Strain identifier
BacDive ID: 2815
Type strain: 
Species: Paramaledivibacter caminithermalis
Strain Designation: DViRD3
Strain history: <- M.-L. Fardeau, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; DViRD3 <- N. Brisbarre {2000}
NCBI tax ID(s): 1121301 (strain), 191027 (species)
version 8.1 (current version)
General
@ref: 5759
BacDive-ID: 2815
DSM-Number: 15212
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive, motile, rod-shaped
description: Paramaledivibacter caminithermalis DViRD3 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent, depth 800 m.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121301 | strain |
| 191027 | species |
strain history
- @ref: 5759
- history: <- M.-L. Fardeau, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; DViRD3 <- N. Brisbarre {2000}
doi: 10.13145/bacdive2815.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptostreptococcaceae
- genus: Paramaledivibacter
- species: Paramaledivibacter caminithermalis
- full scientific name: Paramaledivibacter caminithermalis (Brisbarre et al. 2003) Li et al. 2016
synonyms
- @ref: 20215
- synonym: Clostridium caminithermale
@ref: 5759
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptostreptococcaceae
genus: Paramaledivibacter
species: Paramaledivibacter caminithermalis
full scientific name: Paramaledivibacter caminithermalis (Brisbarre et al. 2003) Li et al. 2016
strain designation: DViRD3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 25020 | positive | rod-shaped | yes | |
| 69480 | yes | 92.836 | ||
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 5759
- name: PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986)
- growth: yes
- link: https://mediadive.dsmz.de/medium/986
- composition: Name: PARAMALEDIVIBACTER MEDIUM (DSMZ Medium 986) Composition: Sea Salt 29.97 g/l D-Glucose 3.996 g/l NaHCO3 1.998 g/l NH4Cl 0.999001 g/l Peptone 0.499501 g/l Yeast extract 0.499501 g/l KH2PO4 0.2997 g/l K2HPO4 0.2997 g/l L-Cysteine HCl x H2O 0.24975 g/l Na2S x 9 H2O 0.24975 g/l Sodium resazurin 0.0004995 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l Riboflavin 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Vitamin B12 9.99001e-07 g/l Distilled water
culture temp
- @ref: 5759
- growth: positive
- type: growth
- temperature: 42
- range: thermophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5759 | anaerobe | |
| 25020 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 25020 | 17057 | cellobiose | - | carbon source |
| 25020 | 27082 | trehalose | - | carbon source |
| 25020 | 22599 | arabinose | + | carbon source |
| 25020 | 17750 | betaine | + | electron acceptor |
| 25020 | 16899 | D-mannitol | + | carbon source |
| 25020 | 16024 | D-mannose | + | carbon source |
| 25020 | esculin ferric citrate | + | carbon source | |
| 25020 | 5291 | gelatin | + | carbon source |
| 25020 | 17234 | glucose | + | carbon source |
| 25020 | 24898 | isoleucine | + | electron donor |
| 25020 | 6731 | melezitose | + | carbon source |
| 25020 | 16811 | methionine | + | electron donor |
| 25020 | 17992 | sucrose | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 5759
- sample type: deep-sea hydrothermal vent, depth 800 m
- geographic location: Mid-Atlantic Ridge
- country: Portugal
- origin.country: PRT
- continent: Europe
- latitude: 37.8333
- longitude: -31.5167
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_60064.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15791;96_25629;97_32147;98_42666;99_60064&stattab=map
- Last taxonomy: Wukongibacter
- 16S sequence: AF458779
- Sequence Identity:
- Total samples: 140
- soil counts: 10
- aquatic counts: 86
- animal counts: 40
- plant counts: 4
Safety information
risk assessment
- @ref: 5759
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5759
- description: Clostridium subatlanticum 16S ribosomal RNA gene, partial sequence
- accession: AF458779
- length: 1577
- database: ena
- NCBI tax ID: 191027
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paramaledivibacter caminithermalis DSM 15212 | GCA_900142245 | scaffold | ncbi | 1121301 |
| 66792 | Clostridium caminithermale DSM 15212 | 1121301.3 | wgs | patric | 1121301 |
| 66792 | Paramaledivibacter caminithermalis DSM 15212 | 2585428176 | draft | img | 1121301 |
GC content
- @ref: 5759
- GC-content: 33.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 86.645 | no |
| flagellated | yes | 54.714 | no |
| gram-positive | yes | 57.575 | yes |
| anaerobic | yes | 99.237 | yes |
| aerobic | no | 97.806 | yes |
| halophile | no | 87.919 | no |
| spore-forming | yes | 94.185 | no |
| thermophile | yes | 95.202 | yes |
| glucose-util | yes | 90.592 | yes |
| glucose-ferment | yes | 53.687 | no |
External links
@ref: 5759
culture collection no.: DSM 15212, CIP 107654
straininfo link
- @ref: 72340
- straininfo: 113585
literature
- topic: Phylogeny
- Pubmed-ID: 12892124
- title: Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney.
- authors: Brisbarre N, Fardeau ML, Cueff V, Cayol JL, Barbier G, Cilia V, Ravot G, Thomas P, Garcia JL, Ollivier B
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02471-0
- year: 2003
- mesh: Atlantic Ocean, Base Composition, Clostridium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5759 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15212) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15212 | |||
| 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 | |||
| 25020 | G. Z. Li, X.,Liu, X.,Zhang, X.,Shao, Z. | 10.1099/ijsem.0.001355 | Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively | IJSEM 66: 4355-4361 2016 | 27473553 | |
| 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 | |||
| 72340 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID113585.1 | StrainInfo: A central database for resolving microbial strain identifiers |