Strain identifier
BacDive ID: 17795
Type strain:
Species: Rhodothermus profundi
Strain Designation: 2037 Souchothèque de Bretagne
Strain history: J.-L. Birrien PRI 2902.
NCBI tax ID(s): 633813 (species)
General
@ref: 16205
BacDive-ID: 17795
DSM-Number: 22212
keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-negative, rod-shaped
description: Rhodothermus profundi 2037 Souchothèque de Bretagne is an aerobe, thermophilic, Gram-negative bacterium that was isolated from hydrothermal chimney material.
NCBI tax id
- NCBI tax id: 633813
- Matching level: species
strain history
@ref | history |
---|---|
16205 | <- J.-L. Birrien, IUEM, Univ. Brest, Plouzané, France; PRI 2902 <- V. T. Marteinsson |
67770 | J.-L. Birrien PRI 2902. |
doi: 10.13145/bacdive17795.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/rhodothermota
- domain: Bacteria
- phylum: Rhodothermota
- class: Rhodothermia
- order: Rhodothermales
- family: Rhodothermaceae
- genus: Rhodothermus
- species: Rhodothermus profundi
- full scientific name: Rhodothermus profundi Marteinsson et al. 2010
@ref: 16205
domain: Bacteria
phylum: Rhodothermaeota
class: Rhodothermia
order: Cytophagales
family: Rhodothermaceae
genus: Rhodothermus
species: Rhodothermus profundi
full scientific name: Rhodothermus profundi Marteinsson et al. 2010
strain designation: 2037 Souchothèque de Bretagne
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29418 | negative | 1.5-3.5 µm | 0.5 µm | rod-shaped | no | |
69480 | negative | 99.74 |
pigmentation
- @ref: 29418
- production: yes
Culture and growth conditions
culture medium
- @ref: 16205
- name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514a
- composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 10.0 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
16205 | positive | growth | 70 | thermophilic | |
29418 | positive | growth | 55-80 | hyperthermophilic | |
29418 | positive | optimum | 70 | thermophilic | |
67770 | positive | growth | 70 | thermophilic | |
69480 | thermophilic | 98.658 |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29418 | positive | growth | 06-08 |
29418 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29418
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29418 | no | |
69480 | no | 99.935 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29418 | NaCl | positive | growth | 01-05 % |
29418 | NaCl | positive | optimum | 02-03 % |
observation
@ref | observation |
---|---|
29418 | aggregates in chains |
67770 | quinones: MK-7 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29418 | 22653 | asparagine | + | carbon source |
29418 | 35391 | aspartate | + | carbon source |
29418 | 5291 | gelatin | + | carbon source |
29418 | 29987 | glutamate | + | carbon source |
29418 | 15361 | pyruvate | + | carbon source |
enzymes
- @ref: 29418
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | latitude | longitude |
---|---|---|---|---|
16205 | hydrothermal chimney material | East Pacific Rise, hydrothermal vent fields of Genesis (12.449844° N 103.56812° W) at a depth of 2634 m | 12.4498 | -103.568 |
67770 | Chimney collected from a deep-sea hydrothermal field at a depth of 2,634 m on the East Pacific Rise |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Hydrothermal vent |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_6891.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_302;96_1200;97_1415;98_1722;99_6891&stattab=map
- Last taxonomy: Rhodothermus profundi
- 16S sequence: FJ624399
- Sequence Identity:
- Total samples: 24
- soil counts: 4
- aquatic counts: 12
- animal counts: 6
- plant counts: 2
Safety information
risk assessment
- @ref: 16205
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16205
- description: Rhodothermus profundi strain PRI 2902 16S ribosomal RNA gene, partial sequence
- accession: FJ624399
- length: 1509
- database: ena
- NCBI tax ID: 633813
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodothermus profundi strain DSM 22212 | 633813.3 | wgs | patric | 633813 |
66792 | Rhodothermus profundi DSM 22212 | 2622736637 | draft | img | 633813 |
67770 | Rhodothermus profundi DSM 22212 | GCA_900142415 | scaffold | ncbi | 633813 |
GC content
@ref | GC-content | method |
---|---|---|
16205 | 60.9 | high performance liquid chromatography (HPLC) |
29418 | 60.9 | |
67770 | 60.7 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 87 | no |
gram-positive | no | 97.173 | no |
anaerobic | no | 96.954 | yes |
halophile | no | 54.766 | no |
spore-forming | no | 92.857 | yes |
glucose-util | yes | 86.922 | no |
thermophile | yes | 99.736 | no |
flagellated | no | 90.798 | yes |
aerobic | yes | 59.815 | no |
motile | yes | 64.708 | no |
glucose-ferment | no | 81.235 | no |
External links
@ref: 16205
culture collection no.: DSM 22212, JCM 15944, PRI 2902
straininfo link
- @ref: 86787
- straininfo: 398419
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20061490 | Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean. | Marteinsson VT, Bjornsdottir SH, Bienvenu N, Kristjansson JK, Birrien JL | Int J Syst Evol Microbiol | 10.1099/ijs.0.012724-0 | 2010 | Amplified Fragment Length Polymorphism Analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodothermus/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 35072600 | Rhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island Surtsey. | Bergsten P, Vannier P, Mougeolle A, Rigaud L, Marteinsson VT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005214 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Iceland, Islands, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodothermus/cytology/isolation & purification, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16205 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22212) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22212 | |||
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 | |||
29418 | 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 | 25825 | 28776041 | |
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) | |||
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. | 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) | |||
86787 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398419.1 | StrainInfo: A central database for resolving microbial strain identifiers |