Strain identifier
BacDive ID: 5536
Type strain: 
Species: Flavobacterium degerlachei
Strain Designation: R-9106
Strain history: <- S. Van Trappen, Univ. Ghent, Belgium; R-9106
NCBI tax ID(s): 229203 (species)
version 9.3 (current version)
General
@ref: 6076
BacDive-ID: 5536
DSM-Number: 15718
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, rod-shaped
description: Flavobacterium degerlachei R-9106 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from microbial mat.
NCBI tax id
- NCBI tax id: 229203
- Matching level: species
strain history
- @ref: 6076
- history: <- S. Van Trappen, Univ. Ghent, Belgium; R-9106
doi: 10.13145/bacdive5536.20250331.9.3
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 degerlachei
- full scientific name: Flavobacterium degerlachei Van Trappen et al. 2004
@ref: 6076
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium degerlachei
full scientific name: Flavobacterium degerlachei Van Trappen et al. 2004
strain designation: R-9106
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 30030 | negative | 03-04 µm | rod-shaped | ||
| 125438 | no | 92 | |||
| 125438 | negative | 99 | |||
| 125439 | negative | 99.8 |
pigmentation
- @ref: 30030
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 6076 | 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 |
| 41927 | MEDIUM 372 - for Aquabacterium | yes | Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Tween 80 (1.000 ml);Casamino acids (0.500 g);Proteose Peptone N°3 (0.500 g);Di Potassium mon |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 6076 | positive | growth | 20 |
| 30030 | positive | growth | 05-30 |
| 30030 | positive | optimum | 20 |
| 41927 | positive | growth | 22 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 93.747 |
| 125439 | no | 98.7 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30030 | NaCl | positive | growth | 0-5 % |
| 30030 | NaCl | positive | optimum | 2.5 % |
observation
- @ref: 30030
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30030 | 17234 | glucose | + | carbon source |
| 30030 | 17306 | maltose | + | carbon source |
| 30030 | 37684 | mannose | + | carbon source |
| 30030 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30030 | catalase | + | 1.11.1.6 |
| 30030 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 6076
- sample type: microbial mat
- geographic location: Vestfold Hills, Lake Ace
- continent: Australia and Oceania
isolation source categories
- Cat1: #Environmental
- Cat2: #Microbial community
- Cat3: #Microbial mat
taxonmaps
- @ref: 69479
- File name: preview.99_50746.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_163;97_1340;98_1624;99_50746&stattab=map
- Last taxonomy: Flavobacterium degerlachei
- 16S sequence: AJ557886
- Sequence Identity:
- Total samples: 1210
- soil counts: 101
- aquatic counts: 985
- animal counts: 105
- plant counts: 19
Safety information
risk assessment
- @ref: 6076
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6076
- description: Flavobacterium degerlachei 16S rRNA gene, strain LMG 21915
- accession: AJ557886
- length: 1475
- database: nuccore
- NCBI tax ID: 229203
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Flavobacterium degerlachei DSM 15718 | GCA_900106645 | scaffold | ncbi | 229203 |
| 66792 | Flavobacterium degerlachei strain DSM 15718 | 229203.5 | wgs | patric | 229203 |
| 66792 | Flavobacterium degerlachei DSM 15718 | 2693429883 | draft | img | 229203 |
GC content
- @ref: 30030
- GC-content: 33.8-34.2
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.105 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.712 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.747 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.222 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 92 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 66.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97 |
External links
@ref: 6076
culture collection no.: DSM 15718, CIP 108386, LMG 21915
straininfo link
- @ref: 75019
- straininfo: 22881
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 14742463 | Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. | Van Trappen S, Vandecandelaere I, Mergaert J, Swings J | Int J Syst Evol Microbiol | 10.1099/ijs.0.02857-0 | 2004 | Antarctic Regions, Classification, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/growth & development/isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics | Genetics |
| Phylogeny | 32038005 | Flavobacterium sandaracinum sp. nov., Flavobacterium caseinilyticum sp. nov., and Flavobacterium hiemivividum sp. nov., novel psychrophilic bacteria isolated from Arctic soil. | Chaudhary DK, Dahal RH, Kim DU, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004031 | 2020 | Arctic Regions, Bacterial Typing Techniques, Base Composition, Canada, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Norway, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6076 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15718) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15718 | |||
| 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 | |||
| 30030 | 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 | 26394 | 28776041 | |
| 41927 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6002 | ||||
| 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) | |||
| 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 | |||
| 75019 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID22881.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |