Strain identifier
BacDive ID: 5703
Type strain:
Species: Chryseobacterium soli
Strain Designation: JS6-6
Strain history: CIP <- 2010, DSMZ <- KACC <- H.Y. Weon, Nat. Inst. Agric. Sci Technol., Suwon, Korea: strain JS6-6
NCBI tax ID(s): 445961 (species)
General
@ref: 8004
BacDive-ID: 5703
DSM-Number: 19298
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Chryseobacterium soli JS6-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample.
NCBI tax id
- NCBI tax id: 445961
- Matching level: species
strain history
@ref | history |
---|---|
8004 | <- S.-W. Kwon, KACC; JS6-6 <- H.-Y. Weon, Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea |
122656 | CIP <- 2010, DSMZ <- KACC <- H.Y. Weon, Nat. Inst. Agric. Sci Technol., Suwon, Korea: strain JS6-6 |
doi: 10.13145/bacdive5703.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Weeksellaceae
- genus: Chryseobacterium
- species: Chryseobacterium soli
- full scientific name: Chryseobacterium soli Weon et al. 2008
@ref: 8004
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium soli
full scientific name: Chryseobacterium soli Weon et al. 2008 emend. Hahnke et al. 2016
strain designation: JS6-6
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32310 | negative | 2.25 µm | 0.7 µm | rod-shaped | no | |
69480 | no | 91.63 | ||||
69480 | negative | 99.99 | ||||
122656 | negative | rod-shaped | no |
pigmentation
- @ref: 32310
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8004 | 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 |
40045 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
122656 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8004 | positive | growth | 30 | mesophilic |
32310 | positive | growth | 05-30 | |
32310 | positive | optimum | 29 | mesophilic |
40045 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32310 | positive | growth | 05-09 | alkaliphile |
32310 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32310 | aerobe |
122656 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
- @ref: 32310
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-3 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32310 | 28087 | glycogen | + | carbon source |
32310 | 17992 | sucrose | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
122656 | 17632 | nitrate | - | reduction |
122656 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 122656
- Chebi-ID: 35581
- metabolite: indole
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
32310 | catalase | + | 1.11.1.6 |
32310 | 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 |
122656 | oxidase | + | |
122656 | catalase | + | 1.11.1.6 |
122656 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122656 | - | + | + | + | + | + | + | + | + | - | + | + | - | - | - | + | - | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122656 | +/- | - | - | - | - | +/- | - | - | - | - | +/- | +/- | +/- | - | - | - | - | - | - | - | - | - | +/- | - | +/- | - | - | +/- | - | - | +/- | +/- | - | - | - | +/- | +/- | - | +/- | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
8004 | soil sample | Jeju | Republic of Korea | KOR | Asia |
122656 | Environment, Soil sample | Jeju Island | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_5979.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_3508;98_4440;99_5979&stattab=map
- Last taxonomy: Chryseobacterium soli subclade
- 16S sequence: EF591302
- Sequence Identity:
- Total samples: 887
- soil counts: 182
- aquatic counts: 215
- animal counts: 396
- plant counts: 94
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8004 | 1 | Risk group (German classification) |
122656 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 8004
- description: Chryseobacterium soli strain JS6-6 16S ribosomal RNA gene, partial sequence
- accession: EF591302
- length: 1390
- database: ena
- NCBI tax ID: 445961
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Chryseobacterium soli DSM 19298 | GCA_000737705 | contig | ncbi | 445961 |
66792 | Chryseobacterium soli strain DSM 19298 | 445961.5 | wgs | patric | 445961 |
66792 | Chryseobacterium soli DSM 19298 | 2617271210 | draft | img | 445961 |
GC content
@ref | GC-content | method |
---|---|---|
8004 | 39.9 | |
8004 | 36.4 | sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.157 | yes |
anaerobic | no | 99.643 | yes |
halophile | no | 94.565 | no |
spore-forming | no | 94.72 | no |
glucose-util | yes | 88.973 | no |
aerobic | yes | 92.784 | yes |
flagellated | no | 97.123 | no |
thermophile | no | 99.521 | no |
motile | no | 93.554 | yes |
glucose-ferment | no | 91.476 | no |
External links
@ref: 8004
culture collection no.: DSM 19298, KACC 12502, CIP 110182
straininfo link
- @ref: 75185
- straininfo: 323958
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18218951 | Chryseobacterium soli sp. nov. and Chryseobacterium jejuense sp. nov., isolated from soil samples from Jeju, Korea. | Weon HY, Kim BY, Yoo SH, Kwon SW, Stackebrandt E, Go SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.65295-0 | 2008 | Bacterial Typing Techniques, Base Composition, Chryseobacterium/classification/genetics/*isolation & purification/physiology, DNA, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
Phylogeny | 19643904 | Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish. | Ilardi P, Fernandez J, Avendano-Herrera R | Int J Syst Evol Microbiol | 10.1099/ijs.0.007021-0 | 2009 | Animals, Chryseobacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Salmonidae/microbiology | Metabolism |
Phylogeny | 20656821 | Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field. | Im WT, Yang JE, Kim SY, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.023614-0 | 2010 | Aerobiosis, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhus/growth & development, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, beta-Glucosidase/metabolism | Metabolism |
Phylogeny | 20889766 | Chryseobacterium piperi sp. nov., isolated from a freshwater creek. | Strahan BL, Failor KC, Batties AM, Hayes PS, Cicconi KM, Mason CT, Newman JD | Int J Syst Evol Microbiol | 10.1099/ijs.0.027805-0 | 2010 | Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Molecular Sequence Data, Pennsylvania, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 34345976 | Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis. | Zhang Z, Yang LL, Li CJ, Jiang XW, Zhi XY | Arch Microbiol | 10.1007/s00203-021-02504-2 | 2021 | Bacterial Typing Techniques, Base Composition, *Chryseobacterium/genetics, DNA, Bacterial/genetics, Fatty Acids, *Liliaceae, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2 | Transcriptome |
Phylogeny | 35503093 | Chryseobacterium subflavum sp. nov., isolated from soil. | Kong D, Wang Y, Li Q, Zhou Y, Jiang X, Xing Z, Wang Z, Ruan Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005345 | 2022 | Bacterial Typing Techniques, Base Composition, *Chryseobacterium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8004 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19298) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19298 | |||
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 | |||
32310 | 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 | 28548 | 28776041 | |
40045 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8012 | ||||
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) | |||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
75185 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID323958.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122656 | Curators of the CIP | Collection of Institut Pasteur (CIP 110182) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110182 |