Strain identifier
BacDive ID: 5575
Type strain:
Species: Flavobacterium rivuli
Strain Designation: WB3.3-2
Strain history: CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB 3.3-2
NCBI tax ID(s): 1121895 (strain), 498301 (species)
General
@ref: 15951
BacDive-ID: 5575
DSM-Number: 21788
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Flavobacterium rivuli WB3.3-2 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from water of a hardwater creek.
NCBI tax id
NCBI tax id | Matching level |
---|---|
498301 | species |
1121895 | strain |
strain history
@ref | history |
---|---|
15951 | <- Z. Ali, DSMZ; WB3.3-2 <- E. Brambilla and O. Päuker, DSMZ |
122243 | CIP <- 2008, DSMZ <- Dr. Tindall, Germany: strain WB 3.3-2 |
doi: 10.13145/bacdive5575.20230509.8.1
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 rivuli
- full scientific name: Flavobacterium rivuli Ali et al. 2009
@ref: 15951
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium rivuli
full scientific name: Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013
strain designation: WB3.3-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29215 | negative | 2 µm | 0.5 µm | rod-shaped | no | |
69480 | negative | 99.998 | ||||
122243 | negative | rod-shaped | no |
colony morphology
- @ref: 61780
- incubation period: 1-2 days
pigmentation
- @ref: 29215
- production: no
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_21788_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21788_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21788_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21788_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21788_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21788_6.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15951 | 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 |
42068 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
122243 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15951 | positive | growth | 20 | psychrophilic |
29215 | positive | growth | 04-29 | |
29215 | positive | optimum | 16-24 | psychrophilic |
42068 | positive | growth | 25 | mesophilic |
61780 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29215 | positive | growth | 6.4-7.8 |
29215 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29215 | aerobe |
61780 | aerobe |
122243 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29215 | NaCl | positive | growth | 0-2 % |
29215 | NaCl | positive | optimum | 1 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29215 | 30089 | acetate | + | carbon source |
29215 | 22599 | arabinose | + | carbon source |
29215 | 17057 | cellobiose | + | carbon source |
29215 | 28757 | fructose | + | carbon source |
29215 | 28260 | galactose | + | carbon source |
29215 | 17234 | glucose | + | carbon source |
29215 | 17716 | lactose | + | carbon source |
29215 | 17306 | maltose | + | carbon source |
29215 | 37684 | mannose | + | carbon source |
29215 | 28053 | melibiose | + | carbon source |
29215 | 51850 | methyl pyruvate | + | carbon source |
29215 | 26271 | proline | + | carbon source |
29215 | 26986 | threonine | + | carbon source |
29215 | 27082 | trehalose | + | carbon source |
29215 | 53423 | tween 40 | + | carbon source |
29215 | 4853 | esculin | + | hydrolysis |
122243 | 17632 | nitrate | - | reduction |
122243 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
29215 | 16136 | hydrogen sulfide | yes |
122243 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29215 | catalase | + | 1.11.1.6 |
29215 | 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 |
122243 | oxidase | + | |
122243 | catalase | + | 1.11.1.6 |
122243 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122243 | - | + | - | + | - | + | + | - | - | - | + | + | + | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15951 | water of a hardwater creek | Harz Mountains, Westerhöfer Bach, Westerhof, 40 km north of Göttingen | Germany | DEU | Europe |
61780 | Water,hardwater creek | Westerhof,Harz Mountains | Germany | DEU | Europe |
122243 | Environment, Hard water, river | Westerhöfer Bach, Harz mountains | Germany | DEU | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
taxonmaps
- @ref: 69479
- File name: preview.99_2658.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1182;97_1690;98_2058;99_2658&stattab=map
- Last taxonomy: Flavobacterium
- 16S sequence: AM934661
- Sequence Identity:
- Total samples: 3441
- soil counts: 370
- aquatic counts: 1682
- animal counts: 1194
- plant counts: 195
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15951 | 1 | Risk group (German classification) |
122243 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 15951
- description: Flavobacterium rivuli partial 16S rRNA gene, type strain WB3.3-2T
- accession: AM934661
- length: 1488
- database: ena
- NCBI tax ID: 498301
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium rivuli WB 3.3-2 = DSM 21788 | GCA_000378485 | scaffold | ncbi | 1121895 |
66792 | Flavobacterium rivuli WB 3.3-2 = DSM 21788 | GCA_000769825 | contig | ncbi | 1121895 |
66792 | Flavobacterium rivuli DSM 21788 | 1121895.5 | wgs | patric | 1121895 |
66792 | Flavobacterium rivuli WB 3.3-2 = DSM 21788 | 1121895.7 | wgs | patric | 1121895 |
66792 | Flavobacterium rivuli DSM 21788 | 2519103183 | draft | img | 1121895 |
GC content
@ref | GC-content | method |
---|---|---|
15951 | 40.4 | high performance liquid chromatography (HPLC) |
29215 | 40.4 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.448 | no |
flagellated | no | 96.452 | yes |
gram-positive | no | 98.303 | no |
anaerobic | no | 99.449 | yes |
aerobic | yes | 90.722 | no |
halophile | no | 92.741 | yes |
spore-forming | no | 95.139 | no |
thermophile | no | 99.202 | no |
glucose-util | yes | 86.619 | yes |
glucose-ferment | no | 91.709 | no |
External links
@ref: 15951
culture collection no.: DSM 21788, CIP 109865, CCUG 58934, WB 3.3-2
straininfo link
- @ref: 75057
- straininfo: 363443
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19622646 | Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. | Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.008771-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/chemistry/classification/genetics/*isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
Genetics | 26380634 | High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. | Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Goker M, Kyrpides NC, Klenk HP | Stand Genomic Sci | 10.1186/s40793-015-0032-y | 2015 | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
15951 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21788) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21788 | ||||
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 | ||||
29215 | 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 | 25636 | 28776041 | ||
42068 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7658 | |||||
61780 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58934) | https://www.ccug.se/strain?id=58934 | ||||
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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
75057 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID363443.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
122243 | Curators of the CIP | Collection of Institut Pasteur (CIP 109865) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109865 |