Strain identifier
BacDive ID: 24022
Type strain: 
Species: Flavobacterium fontis
Strain history: K. Y. Jahng MIC3010.
NCBI tax ID(s): 1124188 (species)
version 8.1 (current version)
General
@ref: 20569
BacDive-ID: 24022
DSM-Number: 25660
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Flavobacterium fontis DSM 25660 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fresh water pond.
NCBI tax id
- NCBI tax id: 1124188
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20569 | <- J. Chun, Chonbuk National Univ., Dept. of Life Scs., Jeonju-si, Korea; MIC3010 |
| 67770 | K. Y. Jahng MIC3010. |
doi: 10.13145/bacdive24022.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Flavobacterium
- species: Flavobacterium fontis
- full scientific name: Flavobacterium fontis Chun et al. 2013
@ref: 20569
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium fontis
full scientific name: Flavobacterium fontis Chun et al. 2013
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 30818 | negative | rod-shaped | no | |
| 69480 | negative | 99.992 |
pigmentation
- @ref: 30818
- production: no
Culture and growth conditions
culture medium
- @ref: 20569
- 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 | range |
|---|---|---|---|---|
| 20569 | positive | growth | 25 | mesophilic |
| 30818 | positive | growth | 15-42 | |
| 30818 | positive | optimum | 25 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30818 | positive | growth | 5.5-8 |
| 30818 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
- @ref: 30818
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
halophily
- @ref: 30818
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 0.5 %
observation
- @ref: 30818
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30818 | 21217 | L-alaninamide | + | carbon source |
| 30818 | 28644 | 2-oxopentanoate | + | carbon source |
| 30818 | 23652 | dextrin | + | carbon source |
| 30818 | 24148 | galactonate | + | carbon source |
| 30818 | 29987 | glutamate | + | carbon source |
| 30818 | 15428 | glycine | + | carbon source |
| 30818 | 28087 | glycogen | + | carbon source |
| 30818 | 26271 | proline | + | carbon source |
| 30818 | 26546 | rhamnose | + | carbon source |
| 30818 | 53423 | tween 40 | + | carbon source |
| 30818 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30818 | gelatinase | + | |
| 30818 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 20569 | fresh water pond | Jeonju (35° 50' N 127° 07' E) | Republic of Korea | KOR | Asia | 35.8333 | 127.117 |
| 67770 | Freshwater pond in Jeonju | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Pond (small) |
taxonmaps
- @ref: 69479
- File name: preview.99_4326.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2169;97_2625;98_3255;99_4326&stattab=map
- Last taxonomy: Flavobacterium
- 16S sequence: JN873147
- Sequence Identity:
- Total samples: 6484
- soil counts: 410
- aquatic counts: 5359
- animal counts: 496
- plant counts: 219
Safety information
risk assessment
- @ref: 20569
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20569
- description: Flavobacterium fontis strain MIC3010 16S ribosomal RNA gene, partial sequence
- accession: JN873147
- length: 1378
- database: ena
- NCBI tax ID: 1124188
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Flavobacterium fontis strain DSM 25660 | 1124188.3 | wgs | patric | 1124188 |
| 66792 | Flavobacterium fontis DSM 25660 | 2695420946 | draft | img | 1124188 |
| 67770 | Flavobacterium fontis DSM 25660 | GCA_900129405 | contig | ncbi | 1124188 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20569 | 41.0 | high performance liquid chromatography (HPLC) |
| 30818 | 41 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 93.674 | yes |
| flagellated | no | 96.633 | yes |
| gram-positive | no | 98.443 | no |
| anaerobic | no | 98.937 | no |
| aerobic | yes | 82.257 | no |
| halophile | no | 96.214 | yes |
| spore-forming | no | 93.829 | no |
| thermophile | no | 93.839 | yes |
| glucose-util | yes | 83.994 | no |
| glucose-ferment | no | 91.536 | no |
External links
@ref: 20569
culture collection no.: DSM 25660, JCM 18212, KACC 16593, MIC 3010
straininfo link
- @ref: 87996
- straininfo: 408227
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22904217 | Flavobacterium fontis sp. nov., isolated from freshwater. | Chun J, Kang JY, Jahng KY | Int J Syst Evol Microbiol | 10.1099/ijs.0.045203-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/analysis, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 26769164 | Flavobacterium lutivivi sp. nov., isolated from activated sludge. | Feng Q, Han L, Nogi Y, Hong Q, Lv J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000892 | 2016 | ||
| Phylogeny | 31157614 | Flavobacterium stagni sp. nov., isolated from a freshwater reservoir. | Chen WM, Guo YP, Kwon SW, Sheu C, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003488 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 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 | ||||
| 20569 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25660 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25660) | ||||
| 30818 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27149 | 28776041 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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 | ||||
| 87996 | 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-ID408227.1 |