Amphibacillus indicireducens C40 is a microaerophile, spore-forming, Gram-positive bacterium that was isolated from Polygonum Indigo fermentation liquor.

NCBI tax id

  • NCBI tax id: 1076330
  • Matching level: species

strain history

@refhistory
20923<- JCM <- I. Yumoto, Natl. Inst. Advanced Industrial Sci. and Technology (AIST), Sapporo, Japan; C40
67770I. Yumoto C40.

doi: 10.13145/bacdive23741.20240510.9

Name and taxonomic classification

LPSN

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

@ref: 20923

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Amphibacillus

species: Amphibacillus indicireducens

full scientific name: Amphibacillus indicireducens Hirota et al. 2013

strain designation: C40

type strain: yes

Morphology

cell morphology

  • @ref: 30506
  • gram stain: positive
  • cell length: 2 µm
  • cell width: 0.4 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 30506
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20923TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
20923CASO 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

culture temp

@refgrowthtypetemperature
20923positivegrowth35
30506positivegrowth17-39
30506positiveoptimum35
67770positivegrowth30

culture pH

@refabilitytypepHPH range
30506positivegrowth09-12alkaliphile
30506positiveoptimum10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
20923microaerophile
30506facultative anaerobe

spore formation

  • @ref: 30506
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
30506NaClpositivegrowth0-7 %
30506NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3050622599arabinose+carbon source
3050617057cellobiose+carbon source
3050628757fructose+carbon source
3050628260galactose+carbon source
3050617234glucose+carbon source
3050617716lactose+carbon source
3050637684mannose+carbon source
3050628053melibiose+carbon source
3050616634raffinose+carbon source
3050626546rhamnose+carbon source
3050617992sucrose+carbon source
3050627082trehalose+carbon source
3050618222xylose+carbon source

enzymes

  • @ref: 30506
  • value: alpha-galactosidase
  • activity: +
  • ec: 3.2.1.22

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
20923Polygonum Indigo (Polygonum tinctorium Lour.) fermentation liquorPolygonum tinctoriumHokkaido, Date CityJapanJPNAsia
67770Polygonum indigo (Polygonum tinctorium Lour.) fermentation liquor from Date CityPolygonum tinctoriumHokkaidoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Host#Plants#Herbaceous plants (Grass,Crops)
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_100760.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1177;97_14872;98_18400;99_100760&stattab=map
  • Last taxonomy: Amphibacillus indicireducens subclade
  • 16S sequence: AB665218
  • Sequence Identity:
  • Total samples: 1671
  • soil counts: 336
  • aquatic counts: 110
  • animal counts: 1181
  • plant counts: 44

Safety information

risk assessment

  • @ref: 20923
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20923
  • description: Amphibacillus indicireducens gene for 16S rRNA, partial sequence
  • accession: AB665218
  • length: 1537
  • database: nuccore
  • NCBI tax ID: 1076330

GC content

@refGC-contentmethod
2092337.5high performance liquid chromatography (HPLC)
3050637.5

External links

@ref: 20923

culture collection no.: DSM 27992, JCM 17250, NCIMB 14686

straininfo link

  • @ref: 87778
  • straininfo: 404006

literature

  • topic: Phylogeny
  • Pubmed-ID: 22493173
  • title: Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye.
  • authors: Hirota K, Aino K, Nodasaka Y, Morita N, Yumoto I
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.037622-0
  • 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, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, 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
20923Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27992Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27992)
30506Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172683828776041
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/
87778Reimer, 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-ID404006.1