Strain identifier
BacDive ID: 17763
Type strain: 
Species: Filimonas lacunae
Strain Designation: YT21
Strain history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; YT21 <- Y. Tagami
NCBI tax ID(s): 477680 (species)
version 9.1 (current version)
General
@ref: 15537
BacDive-ID: 17763
DSM-Number: 21054
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile
description: Filimonas lacunae YT21 is an aerobe, Gram-negative, motile bacterium that was isolated from shallow fresh water.
NCBI tax id
- NCBI tax id: 477680
- Matching level: species
strain history
- @ref: 15537
- history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; YT21 <- Y. Tagami
doi: 10.13145/bacdive17763.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Chitinophagia
- order: Chitinophagales
- family: Chitinophagaceae
- genus: Filimonas
- species: Filimonas lacunae
- full scientific name: Filimonas lacunae Shiratori et al. 2009
@ref: 15537
domain: Bacteria
phylum: Bacteroidetes
class: Chitinophagia
order: Sphingobacteriales
family: Chitinophagaceae
genus: Filimonas
species: Filimonas lacunae
full scientific name: Filimonas lacunae Shiratori et al. 2009 emend. Leandro et al. 2013
strain designation: YT21
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | motility | confidence |
|---|---|---|---|---|---|
| 28958 | negative | 17.5 µm | 0.4 µm | yes | |
| 69480 | negative | 91.139 |
pigmentation
- @ref: 28958
- production: yes
Culture and growth conditions
culture medium
- @ref: 15537
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 15537 | positive | growth | 28 |
| 28958 | positive | growth | 10-35 |
| 28958 | positive | optimum | 29 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 28958 | positive | growth | 05-09 | alkaliphile |
| 28958 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
- @ref: 28958
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 28958 | no | |
| 69481 | no | 91 |
halophily
- @ref: 28958
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <1 %
observation
- @ref: 28958
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28958 | 22599 | arabinose | + | carbon source |
| 28958 | 23652 | dextrin | + | carbon source |
| 28958 | 28260 | galactose | + | carbon source |
| 28958 | 17234 | glucose | + | carbon source |
| 28958 | 17754 | glycerol | + | carbon source |
| 28958 | 17306 | maltose | + | carbon source |
| 28958 | 37684 | mannose | + | carbon source |
| 28958 | 16199 | urea | + | carbon source |
| 28958 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28958 | acid phosphatase | + | 3.1.3.2 |
| 28958 | alkaline phosphatase | + | 3.1.3.1 |
| 28958 | catalase | + | 1.11.1.6 |
| 28958 | gelatinase | + | |
| 28958 | cytochrome oxidase | + | 1.9.3.1 |
| 28958 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 15537
- sample type: shallow fresh water
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Freshwater
taxonmaps
- @ref: 69479
- File name: preview.99_4408.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_2206;97_2671;98_3312;99_4408&stattab=map
- Last taxonomy: Filimonas lacunae subclade
- 16S sequence: AB682148
- Sequence Identity:
- Total samples: 1336
- soil counts: 441
- aquatic counts: 466
- animal counts: 281
- plant counts: 148
Safety information
risk assessment
- @ref: 15537
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Filimonas lacunae gene for 16S rRNA, partial sequence, strain: NBRC 104114 | AB682148 | 1454 | nuccore | 477680 |
| 15537 | Filimonas lacunae gene for 16S rRNA, partial sequence | AB362776 | 1493 | nuccore | 477680 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Filimonas lacunae NBRC 104114 | GCA_002355595 | complete | ncbi | 477680 |
| 66792 | Filimonas lacunae DSM 21054 | GCA_900156765 | scaffold | ncbi | 477680 |
| 66792 | Filimonas lacunae strain DSM 21054 | 477680.4 | wgs | patric | 477680 |
| 66792 | Filimonas lacunae strain NBRC 104114 | 477680.5 | complete | patric | 477680 |
| 66792 | Filimonas lacunae DSM 21054 | 2681813554 | draft | img | 477680 |
| 66792 | Filimonas lacunae NBRC 104114 | 2802429281 | complete | img | 477680 |
GC content
- @ref: 15537
- GC-content: 45.2
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 91 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 91.139 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.93 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.401 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 81.017 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98.481 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.75 | no |
External links
@ref: 15537
culture collection no.: DSM 21054, NBRC 104114
straininfo link
- @ref: 86754
- straininfo: 400231
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19406807 | Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. | Shiratori H, Tagami Y, Morishita T, Kamihara Y, Beppu T, Ueda K | Int J Syst Evol Microbiol | 10.1099/ijs.0.002618-0 | 2009 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 27118116 | Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root. | Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yang MM, Lu M, Sun JG | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001116 | 2016 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 15537 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21054) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21054 | ||||
| 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 | ||
| 28958 | 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 | 25395 | ||
| 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 | ||
| 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 | ||||
| 86754 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400231.1 | StrainInfo: A central database for resolving microbial strain identifiers |