Strain identifier
BacDive ID: 134059
Type strain:
Species: Flavobacterium ginsengisoli
Strain history: CIP <- 2014, JCM <- 2010, DC. Yang, Kyung Hee Univ., Gyeonggi-do, Korea: strain DCY54
NCBI tax ID(s): 871694 (species)
General
@ref: 31154
BacDive-ID: 134059
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Flavobacterium ginsengisoli KCTC 23318 is an aerobe, Gram-negative, motile bacterium that was isolated from Soil of a field cultivated with ginseng.
NCBI tax id
- NCBI tax id: 871694
- Matching level: species
strain history
@ref | history |
---|---|
67770 | D.-C. Yang DCY54. |
67771 | <- YJ KIm, Kyunghee Univ. |
119626 | CIP <- 2014, JCM <- 2010, DC. Yang, Kyung Hee Univ., Gyeonggi-do, Korea: strain DCY54 |
doi: 10.13145/bacdive134059.20230509.8.1
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 ginsengisoli
- full scientific name: Flavobacterium ginsengisoli Kim et al. 2013
@ref: 31154
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium ginsengisoli
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
31154 | negative | 3.85 µm | 0.75 µm | rod-shaped | yes | gliding |
67771 | rod-shaped | yes | gliding | |||
67771 | negative | |||||
119626 | negative | rod-shaped | no |
pigmentation
- @ref: 31154
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
41606 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
119626 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
31154 | positive | growth | 04-35 | |
31154 | positive | optimum | 27.5 | mesophilic |
41606 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31154 | positive | growth | 05-09 | alkaliphile |
31154 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31154 | aerobe |
67771 | aerobe |
spore formation
- @ref: 31154
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31154 | NaCl | positive | growth | 0-2 % |
31154 | NaCl | positive | optimum | 0.5 % |
observation
@ref | observation |
---|---|
31154 | aggregates in clumps |
67771 | quinones: MK-6 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31154 | 22599 | arabinose | + | carbon source |
31154 | 17234 | glucose | + | carbon source |
31154 | 17306 | maltose | + | carbon source |
31154 | 37684 | mannose | + | carbon source |
31154 | 506227 | N-acetylglucosamine | + | carbon source |
31154 | 4853 | esculin | + | hydrolysis |
31154 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31154 | acid phosphatase | + | 3.1.3.2 |
31154 | alkaline phosphatase | + | 3.1.3.1 |
31154 | alpha-galactosidase | + | 3.2.1.22 |
31154 | catalase | + | 1.11.1.6 |
31154 | gelatinase | + | |
31154 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
67770 | Soil of a field cultivated with ginseng | Yongin Province | Republic of Korea | KOR | Asia |
67771 | From soil of a field cultivated with ginseng | Yongin province | Republic of Korea | KOR | Asia |
119626 | Environment, Soil of a field cultivated with ginseng | Yongin Province | Republic of Korea | KOR | Asia |
taxonmaps
- @ref: 69479
- File name: preview.99_159038.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_207;97_5673;98_38607;99_159038&stattab=map
- Last taxonomy: Flavobacterium
- 16S sequence: HM776705
- Sequence Identity:
- Total samples: 30
- soil counts: 15
- aquatic counts: 12
- animal counts: 2
- plant counts: 1
Safety information
risk assessment
- @ref: 119626
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 31154
- description: Flavobacterium ginsengisoli strain DCY54 16S ribosomal RNA gene, partial sequence
- accession: HM776705
- length: 1408
- database: nuccore
- NCBI tax ID: 871694
Genome sequences
- @ref: 66792
- description: Flavobacterium ginsengisoli KCTC 23318
- accession: GCA_029625315
- assembly level: complete
- database: ncbi
- NCBI tax ID: 871694
GC content
- @ref: 31154
- GC-content: 33.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 89.626 | no |
flagellated | no | 94.514 | no |
gram-positive | no | 97.193 | yes |
anaerobic | no | 98.393 | yes |
aerobic | yes | 81.786 | no |
halophile | no | 92.97 | no |
spore-forming | no | 94.077 | yes |
glucose-ferment | no | 84.098 | no |
thermophile | no | 97.483 | no |
glucose-util | yes | 88.711 | yes |
External links
@ref: 31154
culture collection no.: KCTC 23318, JCM 17336, DCY 54, BCRC 81040, CIP 110819
straininfo link
- @ref: 91686
- straininfo: 413994
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23912719 | Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field. | Kim YJ, Kim SR, Nguyen NL, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.053819-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 25563919 | Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil. | Ngo HTT, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.000051 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 29498618 | Flavobacterium fluviatile sp. nov., isolated from a freshwater creek. | Chen WM, Su CL, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002659 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/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, *Water Microbiology | Transcriptome |
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | |||
31154 | 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 | 27482 | 28776041 | |
41606 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/30632 | ||||
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/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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/ | |||
91686 | 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-ID413994.1 | |||
119626 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110819 | Collection of Institut Pasteur (CIP 110819) |