Strain identifier
BacDive ID: 13877
Type strain: 
Species: Tepidamorphus gemmatus
Strain Designation: CB-27A
Strain history: <- M. da Costa, Univ. Coimbra, Portugal; CB-27A <- L. Albuquerque
NCBI tax ID(s): 747076 (species)
version 8.1 (current version)
General
@ref: 8061
BacDive-ID: 13877
DSM-Number: 19345
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Tepidamorphus gemmatus CB-27A is a thermophilic, Gram-negative bacterium that was isolated from runoff of a hot spring.
NCBI tax id
- NCBI tax id: 747076
- Matching level: species
strain history
- @ref: 8061
- history: <- M. da Costa, Univ. Coimbra, Portugal; CB-27A <- L. Albuquerque
doi: 10.13145/bacdive13877.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Tepidamorphaceae
- genus: Tepidamorphus
- species: Tepidamorphus gemmatus
- full scientific name: Tepidamorphus gemmatus Albuquerque et al. 2010
@ref: 8061
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Tepidamorphaceae
genus: Tepidamorphus
species: Tepidamorphus gemmatus
full scientific name: Tepidamorphus gemmatus Albuquerque et al. 2010
strain designation: CB-27A
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.99
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 8061 | 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 |
| 8061 | THERMUS 162 MEDIUM (DSMZ Medium 878) | yes | https://mediadive.dsmz.de/medium/878 | Name: THERMUS 162 MEDIUM (DSMZ Medium 878) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l ZnSO4 x 7 H2O 0.00025 g/l H3BO3 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water |
culture temp
- @ref: 8061
- growth: positive
- type: growth
- temperature: 50
- range: thermophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
Isolation, sampling and environmental information
isolation
- @ref: 8061
- sample type: runoff of a hot spring
- geographic location: Azores, Island of São Miguel, Furnas, Caldeira daBarrela
- country: Portugal
- origin.country: PRT
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_94703.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_38860;97_49493;98_65060;99_94703&stattab=map
- Last taxonomy: Tepidamorphus gemmatus subclade
- 16S sequence: GU187912
- Sequence Identity:
- Total samples: 1732
- soil counts: 699
- aquatic counts: 789
- animal counts: 127
- plant counts: 117
Safety information
risk assessment
- @ref: 8061
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8061
- description: Tepidamorphus gemmatus strain CB-27A 16S ribosomal RNA gene, partial sequence
- accession: GU187912
- length: 1391
- database: ena
- NCBI tax ID: 747076
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tepidamorphus gemmatus DSM 19345 | GCA_004346195 | scaffold | ncbi | 747076 |
| 66792 | Tepidamorphus gemmatus strain DSM 19345 | 747076.3 | wgs | patric | 747076 |
| 66792 | Tepidamorphus gemmatus DSM 19345 | 2784746801 | draft | img | 747076 |
GC content
- @ref: 8061
- GC-content: 66.9±0.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 86.468 | no |
| flagellated | no | 56.633 | no |
| gram-positive | no | 98.72 | no |
| anaerobic | no | 95.204 | no |
| aerobic | yes | 84.418 | no |
| halophile | no | 61.557 | no |
| spore-forming | no | 97.2 | no |
| glucose-util | yes | 72.77 | no |
| thermophile | no | 59.469 | yes |
| glucose-ferment | no | 92.123 | no |
External links
@ref: 8061
culture collection no.: DSM 19345, LMG 24113
straininfo link
- @ref: 83052
- straininfo: 400772
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20116192 | Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. | Albuquerque L, Rainey FA, Pena A, Tiago I, Verissimo A, Nobre MF, da Costa MS | Syst Appl Microbiol | 10.1016/j.syapm.2010.01.002 | 2010 | Alphaproteobacteria/*classification/genetics/isolation & purification/*physiology, Azores, Bacterial Proteins/metabolism, Bacterial Typing Techniques, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hot Springs/*microbiology, Hot Temperature, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| Phylogeny | 27902327 | Microbaculum marinum gen. nov., sp. nov., isolated from deep seawater. | Su Y, Han S, Wang R, Yu X, Fu G, Chen C, Zhang C, Li Y, Sun C, Wu M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001647 | 2017 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 28829015 | Butyratibacter algicola gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. | Wang G, Wang Y, Su H, Wu H, Li T, Liang J, Huang W, Xiang W, Yu K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002081 | 2017 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chlorophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8061 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19345) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19345 | |||
| 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 | |||
| 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) | |||
| 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 | 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. | 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 | |||
| 83052 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400772.1 | StrainInfo: A central database for resolving microbial strain identifiers |