Strain identifier
BacDive ID: 131394
Type strain: 
Species: Gemmatimonas phototrophica
Strain Designation: AP64
Strain history: <- Y. Zeng, Academy of Science, Inst. of Microbiol., Trebon, Czech Republic; AP64
NCBI tax ID(s): 1379270 (species)
version 8.1 (current version)
General
@ref: 22621
BacDive-ID: 131394
DSM-Number: 29774
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative
description: Gemmatimonas phototrophica AP64 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from near-shore water from a freshwater desert lake.
NCBI tax id
- NCBI tax id: 1379270
- Matching level: species
strain history
- @ref: 22621
- history: <- Y. Zeng, Academy of Science, Inst. of Microbiol., Trebon, Czech Republic; AP64
doi: 10.13145/bacdive131394.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/gemmatimonadota
- domain: Bacteria
- phylum: Gemmatimonadota
- class: Gemmatimonadia
- order: Gemmatimonadales
- family: Gemmatimonadaceae
- genus: Gemmatimonas
- species: Gemmatimonas phototrophica
- full scientific name: Gemmatimonas phototrophica Zeng et al. 2015
@ref: 22621
domain: Bacteria
phylum: Gemmatimonadetes
class: Gemmatimonadetes
order: Gemmatimonadales
family: Gemmatimonadaceae
genus: Gemmatimonas
species: Gemmatimonas phototrophica
full scientific name: Gemmatimonas phototrophica Zeng et al. 2017
strain designation: AP64
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.951
Culture and growth conditions
culture medium
- @ref: 22621
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: 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
culture temp
- @ref: 22621
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 22621
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 94 |
| 69480 | no | 99.983 |
Isolation, sampling and environmental information
isolation
- @ref: 22621
- sample type: near-shore water from a freshwater desert lake
- geographic location: Inner Mongolia, western Gobi Desert, Swan Lake (42.005 N, 101.585 E) at a depth of 0.5 m
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 42.005
- longitude: 101.585
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Terrestrial | #Desert |
taxonmaps
- @ref: 69479
- File name: preview.99_151.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_51;96_112;97_119;98_132;99_151&stattab=map
- Last taxonomy: Gemmatimonas phototrophica subclade
- 16S sequence: KF481682
- Sequence Identity:
- Total samples: 6668
- soil counts: 1795
- aquatic counts: 4358
- animal counts: 307
- plant counts: 208
Safety information
risk assessment
- @ref: 22621
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22621
- description: Gemmatimonas phototrophica strain AP64 16S ribosomal RNA gene, complete sequence
- accession: KF481682
- length: 1525
- database: ena
- NCBI tax ID: 1379270
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gemmatimonas phototrophica AP64 | GCA_000695095 | complete | ncbi | 1379270 |
| 66792 | Gemmatimonas phototrophica AP64 | 2775507241 | complete | img | 1379270 |
GC content
- @ref: 22621
- GC-content: 64.4
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 94 | no |
| motile | yes | 69.889 | no |
| motile | yes | 69.889 | no |
| flagellated | no | 81.275 | no |
| flagellated | no | 81.275 | no |
| gram-positive | no | 97.358 | no |
| gram-positive | no | 97.358 | no |
| anaerobic | no | 97.321 | yes |
| anaerobic | no | 97.321 | yes |
| halophile | no | 93.187 | no |
| halophile | no | 93.187 | no |
| spore-forming | no | 93.352 | no |
| spore-forming | no | 93.352 | no |
| glucose-util | yes | 76.279 | no |
| glucose-util | yes | 76.279 | no |
| aerobic | yes | 72.726 | no |
| aerobic | yes | 72.726 | no |
| thermophile | no | 85.548 | yes |
| thermophile | no | 85.548 | yes |
| glucose-ferment | no | 90.34 | no |
| glucose-ferment | no | 90.34 | no |
External links
@ref: 22621
culture collection no.: DSM 29774, MCCC 1K00455
straininfo link
- @ref: 89827
- straininfo: 401767
literature
- topic: Phylogeny
- Pubmed-ID: 25899503
- title: Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca.
- authors: Zeng Y, Selyanin V, Lukes M, Dean J, Kaftan D, Feng F, Koblizek M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000272
- year: 2015
- mesh: Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, Base Sequence, China, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/chemistry, Fresh Water/microbiology, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/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 | |||
| 22621 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29774 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29774) | |||
| 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 | |
| 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 | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89827 | 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-ID401767.1 |