Strain identifier
BacDive ID: 24488
Type strain: 
Species: Gemmobacter megaterium
Strain Designation: CF17
Strain history: X.-Q. Zhang CF17.
NCBI tax ID(s): 1086013 (species)
version 8.1 (current version)
General
@ref: 20578
BacDive-ID: 24488
DSM-Number: 26375
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Gemmobacter megaterium CF17 is a mesophilic, Gram-negative bacterium that was isolated from planktonic seaweed from coastal seawater.
NCBI tax id
- NCBI tax id: 1086013
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20578 | <- J. Liu, Zhejiang Univ., College of Life Scs., Hangzhou, China; CF17 <- F.-T. Chi |
| 67770 | X.-Q. Zhang CF17. |
doi: 10.13145/bacdive24488.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Gemmobacter
- species: Gemmobacter megaterium
- full scientific name: Gemmobacter megaterium Liu et al. 2014
synonyms
- @ref: 20215
- synonym: Wagnerdoeblera megaterium
@ref: 20578
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Gemmobacter
species: Gemmobacter megaterium
full scientific name: Gemmobacter megaterium Liu et al. 2014
strain designation: CF17
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 20578 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
| 20578 | ONR7a MEDIUM (DSMZ Medium 950) | yes | https://mediadive.dsmz.de/medium/950 | Name: ONR7a MEDIUM (DSMZ Medium 950; with strain-specific modifications) Composition: NaCl 22.79 g/l Agar 15.0 g/l Agarose 12.0 g/l MgCl2 x 6 H2O 11.18 g/l Sodium pyruvate 10.0 g/l Na2SO4 3.98 g/l CaCl2 x 2 H2O 1.46 g/l TAPSO 1.3 g/l KCl 0.72 g/l NH4Cl 0.27 g/l Na2HPO4 x 7 H2O 0.089 g/l NaBr 0.083 g/l NaHCO3 0.031 g/l H3BO3 0.027 g/l SrCl2 x 6 H2O 0.024 g/l NaF 0.0026 g/l FeCl2 x 4 H2O 0.002 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20578 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 27 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.996
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 20578 | planktonic seaweed from coastal seawater | East China Sea, Zhoushan sea area | China | CHN | Asia |
| 67770 | Coastal planktonic seaweeds | East China Sea |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Coast |
| #Host | #Algae |
taxonmaps
- @ref: 69479
- File name: preview.99_5155.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_1078;98_3842;99_5155&stattab=map
- Last taxonomy: Gemmobacter megaterium subclade
- 16S sequence: JN620361
- Sequence Identity:
- Total samples: 110
- soil counts: 6
- aquatic counts: 85
- animal counts: 17
- plant counts: 2
Safety information
risk assessment
- @ref: 20578
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20578
- description: Gemmobacter megaterium strain CF17 16S ribosomal RNA gene, partial sequence
- accession: JN620361
- length: 1428
- database: ena
- NCBI tax ID: 1086013
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gemmobacter megaterium CGMCC 1.11024 | GCA_014636395 | scaffold | ncbi | 1086013 |
| 66792 | Gemmobacter megaterium strain CGMCC 1.11024 | 1086013.8 | wgs | patric | 1086013 |
| 66792 | Gemmobacter megaterium strain DSM 26375 | 1086013.3 | wgs | patric | 1086013 |
| 66792 | Gemmobacter megaterium DSM 26375 | 2681813556 | draft | img | 1086013 |
| 67770 | Gemmobacter megaterium DSM 26375 | GCA_900156815 | contig | ncbi | 1086013 |
GC content
- @ref: 20578
- GC-content: 61.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 69 | no |
| flagellated | no | 90.577 | no |
| gram-positive | no | 98.094 | no |
| anaerobic | no | 98.444 | no |
| aerobic | yes | 89.47 | no |
| halophile | no | 56.505 | no |
| spore-forming | no | 95.813 | no |
| glucose-util | yes | 51.661 | no |
| thermophile | no | 97.507 | yes |
| motile | no | 66.344 | no |
| glucose-ferment | no | 89.77 | no |
External links
@ref: 20578
culture collection no.: DSM 26375, CGMCC 1.11024, JCM 18498
straininfo link
- @ref: 88348
- straininfo: 407198
literature
- topic: Phylogeny
- Pubmed-ID: 24014623
- title: Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds.
- authors: Liu JJ, Zhang XQ, Chi FT, Pan J, Sun C, Wu M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.050955-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater, Seaweed/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20578 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26375 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26375) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 88348 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407198.1 |