Strain identifier
BacDive ID: 6682
Type strain:
Species: Lactiplantibacillus fabifermentans
Strain Designation: R-34115
Strain history: <- L. De Vuyst and K. De Bruyne <- N. Camu, Vrije Univ. Brussels, Belgium; R-34115
NCBI tax ID(s): 1413187 (strain), 483011 (species)
General
@ref: 15486
BacDive-ID: 6682
DSM-Number: 21115
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Lactiplantibacillus fabifermentans R-34115 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from cocoa bean heap fermentation.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1413187 | strain |
483011 | species |
strain history
- @ref: 15486
- history: <- L. De Vuyst and K. De Bruyne <- N. Camu, Vrije Univ. Brussels, Belgium; R-34115
doi: 10.13145/bacdive6682.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Lactiplantibacillus
- species: Lactiplantibacillus fabifermentans
- full scientific name: Lactiplantibacillus fabifermentans (De Bruyne et al. 2009) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus fabifermentans
@ref: 15486
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Lactiplantibacillus
species: Lactiplantibacillus fabifermentans
full scientific name: Lactiplantibacillus fabifermentans (De Bruyne et al. 2009) Zheng et al. 2020
strain designation: R-34115
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
28904 | positive | 10 µm | 2 µm | rod-shaped | no | |
69480 | no | 95.765 | ||||
69480 | positive | 100 |
pigmentation
- @ref: 28904
- production: no
Culture and growth conditions
culture medium
- @ref: 15486
- name: MRS MEDIUM (DSMZ Medium 11)
- growth: yes
- link: https://mediadive.dsmz.de/medium/11
- composition: Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15486 | positive | growth | 30 | mesophilic |
28904 | positive | growth | 10-37 | |
28904 | positive | optimum | 23.5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
15486 | microaerophile |
28904 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
28904 | 22599 | arabinose | + | carbon source |
28904 | 17057 | cellobiose | + | carbon source |
28904 | 28757 | fructose | + | carbon source |
28904 | 28260 | galactose | + | carbon source |
28904 | 17234 | glucose | + | carbon source |
28904 | 17306 | maltose | + | carbon source |
28904 | 29864 | mannitol | + | carbon source |
28904 | 37684 | mannose | + | carbon source |
28904 | 33942 | ribose | + | carbon source |
28904 | 17814 | salicin | + | carbon source |
28904 | 17992 | sucrose | + | carbon source |
28904 | 27082 | trehalose | + | carbon source |
28904 | 18222 | xylose | + | carbon source |
28904 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | + | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15486 | - | - | - | - | + | - | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
15486 | - | - | - | - | + | + | + | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 15486
- sample type: cocoa bean heap fermentation
- country: Ghana
- origin.country: GHA
- continent: Africa
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | |
#Host Body-Site | #Plant | #Fruit (Seed) |
taxonmaps
- @ref: 69479
- File name: preview.99_195.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_140;97_151;98_168;99_195&stattab=map
- Last taxonomy: Lactobacillaceae
- 16S sequence: AM905388
- Sequence Identity:
- Total samples: 38637
- soil counts: 2696
- aquatic counts: 4479
- animal counts: 29069
- plant counts: 2393
Safety information
risk assessment
- @ref: 15486
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactobacillus fabifermentans gene for 16S rRNA, partial sequence, strain: DSM 21115 | AB626075 | 1491 | ena | 483011 |
15486 | Lactobacillus fabifermentans partial 16S rRNA gene, type strain LMG 24284T | AM905388 | 1532 | ena | 483011 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactiplantibacillus fabifermentans DSM 21115 | GCA_000498955 | scaffold | ncbi | 1413187 |
66792 | Lactobacillus fabifermentans DSM 21115 | 1578.21 | wgs | patric | 1413187 |
66792 | Lactiplantibacillus fabifermentans DSM 21115 | 2563367174 | draft | img | 1413187 |
GC content
- @ref: 15486
- GC-content: 44.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.88 | yes |
motile | no | 95.88 | yes |
flagellated | no | 96.917 | no |
flagellated | no | 96.917 | no |
gram-positive | yes | 95.799 | yes |
gram-positive | yes | 95.799 | yes |
anaerobic | no | 80.682 | yes |
anaerobic | no | 80.682 | yes |
aerobic | no | 97.908 | yes |
aerobic | no | 97.908 | yes |
halophile | yes | 86.953 | no |
halophile | yes | 86.953 | no |
spore-forming | no | 93.315 | no |
spore-forming | no | 93.315 | no |
thermophile | no | 99.592 | yes |
thermophile | no | 99.592 | yes |
glucose-util | yes | 92.71 | yes |
glucose-util | yes | 92.71 | yes |
glucose-ferment | yes | 84.751 | no |
glucose-ferment | yes | 84.751 | no |
External links
@ref: 15486
culture collection no.: DSM 21115, LMG 24284
straininfo link
- @ref: 76156
- straininfo: 311003
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19126714 | Lactobacillus fabifermentans sp. nov. and Lactobacillus cacaonum sp. nov., isolated from Ghanaian cocoa fermentations. | De Bruyne K, Camu N, De Vuyst L, Vandamme P | Int J Syst Evol Microbiol | 10.1099/ijs.0.001172-0 | 2009 | Bacterial Proteins/chemistry/genetics, Bacterial Typing Techniques, Cacao/*metabolism/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Ghana, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Metabolism |
Phylogeny | 23950151 | Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough. | Gu CT, Li CY, Yang LJ, Huo GC | Int J Syst Evol Microbiol | 10.1099/ijs.0.054296-0 | 2013 | Bacterial Typing Techniques, Base Composition, Bread/microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Genes, Bacterial, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/microbiology | Biotechnology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
15486 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21115) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21115 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
28904 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 25343 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
68371 | Automatically annotated from API 50CH acid | ||||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
76156 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID311003.1 | StrainInfo: A central database for resolving microbial strain identifiers |