Strain identifier
BacDive ID: 5565
Type strain:
Species: Flavobacterium cucumis
Strain Designation: R2A45-3
Strain history: CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18830
NCBI tax ID(s): 416016 (species)
General
@ref: 7727
BacDive-ID: 5565
DSM-Number: 18830
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Flavobacterium cucumis R2A45-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil cultivated with cucumber.
NCBI tax id
- NCBI tax id: 416016
- Matching level: species
strain history
@ref | history |
---|---|
7727 | <- S.-W. Kwon, KACC; R2A45-3 <- H.-Y. Weon et al., Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea |
118807 | CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18830 |
doi: 10.13145/bacdive5565.20230509.8.1
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 cucumis
- full scientific name: Flavobacterium cucumis Weon et al. 2007
@ref: 7727
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium cucumis
full scientific name: Flavobacterium cucumis Weon et al. 2007
strain designation: R2A45-3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
32083 | negative | 2.5 µm | 0.5 µm | rod-shaped | yes | gliding | |
69480 | negative | 99.998 | |||||
118807 | negative | rod-shaped | no |
pigmentation
- @ref: 32083
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7727 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
33335 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
118807 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7727 | positive | growth | 30 | mesophilic |
32083 | positive | growth | 05-37 | |
32083 | positive | optimum | 30 | mesophilic |
33335 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32083 | positive | growth | 06-08 |
32083 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32083 | aerobe |
118807 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32083 | no | |
69481 | no | 100 |
69480 | no | 99.998 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32083 | NaCl | positive | growth | 0-2 % |
32083 | NaCl | positive | optimum | 0-2 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32083 | 4853 | esculin | + | hydrolysis |
118807 | 17632 | nitrate | - | reduction |
118807 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 118807
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
32083 | acid phosphatase | + | 3.1.3.2 |
32083 | alkaline phosphatase | + | 3.1.3.1 |
32083 | alpha-galactosidase | + | 3.2.1.22 |
32083 | catalase | + | 1.11.1.6 |
32083 | cytochrome oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118807 | oxidase | + | |
118807 | catalase | + | 1.11.1.6 |
118807 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118807 | - | + | + | + | - | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
7727 | greenhouse soil cultivated with cucumber | Sangju region | Republic of Korea | KOR | Asia | |
118807 | Environment, Greenhouse soils | Suwon | Republic of Korea | KOR | Asia | 2007 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Greenhouse |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_1103.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_644;97_747;98_866;99_1103&stattab=map
- Last taxonomy: Flavobacterium
- 16S sequence: EF126993
- Sequence Identity:
- Total samples: 3245
- soil counts: 257
- aquatic counts: 2595
- animal counts: 363
- plant counts: 30
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7727 | 1 | Risk group (German classification) |
118807 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7727
- description: Flavobacterium cucumis strain R2A45-3 16S ribosomal RNA gene, partial sequence
- accession: EF126993
- length: 1439
- database: ena
- NCBI tax ID: 416016
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium cucumis DSM 18830 | GCA_900148835 | contig | ncbi | 416016 |
66792 | Flavobacterium cucumis strain DSM 18830 | 416016.4 | wgs | patric | 416016 |
66792 | Flavobacterium cucumis DSM 18830 | 2698536819 | draft | img | 416016 |
GC content
@ref | GC-content |
---|---|
7727 | 38.0 |
32083 | 38 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.916 | no |
anaerobic | no | 98.604 | yes |
halophile | no | 93.29 | no |
spore-forming | no | 95.501 | no |
glucose-util | yes | 84.901 | no |
aerobic | yes | 85.83 | no |
flagellated | no | 94.137 | yes |
thermophile | no | 98.247 | no |
motile | no | 89.818 | no |
glucose-ferment | no | 92.989 | no |
External links
@ref: 7727
culture collection no.: DSM 18830, CIP 109888, KACC 11732
straininfo link
- @ref: 75047
- straininfo: 309451
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17625200 | Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil. | Weon HY, Song MH, Son JA, Kim BY, Kwon SW, Go SJ, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.64935-0 | 2007 | Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology | Genetics |
Phylogeny | 18768627 | Flavobacterium cheniae sp. nov., isolated from sediment of a eutrophic reservoir. | Qu JH, Li HF, Yang JS, Yuan HL | Int J Syst Evol Microbiol | 10.1099/ijs.0.65586-0 | 2008 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Genetics |
Phylogeny | 19406812 | Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals. | Yoon HS, Aslam Z, Song GC, Kim SW, Jeon CO, Chon TS, Chung YR | Int J Syst Evol Microbiol | 10.1099/ijs.0.004978-0 | 2009 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Industrial Waste, Korea, *Metals, Heavy, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*chemistry/*microbiology, Sequence Analysis, DNA, Species Specificity, *Water Pollution, Chemical | Genetics |
Phylogeny | 23543500 | Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field. | Subhash Y, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.050047-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triterpenes/analysis, *Water Microbiology, beta Carotene/analysis | Genetics |
Phylogeny | 31758394 | Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. | Kim I, Kim J, Chhetri G, Seo T | J Microbiol | 10.1007/s12275-019-9350-x | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/*metabolism, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Pigments, Biological/*metabolism, Polyenes/*metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Metabolism |
Phylogeny | 35059830 | Flavobacterium proteolyticum sp. nov., isolated from aquaculture water. | Du J, Liu Y, Pei T, Li A, Deng MR, Zhu H | Arch Microbiol | 10.1007/s00203-021-02744-2 | 2022 | Aquaculture, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Flavobacterium/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water | Transcriptome |
Phylogeny | 35731344 | Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead). | Kang S, Lee JY, Han JE, Jeong YS, Gim DH, Bae JW | J Microbiol | 10.1007/s12275-022-2075-2 | 2022 | Animals, Bacterial Typing Techniques, Bivalvia, Cordyceps, DNA, Bacterial/genetics, *Fatty Acids/analysis, Fishes, *Flavobacterium, Intestines, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2 | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7727 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18830) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18830 | |||
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 | |||
32083 | 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 | 28329 | 28776041 | |
33335 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7683 | ||||
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) | |||
68382 | Automatically annotated from API zym | |||||
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 | |||
75047 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID309451.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118807 | Curators of the CIP | Collection of Institut Pasteur (CIP 109888) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109888 |