Strain identifier
BacDive ID: 140884
Type strain:
Species: Bifidobacterium aquikefiri
Strain Designation: R 54638
NCBI tax ID(s): 1653207 (species)
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43708 | positive | 1-2 µm | 0.5-1 µm | rod-shaped | no | |
69480 | positive | 99.998 |
colony morphology
@ref | colony size | colony color | colony shape | incubation period | medium used |
---|---|---|---|---|---|
43708 | 1 mm | Cream | circular | 6 days | M144 agar medium |
63386 | 2 days |
Culture and growth conditions
culture medium
- @ref: 43708
- name: M144 agar medium
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43708 | positive | growth | 4-37 | |
43708 | positive | optimum | 28 | mesophilic |
63386 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 43708
- ability: positive
- type: growth
- pH: 4-8
- PH range: acidophile
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
43708 | anaerobe | |
63386 | anaerobe | |
69480 | anaerobe | 98.234 |
spore formation
@ref | spore formation | confidence |
---|---|---|
43708 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43708 | 18305 | arbutin | - | builds acid from |
43708 | 17057 | cellobiose | - | builds acid from |
43708 | 15963 | ribitol | - | builds acid from |
43708 | 17108 | D-arabinose | - | builds acid from |
43708 | 18333 | D-arabitol | - | builds acid from |
43708 | 28847 | D-fucose | - | builds acid from |
43708 | 62318 | D-lyxose | - | builds acid from |
43708 | 17924 | D-sorbitol | - | builds acid from |
43708 | 16443 | D-tagatose | - | builds acid from |
43708 | 65327 | D-xylose | - | builds acid from |
43708 | 16813 | galactitol | - | builds acid from |
43708 | 17113 | erythritol | - | builds acid from |
43708 | esculin ferric citrate | - | builds acid from | |
43708 | 17754 | glycerol | - | builds acid from |
43708 | 28087 | glycogen | - | builds acid from |
43708 | 17268 | myo-inositol | - | builds acid from |
43708 | 15443 | inulin | - | builds acid from |
43708 | 18403 | L-arabitol | - | builds acid from |
43708 | 18287 | L-fucose | - | builds acid from |
43708 | 62345 | L-rhamnose | - | builds acid from |
43708 | 17266 | L-sorbose | - | builds acid from |
43708 | 65328 | L-xylose | - | builds acid from |
43708 | 17716 | lactose | - | builds acid from |
43708 | 6731 | melezitose | - | builds acid from |
43708 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
43708 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
43708 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
43708 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
43708 | 17814 | salicin | - | builds acid from |
43708 | 28017 | starch | - | builds acid from |
43708 | 27082 | trehalose | - | builds acid from |
43708 | 17151 | xylitol | - | builds acid from |
43708 | casein | - | degradation | |
43708 | 5291 | gelatin | - | degradation |
43708 | 15824 | D-fructose | + | builds acid from |
43708 | 12936 | D-galactose | + | builds acid from |
43708 | 17634 | D-glucose | + | builds acid from |
43708 | 16024 | D-mannose | + | builds acid from |
43708 | 16988 | D-ribose | + | builds acid from |
43708 | 28066 | gentiobiose | + | builds acid from |
43708 | 30849 | L-arabinose | + | builds acid from |
43708 | 17306 | maltose | + | builds acid from |
43708 | 28053 | melibiose | + | builds acid from |
43708 | 32032 | potassium gluconate | + | builds acid from |
43708 | 16634 | raffinose | + | builds acid from |
43708 | 17992 | sucrose | + | builds acid from |
43708 | 32528 | turanose | + | builds acid from |
43708 | 27613 | amygdalin | +/- | builds acid from |
43708 | 16899 | D-mannitol | +/- | builds acid from |
43708 | 320061 | methyl alpha-D-glucopyranoside | +/- | builds acid from |
43708 | 506227 | N-acetylglucosamine | +/- | builds acid from |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43708 | leucine arylamidase | + | 3.4.11.1 |
43708 | alpha-galactosidase | + | 3.2.1.22 |
43708 | beta-galactosidase | + | 3.2.1.23 |
43708 | alpha-glucosidase | + | 3.2.1.20 |
43708 | beta-glucosidase | + | 3.2.1.21 |
43708 | acid phosphatase | +/- | 3.1.3.2 |
43708 | naphthol-AS-BI-phosphohydrolase | +/- | |
43708 | alkaline phosphatase | - | 3.1.3.1 |
43708 | esterase (C 4) | - | |
43708 | esterase Lipase (C 8) | - | |
43708 | lipase (C 14) | - | |
43708 | valine arylamidase | - | |
43708 | cystine arylamidase | - | 3.4.11.3 |
43708 | trypsin | - | 3.4.21.4 |
43708 | alpha-chymotrypsin | - | 3.4.21.1 |
43708 | beta-glucuronidase | - | 3.2.1.31 |
43708 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43708 | alpha-mannosidase | - | 3.2.1.24 |
43708 | alpha-fucosidase | - | 3.2.1.51 |
43708 | cytochrome oxidase | - | 1.9.3.1 |
43708 | catalase | - | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date | sampling date |
---|---|---|---|---|---|---|---|
43708 | A household water kefir fermentation process carried out in 2014 | Brussels | Belgium | BEL | Europe | 2014 | |
63386 | Water kefir | Brussels | Belgium | BEL | Europe | 2014-11-13 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium aquikefiri LMG 28769 | GCA_002259795 | contig | ncbi | 1653207 |
66792 | Bifidobacterium aquikefiri strain LMG 28769 | 1653207.3 | wgs | patric | 1653207 |
66792 | Bifidobacterium aquikefiri LMG 28769 | 2791355241 | draft | img | 1653207 |
GC content
- @ref: 43708
- GC-content: 52.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.716 | yes |
gram-positive | yes | 92.782 | yes |
anaerobic | yes | 89.659 | no |
aerobic | no | 93.691 | yes |
halophile | no | 70.194 | no |
spore-forming | no | 96.594 | no |
thermophile | no | 97.036 | no |
glucose-util | yes | 86.18 | no |
flagellated | no | 97.332 | yes |
glucose-ferment | yes | 80.654 | no |
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
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
43708 | David Laureys, Margo Cnockaert, Luc De Vuyst, Peter Vandamme | Bifidobacterium aquikefiri sp. nov., isolated from water kefir | 10.1099/ijsem.0.000877 | IJSEM 66: 1281-1286 2016 | 26739269 | |
63386 | Curators of the CCUG | https://www.ccug.se/strain?id=67145 | Culture Collection University of Gothenburg (CCUG) (CCUG 67145) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João 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 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
96807 | Reimer, 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 identifiers | 10.60712/SI-ID396435.1 |