Strain identifier
BacDive ID: 6698
Type strain:
Species: Holzapfeliella floricola
Strain Designation: Ryu1-2
Strain history: S. Kawasaki Ryu1-2.
NCBI tax ID(s): 679249 (species)
General
@ref: 16663
BacDive-ID: 6698
DSM-Number: 23037
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Holzapfeliella floricola Ryu1-2 is a mesophilic bacterium that was isolated from flower of Caltha palustris.
NCBI tax id
- NCBI tax id: 679249
- Matching level: species
strain history
@ref | history |
---|---|
16663 | <- S. Kawasaki, Dept. Bio-Science, Tokyo Univ. Agriculture, Japan; NRIC 0774 |
67770 | S. Kawasaki Ryu1-2. |
doi: 10.13145/bacdive6698.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Holzapfeliella
- species: Holzapfeliella floricola
- full scientific name: Holzapfeliella floricola (Kawasaki et al. 2011) Deshmukh and Oren 2023
synonyms
@ref synonym 20215 Holzapfelia floricola 20215 Lactobacillus floricola
@ref: 16663
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Holzapfelia
species: Holzapfelia floricola
full scientific name: Holzapfelia floricola (Kawasaki et al. 2011) Zheng et al. 2020
strain designation: Ryu1-2
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 98.075 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 16663
- 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 |
---|---|---|---|---|
16663 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.991 |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16663 | - | - | - | - | - | - | - | - | - | - | +/- | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
16663 | flower of Caltha palustris | Caltha palustris | Oze National Park | Japan | JPN | Asia |
67770 | Flower, buttercup (Caltha palustris) | Caltha palustris | Oze National Park | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Flower |
taxonmaps
- @ref: 69479
- File name: preview.99_7131.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_3344;97_4101;98_5246;99_7131&stattab=map
- Last taxonomy: Holzapfelia floricola subclade
- 16S sequence: LC519858
- Sequence Identity:
- Total samples: 2442
- soil counts: 88
- aquatic counts: 112
- animal counts: 2097
- plant counts: 145
Safety information
risk assessment
- @ref: 16663
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
16663 | Lactobacillus floricola gene for 16S rRNA, partial sequence, strain: Ryu1-2 | AB523780 | 1566 | ena | 1423744 |
67770 | Lactobacillus floricola JCM 16512 gene for 16S rRNA, partial sequence | LC519858 | 1514 | ena | 679249 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus floricola DSM 23037 = JCM 16512 | 1423744.4 | wgs | patric | 1423744 |
66792 | Lactobacillus floricola DSM 23037 = JCM 16512 | 1423744.3 | wgs | patric | 1423744 |
66792 | Lactobacillus floricola JCM 16512 | 2728369687 | draft | img | 1423744 |
66792 | Lactobacillus floricola DSM 23037 | 2667527860 | draft | img | 1423744 |
67770 | Holzapfeliella floricola DSM 23037 = JCM 16512 | GCA_001436605 | scaffold | ncbi | 1423744 |
67770 | Holzapfeliella floricola DSM 23037 = JCM 16512 | GCA_001311465 | contig | ncbi | 1423744 |
GC content
@ref | GC-content | method |
---|---|---|
16663 | 48.0 | high performance liquid chromatography (HPLC) |
67770 | 34.5 | genome sequence analysis |
67770 | 48 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 97.392 | no |
gram-positive | yes | 94.493 | no |
anaerobic | no | 84.607 | no |
halophile | yes | 88.558 | no |
spore-forming | no | 96.425 | no |
glucose-util | yes | 84.245 | no |
thermophile | no | 98.616 | no |
aerobic | no | 94.521 | no |
flagellated | no | 99.082 | no |
glucose-ferment | yes | 81.831 | no |
External links
@ref: 16663
culture collection no.: DSM 23037, JCM 16512, NRIC 0774, KCTC 21006
straininfo link
- @ref: 76172
- straininfo: 406305
literature
- topic: Phylogeny
- Pubmed-ID: 20601482
- title: Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers.
- authors: Kawasaki S, Kurosawa K, Miyazaki M, Yagi C, Kitajima Y, Tanaka S, Irisawa T, Okada S, Sakamoto M, Ohkuma M, Niimura Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.022988-0
- year: 2010
- mesh: Bacterial Typing Techniques, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Flowers/*microbiology, Japan, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16663 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23037) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23037 | |||
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 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
76172 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406305.1 | StrainInfo: A central database for resolving microbial strain identifiers |