Strain identifier
BacDive ID: 24011
Type strain:
Species: Flammeovirga kamogawensis
Strain Designation: YS10
Strain history: IAM 15451 <-- S. Hosoya and A. Yokota YS10.
NCBI tax ID(s): 373891 (species)
General
@ref: 20563
BacDive-ID: 24011
DSM-Number: 26273
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Flammeovirga kamogawensis YS10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.
NCBI tax id
- NCBI tax id: 373891
- Matching level: species
strain history
@ref | history |
---|---|
20563 | <- JCM <- IAM <- S. Hosoya and A. Yokota, Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan; YS10 |
67770 | IAM 15451 <-- S. Hosoya and A. Yokota YS10. |
doi: 10.13145/bacdive24011.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Flammeovirgaceae
- genus: Flammeovirga
- species: Flammeovirga kamogawensis
- full scientific name: Flammeovirga kamogawensis Hosoya and Yokota 2007
@ref: 20563
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Flammeovirgaceae
genus: Flammeovirga
species: Flammeovirga kamogawensis
full scientific name: Flammeovirga kamogawensis Hosoya and Yokota 2007
strain designation: YS10
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
32110 | negative | 02-40 µm | 0.6-1 µm | rod-shaped | yes | gliding | |
69480 | negative | 99.911 |
pigmentation
- @ref: 32110
- production: yes
Culture and growth conditions
culture medium
- @ref: 20563
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20563 | positive | growth | 28 | mesophilic |
32110 | positive | growth | 15-30 | |
32110 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32110 | positive | growth | 06-08 |
32110 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32110
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32110 | no | |
69481 | no | 100 |
69480 | no | 99.983 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32110 | NaCl | positive | growth | 02-04 % |
32110 | NaCl | positive | optimum | 3 % |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32110 | 17057 | cellobiose | + | carbon source |
32110 | 28260 | galactose | + | carbon source |
32110 | 17234 | glucose | + | carbon source |
32110 | 17716 | lactose | + | carbon source |
32110 | 17306 | maltose | + | carbon source |
32110 | 37684 | mannose | + | carbon source |
32110 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 32110
- value: alkaline phosphatase
- activity: +
- ec: 3.1.3.1
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
20563 | coastal seawater | Kamogawa, Yoshiura | Japan | JPN | Asia |
67770 | Coastal seawater off Yoshiura | Kamogawa | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_45735.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16066;96_20929;97_26070;98_33127;99_45735&stattab=map
- Last taxonomy: Flammeovirga kamogawensis subclade
- 16S sequence: AB251933
- Sequence Identity:
- Total samples: 618
- soil counts: 4
- aquatic counts: 571
- animal counts: 43
Safety information
risk assessment
- @ref: 20563
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20563
- description: Flammeovirga kamogawensis gene for 16S rRNA, partial sequence, strain: YS10
- accession: AB251933
- length: 1466
- database: ena
- NCBI tax ID: 373891
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flammeovirga kamogawensis YS10 | GCA_018736065 | complete | ncbi | 373891 |
66792 | Flammeovirga kamogawensis YS10 | GCA_007097495 | contig | ncbi | 373891 |
66792 | Flammeovirga kamogawensis DSM 26273 | GCA_014207545 | scaffold | ncbi | 373891 |
66792 | Flammeovirga kamogawensis strain DSM 26273 | 373891.5 | wgs | patric | 373891 |
66792 | Flammeovirga kamogawensis strain YS10 | 373891.4 | wgs | patric | 373891 |
66792 | Flammeovirga kamogawensis DSM 26273 | 2861514905 | draft | img | 373891 |
GC content
@ref | GC-content | method |
---|---|---|
20563 | 32-33 | high performance liquid chromatography (HPLC) |
32110 | 32-33 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 91.841 | yes |
gram-positive | no | 98.389 | no |
anaerobic | no | 96.879 | yes |
aerobic | yes | 79.245 | yes |
halophile | no | 79.413 | no |
spore-forming | no | 91.162 | yes |
thermophile | no | 97.821 | yes |
motile | no | 84.828 | no |
glucose-util | yes | 85.026 | no |
glucose-ferment | no | 78.329 | no |
External links
@ref: 20563
culture collection no.: DSM 26273, IAM 15451, JCM 23196, NCIMB 14281
straininfo link
- @ref: 87985
- straininfo: 309447
literature
- topic: Phylogeny
- Pubmed-ID: 17551052
- title: Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan.
- authors: Hosoya S, Yokota A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64977-0
- year: 2007
- mesh: Agar/metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Japan, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
- topic2: Metabolism
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
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 | |||
20563 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26273 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26273) | |||
32110 | 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 | 28355 | 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 | |||
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 | |||
87985 | 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-ID309447.1 |