Strain identifier
BacDive ID: 130468
Type strain: 
Species: Caminibacter pacificus
Strain Designation: EPR-TB6, TB-6
Strain history: C. Vetriani TB-6.
NCBI tax ID(s): 1424653 (species)
version 8.1 (current version)
General
@ref: 22153
BacDive-ID: 130468
DSM-Number: 27783
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic
description: Caminibacter pacificus EPR-TB6 is an anaerobe, thermophilic bacterium that was isolated from sulfide chimney fragments from an active deep-sea hydrothermal vent, depth 2500 m.
NCBI tax id
- NCBI tax id: 1424653
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22153 | <- C. Vetriani, Rutgers, State Univ. New Jersey, New Brunswick, USA; EPR-TB6 <- I. Pérez-Rodríguez {2007} |
| 67770 | C. Vetriani TB-6. |
doi: 10.13145/bacdive130468.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Nautiliales
- family: Nautiliaceae
- genus: Caminibacter
- species: Caminibacter pacificus
- full scientific name: Caminibacter pacificus (Grosche et al. 2015) Shiotani et al. 2021
synonyms
- @ref: 20215
- synonym: Cetia pacifica
@ref: 22153
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Nautiliales
family: Nautiliaceae
genus: Cetia
species: Cetia pacifica
full scientific name: Cetia pacifica Grosche et al. 2015
strain designation: EPR-TB6, TB-6
type strain: yes
Culture and growth conditions
culture medium
- @ref: 22153
- name: THERMOVIBRIO AMMONIFICANS MEDIUM (DSMZ Medium 792a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/792a
- composition: Name: THERMOVIBRIO AMMONIFICANS MEDIUM (DSMZ Medium 792a) Composition: MgCl2 x 6 H2O 2.72547 g/l KNO3 0.99108 g/l KH2PO4 0.49554 g/l KCl 0.327056 g/l Na2S x 9 H2O 0.148662 g/l NaBr 0.049554 g/l MgSO4 x 7 H2O 0.0297324 g/l NaCl 0.0099108 g/l SrCl2 x 6 H2O 0.00693757 g/l MnSO4 x H2O 0.0049554 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00277502 g/l CoCl2 x 6 H2O 0.00178394 g/l ZnSO4 x 7 H2O 0.00178394 g/l FeSO4 x 7 H2O 0.00099108 g/l CaCl2 x 2 H2O 0.00099108 g/l Sodium resazurin 0.00049554 g/l AlK(SO4)2 x 12 H2O 0.000178394 g/l Na2SeO4 9.9108e-05 g/l Na2WO4 x 2 H2O 9.9108e-05 g/l H3BO3 9.9108e-05 g/l CuSO4 x 5 H2O 9.9108e-05 g/l Na2MoO4 x 2 H2O 9.9108e-05 g/l KI 4.9554e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 22153 | positive | growth | 55 | thermophilic |
| 67770 | positive | growth | 55 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 22153
- oxygen tolerance: anaerobe
observation
- @ref: 67770
- observation: quinones: MK-7, MMK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | latitude | longitude |
|---|---|---|---|---|---|
| 22153 | sulfide chimney fragments from an active deep-sea hydrothermal vent, depth 2500 m | East Pacific Rise, Bio 9 Vent | International waters | 9.8167 | -104.283 |
| 67770 | Chimney fragments from an active deep-sea hydrothermal vent on the East Pacific Rise |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Sulfuric | |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_67359.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_250;96_29097;97_36692;98_47481;99_67359&stattab=map
- Last taxonomy: Cetia pacifica subclade
- 16S sequence: KF648717
- Sequence Identity:
- Total samples: 141
- aquatic counts: 130
- animal counts: 11
Safety information
risk assessment
- @ref: 22153
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22153
- description: Cetia pacifica strain TB-6 16S ribosomal RNA gene, partial sequence
- accession: KF648717
- length: 1482
- database: ena
- NCBI tax ID: 1424653
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Cetia pacifica strain DSM 27783 | 1424653.31 | wgs | patric | 1424653 |
| 66792 | Cetia pacifica DSM 27783 | 2788499860 | draft | img | 1424653 |
| 67770 | Caminibacter pacificus DSM 27783 | GCA_003752135 | contig | ncbi | 1424653 |
GC content
- @ref: 22153
- GC-content: 36.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 86.687 | no |
| gram-positive | no | 98.491 | no |
| anaerobic | yes | 97.113 | yes |
| halophile | no | 76.478 | no |
| spore-forming | no | 94.034 | no |
| thermophile | yes | 99.595 | yes |
| glucose-util | no | 77.382 | no |
| aerobic | no | 98.86 | no |
| flagellated | no | 82.275 | no |
| glucose-ferment | no | 82.116 | no |
External links
@ref: 22153
culture collection no.: DSM 27783, JCM 19563
straininfo link
- @ref: 88997
- straininfo: 402491
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25604337 | Cetia pacifica gen. nov., sp. nov., a chemolithoautotrophic, thermophilic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent. | Grosche A, Sekaran H, Perez-Rodriguez I, Starovoytov V, Vetriani C | Int J Syst Evol Microbiol | 10.1099/ijs.0.000070 | 2015 | Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Epsilonproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Nitrates/metabolism, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Enzymology |
| Phylogeny | 33301463 | Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". | Shiotani T, Mino S, Sato W, Nishikawa S, Yonezawa M, Sievert SM, Sawabe T | PLoS One | 10.1371/journal.pone.0241366 | 2020 | DNA, Bacterial/genetics, Epsilonproteobacteria/*classification/genetics/metabolism, Genome, Bacterial, Hydrogen/metabolism, Hydrothermal Vents/*microbiology, Oxidation-Reduction, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Species Specificity, Terminology as Topic | Metabolism |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22153 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27783 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27783) | |
| 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 | |
| 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/ | |
| 88997 | 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-ID402491.1 |