Strain identifier

BacDive ID: 140884

Type strain: Yes

Species: Bifidobacterium aquikefiri

Strain Designation: R 54638

NCBI tax ID(s): 1653207 (species)

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

@ref: 43708

BacDive-ID: 140884

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-positive, rod-shaped, colony-forming

description: Bifidobacterium aquikefiri R 54638 is an anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from A household water kefir fermentation process carried out in 2014.

NCBI tax id

  • NCBI tax id: 1653207
  • Matching level: species

doi: 10.13145/bacdive140884.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Bifidobacterium
  • species: Bifidobacterium aquikefiri
  • full scientific name: Bifidobacterium aquikefiri Laureys et al. 2016

@ref: 43708

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium aquikefiri

strain designation: R 54638

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43708positive1-2 µm0.5-1 µmrod-shapedno
69480positive99.998

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
437081 mmCreamcircular6 daysM144 agar medium
633862 days

Culture and growth conditions

culture medium

  • @ref: 43708
  • name: M144 agar medium
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43708positivegrowth4-37
43708positiveoptimum28mesophilic
63386positivegrowth30mesophilic

culture pH

  • @ref: 43708
  • ability: positive
  • type: growth
  • pH: 4-8
  • PH range: acidophile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43708anaerobe
63386anaerobe
69480anaerobe98.234

spore formation

@refspore formationconfidence
43708no
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4370818305arbutin-builds acid from
4370817057cellobiose-builds acid from
4370815963ribitol-builds acid from
4370817108D-arabinose-builds acid from
4370818333D-arabitol-builds acid from
4370828847D-fucose-builds acid from
4370862318D-lyxose-builds acid from
4370817924D-sorbitol-builds acid from
4370816443D-tagatose-builds acid from
4370865327D-xylose-builds acid from
4370816813galactitol-builds acid from
4370817113erythritol-builds acid from
43708esculin ferric citrate-builds acid from
4370817754glycerol-builds acid from
4370828087glycogen-builds acid from
4370817268myo-inositol-builds acid from
4370815443inulin-builds acid from
4370818403L-arabitol-builds acid from
4370818287L-fucose-builds acid from
4370862345L-rhamnose-builds acid from
4370817266L-sorbose-builds acid from
4370865328L-xylose-builds acid from
4370817716lactose-builds acid from
437086731melezitose-builds acid from
4370843943methyl alpha-D-mannoside-builds acid from
4370874863methyl beta-D-xylopyranoside-builds acid from
43708potassium 2-dehydro-D-gluconate-builds acid from
43708potassium 5-dehydro-D-gluconate-builds acid from
4370817814salicin-builds acid from
4370828017starch-builds acid from
4370827082trehalose-builds acid from
4370817151xylitol-builds acid from
43708casein-degradation
437085291gelatin-degradation
4370815824D-fructose+builds acid from
4370812936D-galactose+builds acid from
4370817634D-glucose+builds acid from
4370816024D-mannose+builds acid from
4370816988D-ribose+builds acid from
4370828066gentiobiose+builds acid from
4370830849L-arabinose+builds acid from
4370817306maltose+builds acid from
4370828053melibiose+builds acid from
4370832032potassium gluconate+builds acid from
4370816634raffinose+builds acid from
4370817992sucrose+builds acid from
4370832528turanose+builds acid from
4370827613amygdalin+/-builds acid from
4370816899D-mannitol+/-builds acid from
43708320061methyl alpha-D-glucopyranoside+/-builds acid from
43708506227N-acetylglucosamine+/-builds acid from

enzymes

@refvalueactivityec
43708leucine arylamidase+3.4.11.1
43708alpha-galactosidase+3.2.1.22
43708beta-galactosidase+3.2.1.23
43708alpha-glucosidase+3.2.1.20
43708beta-glucosidase+3.2.1.21
43708acid phosphatase+/-3.1.3.2
43708naphthol-AS-BI-phosphohydrolase+/-
43708alkaline phosphatase-3.1.3.1
43708esterase (C 4)-
43708esterase Lipase (C 8)-
43708lipase (C 14)-
43708valine arylamidase-
43708cystine arylamidase-3.4.11.3
43708trypsin-3.4.21.4
43708alpha-chymotrypsin-3.4.21.1
43708beta-glucuronidase-3.2.1.31
43708N-acetyl-beta-glucosaminidase-3.2.1.52
43708alpha-mannosidase-3.2.1.24
43708alpha-fucosidase-3.2.1.51
43708cytochrome oxidase-1.9.3.1
43708catalase-1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation datesampling date
43708A household water kefir fermentation process carried out in 2014BrusselsBelgiumBELEurope2014
63386Water kefirBrusselsBelgiumBELEurope2014-11-13

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#House
#Engineered#Food production#Dairy product
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_51641.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_2944;97_3619;98_37080;99_51641&stattab=map
  • Last taxonomy: Bifidobacterium aquikefiri subclade
  • 16S sequence: LN849254
  • Sequence Identity:
  • Total samples: 2939
  • soil counts: 29
  • aquatic counts: 40
  • animal counts: 2851
  • plant counts: 19

Sequence information

16S sequences

  • @ref: 43708
  • description: 16S rRNA gene sequence
  • accession: LN849254
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium aquikefiri LMG 28769GCA_002259795contigncbi1653207
66792Bifidobacterium aquikefiri strain LMG 287691653207.3wgspatric1653207
66792Bifidobacterium aquikefiri LMG 287692791355241draftimg1653207

GC content

  • @ref: 43708
  • GC-content: 52.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.716yes
gram-positiveyes92.782yes
anaerobicyes89.659no
aerobicno93.691yes
halophileno70.194no
spore-formingno96.594no
thermophileno97.036no
glucose-utilyes86.18no
flagellatedno97.332yes
glucose-fermentyes80.654no

External links

@ref: 43708

culture collection no.: LMG 28769, CCUG 67145

straininfo link

  • @ref: 96807
  • straininfo: 396435

literature

  • topic: Phylogeny
  • Pubmed-ID: 26739269
  • title: Bifidobacterium aquikefiri sp. nov., isolated from water kefir.
  • authors: Laureys D, Cnockaert M, De Vuyst L, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000877
  • year: 2016

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43708David Laureys, Margo Cnockaert, Luc De Vuyst, Peter VandammeBifidobacterium aquikefiri sp. nov., isolated from water kefir10.1099/ijsem.0.000877IJSEM 66: 1281-1286 201626739269
63386Curators of the CCUGhttps://www.ccug.se/strain?id=67145Culture Collection University of Gothenburg (CCUG) (CCUG 67145)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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
96807Reimer, 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-ID396435.1