Strain identifier
BacDive ID: 5526
Type strain:
Species: Flavobacterium succinicans
Strain Designation: 8
Strain history: CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- H. Reichenbach: strain Cy su 3 <- J.T. Staley <- R.L. Anderson and E.J. Ordal: strain 8, Washington Univ., USA
NCBI tax ID(s): 1450525 (strain), 29536 (species)
General
@ref: 1569
BacDive-ID: 5526
DSM-Number: 4002
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped
description: Flavobacterium succinicans 8 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from eroded caudal fin of a fingerling chinook salmon.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1450525 | strain |
29536 | species |
strain history
@ref | history |
---|---|
1569 | <- H. Reichenbach, Cy su3 <- J.T. Staley <- R.L. Anderson, E.J. Ordal, 8 (Cytophaga succinicans) |
67770 | IAM 14311 <-- IFO 14905 <-- DSM 4002 ("Flexibacter succinicans") <-- H. Reichenbach Cy su3 <-- J. T. Staley <-- R. L. Anderson and E. J. Ordal 8. |
123365 | CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- H. Reichenbach: strain Cy su 3 <- J.T. Staley <- R.L. Anderson and E.J. Ordal: strain 8, Washington Univ., USA |
doi: 10.13145/bacdive5526.20230509.8.1
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 succinicans
- full scientific name: Flavobacterium succinicans (Reichenbach 1989 ex Anderson and Ordal 1961) Bernardet et al. 1996
synonyms
- @ref: 20215
- synonym: Cytophaga succinicans
@ref: 1569
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium succinicans
full scientific name: Flavobacterium succinicans (Reichenbach 1989) Bernardet et al. 1996
strain designation: 8
type strain: yes
Morphology
cell morphology
- @ref: 123365
- gram stain: negative
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1569 | CY-AGAR (DSMZ Medium 67) | yes | https://mediadive.dsmz.de/medium/67 | Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water |
39086 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
1569 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf | |
123365 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
123365 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1569 | positive | growth | 28 | mesophilic |
39086 | positive | growth | 22 | psychrophilic |
67770 | positive | growth | 25 | mesophilic |
123365 | positive | growth | 10-22 | psychrophilic |
123365 | no | growth | 30 | mesophilic |
123365 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
1569 | facultative anaerobe |
123365 | facultative anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123365 | NaCl | positive | growth | 0 % |
123365 | NaCl | no | growth | 2 % |
123365 | NaCl | no | growth | 4 % |
123365 | NaCl | no | growth | 6 % |
123365 | NaCl | no | growth | 8 % |
123365 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | starch | + | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
123365 | citrate | - | carbon source | 16947 |
123365 | glucose | - | fermentation | 17234 |
123365 | lactose | - | fermentation | 17716 |
123365 | nitrate | + | reduction | 17632 |
123365 | nitrite | - | reduction | 16301 |
123365 | sodium thiosulfate | - | builds gas from | 132112 |
metabolite production
- @ref: 123365
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
123365 | oxidase | - | |
123365 | beta-galactosidase | + | 3.2.1.23 |
123365 | alcohol dehydrogenase | - | 1.1.1.1 |
123365 | gelatinase | - | |
123365 | DNase | + | |
123365 | caseinase | - | 3.4.21.50 |
123365 | catalase | - | 1.11.1.6 |
123365 | gamma-glutamyltransferase | + | 2.3.2.2 |
123365 | lecithinase | - | |
123365 | lysine decarboxylase | - | 4.1.1.18 |
123365 | ornithine decarboxylase | - | 4.1.1.17 |
123365 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123365 | tryptophan deaminase | - | |
123365 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123365 | - | + | + | + | - | + | + | + | - | - | + | + | - | - | - | + | + | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123365 | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | + | - | + | - | - | + | + | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - | - | - | +/- |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123365 | + | - | + | - | - | - | - | - | - | + | + | - | - | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
1569 | eroded caudal fin of a fingerling chinook salmon | Washington | USA | USA | North America | |
67770 | Eroded caudal fin of a fingerling chinook salmon inflicted with furunculosis disease | University of Washington, Hatchery | USA | USA | North America | |
123365 | Animal, Eroded caudal fin of a farmed chinook salmon | Washington | United States of America | USA | North America | 1954 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Fishes | #Salmonidae |
#Host Body-Site | #Limb |
taxonmaps
- @ref: 69479
- File name: preview.99_1141.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_352;97_772;98_895;99_1141&stattab=map
- Last taxonomy: Flavobacterium
- 16S sequence: AM230492
- Sequence Identity:
- Total samples: 4251
- soil counts: 465
- aquatic counts: 2713
- animal counts: 986
- plant counts: 87
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1569 | 1 | Risk group (German classification) |
123365 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Flavobacterium succinicans strain DSM 4002 16S ribosomal RNA gene, partial sequence | JX657046 | 1256 | ena | 29536 |
20218 | Flavobacterium succinicans gene for 16S ribosomal RNA, partial sequence, strain: IFO 14905 | D12673 | 1256 | ena | 29536 |
1569 | Flavobacterium succinicans partial 16S rRNA gene, type strain DSM 4002 | AM230492 | 1501 | ena | 29536 |
1569 | Flavobacterium succinicans gene for 16S rRNA, partial sequence, strain: NBRC 14905 | AB680695 | 1439 | ena | 29536 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium succinicans LMG 10402 | 1450525.5 | wgs | patric | 1450525 |
66792 | Flavobacterium succinicans strain DSM 4002 | 29536.15 | wgs | patric | 29536 |
66792 | Flavobacterium succinicans DSM 4002 | 2693429891 | draft | img | 29536 |
66792 | Flavobacterium succinicans LMG 10402 | 2585427837 | draft | img | 1450525 |
67770 | Flavobacterium succinicans DSM 4002 | GCA_900114945 | scaffold | ncbi | 29536 |
67770 | Flavobacterium succinicans LMG 10402 | GCA_000611675 | contig | ncbi | 1450525 |
GC content
@ref | GC-content |
---|---|
1569 | 38.0 |
1569 | 35.0 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 90.542 | no |
gram-positive | no | 98.187 | no |
anaerobic | no | 98.891 | no |
halophile | no | 97.241 | no |
spore-forming | no | 94.394 | no |
glucose-util | yes | 88.535 | no |
thermophile | no | 98.983 | no |
aerobic | yes | 71.895 | yes |
flagellated | no | 94.874 | no |
glucose-ferment | no | 88.434 | no |
External links
@ref: 1569
culture collection no.: DSM 4002, IAM 14311, IFO 14905, NBRC 14905, Cy su3, JCM 21151, BCRC 81041, CIP 104744, LMG 10402, NCIMB 2277, Cy su 3
straininfo link
- @ref: 75009
- straininfo: 10490
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25563922 | Flavobacterium palustre sp. nov., isolated from wetland soil. | Feng H, Zeng Y, Huang Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.000054 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *Wetlands | Genetics |
Phylogeny | 28671526 | Flavobacterium keumense sp. nov., isolated from freshwater. | Ekwe AP, Ahn JH, Kim SB | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001920 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 30320544 | Flavobacterium riviphilum sp. nov., isolated from a freshwater creek. | Sheu SY, Su CL, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003070 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Water Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1569 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4002) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4002 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
39086 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16686 | ||||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
75009 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10490.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123365 | Curators of the CIP | Collection of Institut Pasteur (CIP 104744) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104744 |