Strain identifier
BacDive ID: 5531
Type strain:
Species: Flavobacterium hibernum
Strain Designation: LCI
Strain history: CIP <- 1998, JF. Bernardet, INRA, Jouy en Josas, France, "Flavobacterium ameridies" <- P. Franzmann <- Mc Cammon
NCBI tax ID(s): 37752 (species)
General
@ref: 4772
BacDive-ID: 5531
DSM-Number: 12611
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, psychrophilic, Gram-negative
description: Flavobacterium hibernum LCI is an obligate aerobe, psychrophilic, Gram-negative bacterium that was isolated from surface water.
NCBI tax id
- NCBI tax id: 37752
- Matching level: species
strain history
@ref | history |
---|---|
4772 | <- ACAM <- P. D. Franzmann; LCI |
119890 | CIP <- 1998, JF. Bernardet, INRA, Jouy en Josas, France, "Flavobacterium ameridies" <- P. Franzmann <- Mc Cammon |
doi: 10.13145/bacdive5531.20230509.8.1
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 hibernum
- full scientific name: Flavobacterium hibernum McCammon et al. 1998
@ref: 4772
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium hibernum
full scientific name: Flavobacterium hibernum McCammon et al. 1998
strain designation: LCI
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.996 | ||
119890 | negative | rod-shaped | yes |
colony morphology
- @ref: 119890
pigmentation
- @ref: 119890
- production: no
- name: Flexirubin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4772 | 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 |
32829 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
119890 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
119890 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4772 | positive | growth | 20 | psychrophilic |
32829 | positive | growth | 25 | mesophilic |
119890 | positive | growth | 5-30 | |
119890 | no | growth | 37 | mesophilic |
119890 | no | growth | 41 | thermophilic |
119890 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 119890
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
119890 | NaCl | positive | growth | 0 % |
119890 | NaCl | no | growth | 2 % |
119890 | NaCl | no | growth | 4 % |
119890 | NaCl | no | growth | 6 % |
119890 | NaCl | no | growth | 8 % |
119890 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
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 | 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 |
119890 | citrate | - | carbon source | 16947 |
119890 | esculin | + | hydrolysis | 4853 |
119890 | hippurate | - | hydrolysis | 606565 |
119890 | nitrate | - | builds gas from | 17632 |
119890 | nitrate | + | reduction | 17632 |
119890 | nitrite | - | builds gas from | 16301 |
119890 | nitrite | - | reduction | 16301 |
119890 | tributyrin | - | hydrolysis | 35020 |
119890 | malonate | - | assimilation | 15792 |
119890 | glucose | + | degradation | 17234 |
antibiotic resistance
- @ref: 119890
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 119890
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
119890 | 15688 | acetoin | - | |
119890 | 17234 | glucose | - |
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 |
119890 | oxidase | - | |
119890 | beta-galactosidase | + | 3.2.1.23 |
119890 | alcohol dehydrogenase | + | 1.1.1.1 |
119890 | gelatinase | +/- | |
119890 | amylase | + | |
119890 | DNase | - | |
119890 | caseinase | + | 3.4.21.50 |
119890 | catalase | + | 1.11.1.6 |
119890 | tween esterase | + | |
119890 | gamma-glutamyltransferase | + | 2.3.2.2 |
119890 | lecithinase | - | |
119890 | lipase | - | |
119890 | lysine decarboxylase | - | 4.1.1.18 |
119890 | ornithine decarboxylase | - | 4.1.1.17 |
119890 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
119890 | protease | - | |
119890 | tryptophan deaminase | - | |
119890 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119890 | - | + | + | + | + | + | + | + | - | + | + | + | - | + | - | + | + | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119890 | - | - | + | + | - | + | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | + | + | - | + | + | + | +/- | - | + | + | + | - | - | + | + | - | + | + | - | - | - | + | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119890 | - | - | + | - | - | - | - | - | + | + | - | - | - | - | - | + | + | + | + | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | latitude | longitude | country | origin.country |
---|---|---|---|---|---|---|---|
4772 | surface water | Vestfold Hills, Crooked Lake, 68°38'S, 18°17'E | Australia and Oceania | -68.6333 | 18.2833 | ||
119890 | Environment, Water, surface | Crooked lake | Antarctica | Antarctica | ATA |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Surface water
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4772 | 1 | Risk group (German classification) |
119890 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Flavobacterium hibernum 16S ribosomal RNA gene, partial sequence
- accession: L39067
- length: 1461
- database: ena
- NCBI tax ID: 37752
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium hibernum DSM 12611 | GCA_000832125 | contig | ncbi | 37752 |
66792 | Flavobacterium hibernum ATCC 51468 | GCA_002217315 | scaffold | ncbi | 37752 |
66792 | Flavobacterium hibernum DSM 12611 | 37752.5 | wgs | patric | 37752 |
66792 | Flavobacterium hibernum strain ATCC 51468 | 37752.9 | wgs | patric | 37752 |
66792 | Flavobacterium hibernum DSM 12611 | 2648501293 | draft | img | 37752 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 93.5 | no |
gram-positive | no | 98.095 | no |
anaerobic | no | 99.785 | no |
aerobic | yes | 92.405 | no |
halophile | no | 97.863 | no |
spore-forming | no | 93.94 | no |
thermophile | no | 99.651 | yes |
glucose-util | yes | 89.643 | no |
motile | no | 84.436 | no |
glucose-ferment | no | 87.724 | no |
External links
@ref: 4772
culture collection no.: DSM 12611, ACAM 376, ATCC 51468, CIP 105745
straininfo link
- @ref: 75014
- straininfo: 46908
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9828443 | Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. | McCammon SA, Innes BH, Bowman JP, Franzmann PD, Dobson SJ, Holloway PE, Skerratt JH, Nichols PD, Rankin LM | Int J Syst Bacteriol | 10.1099/00207713-48-4-1405 | 1998 | Antarctic Regions, Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Flavobacterium/*classification/enzymology/isolation & purification/physiology, Fresh Water/*microbiology, Lactose/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Terminology as Topic, *Water Microbiology, beta-Galactosidase/metabolism | Enzymology |
Phylogeny | 25313092 | Flavobacterium maotaiense sp. nov., isolated from freshwater. | Feng Q, Gao Y, Nogi Y, Tan X, Han L, Zhang Y, Lv J | Int J Syst Evol Microbiol | 10.1099/ijs.0.064139-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 29804222 | Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil. | Dahal RH, Kim J | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1105-x | 2018 | Bacterial Typing Techniques, Base Composition/genetics, Flavobacterium/*genetics/*metabolism, Genotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Urea/*metabolism | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4772 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12611) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12611 | |||
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 | |
32829 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17798 | ||||
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 | |||||
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 | |||
75014 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46908.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119890 | Curators of the CIP | Collection of Institut Pasteur (CIP 105745) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105745 |