Strain identifier
BacDive ID: 509
Type strain: 
Species: Hydrogenivirga caldilitoris
Strain Designation: ISBSK3
Strain history: S. Nakagawa IBSK3.
NCBI tax ID(s): 246264 (species)
version 8.1 (current version)
General
@ref: 6383
BacDive-ID: 509
DSM-Number: 16510
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped
description: Hydrogenivirga caldilitoris ISBSK3 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from coastal hot spring.
NCBI tax id
- NCBI tax id: 246264
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6383 | <- S. Nakagawa; ISBSK3 |
| 67770 | S. Nakagawa IBSK3. |
doi: 10.13145/bacdive509.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/aquificota
- domain: Bacteria
- phylum: Aquificota
- class: Aquificia
- order: Aquificales
- family: Aquificaceae
- genus: Hydrogenivirga
- species: Hydrogenivirga caldilitoris
- full scientific name: Hydrogenivirga caldilitoris Nakagawa et al. 2004
@ref: 6383
domain: Bacteria
phylum: Aquificae
class: Aquificae
order: Aquificales
family: Aquificaceae
genus: Hydrogenivirga
species: Hydrogenivirga caldilitoris
full scientific name: Hydrogenivirga caldilitoris Nakagawa et al. 2004
strain designation: ISBSK3
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30178 | negative | 2 µm | 0.3 µm | rod-shaped | yes | |
| 69480 | yes | 93.256 | ||||
| 69480 | negative | 99.999 |
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_16510_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_16510_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_16510_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_16510_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_16510_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 6383
- name: HNW MEDIUM (DSMZ Medium 997)
- growth: yes
- link: https://mediadive.dsmz.de/medium/997
- composition: Name: HNW MEDIUM (DSMZ Medium 997) Composition: MgCl2 x 6 H2O 418.0 g/l Na2S 100.0 g/l NaHCO3 100.0 g/l NaNO3 100.0 g/l KCl 33.0 g/l NH4Cl 25.0 g/l K2HPO4 14.0 g/l MgSO4 x 7 H2O 3.0 g/l C6H9NO6 1.5 g/l NaCl 1.0 g/l Fe(NH4)2(SO4)2 x 6 H2O 1.0 g/l MnSO4 x 2 H2O 0.5 g/l CoSO4 x 7 H2O 0.18 g/l ZnSO4 x 7 H2O 0.18 g/l FeSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.1 g/l NiCl2 x 6 H2O 0.025 g/l AlK(SO4)2 x 12 H2O 0.02 g/l CuSO4 x 5 H2O 0.01 g/l H3BO3 0.01 g/l Na2MoO4 x 2 H2O 0.01 g/l Na2SeO3 x 5 H2O 0.0003 g/l Na2WO4 x 2 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l Nicotinic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 6383 | positive | growth | 75 | thermophilic | |
| 30178 | positive | growth | 55-77 | thermophilic | |
| 30178 | positive | optimum | 75 | thermophilic | |
| 67770 | positive | growth | 75 | thermophilic | |
| 69480 | thermophilic | 99.999 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30178 | positive | growth | 5.5-8.3 |
| 30178 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 30178 | anaerobe | |
| 69480 | anaerobe | 98.606 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.567
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30178 | NaCl | positive | growth | 0.5-4 % |
| 30178 | NaCl | positive | optimum | 2 % |
observation
- @ref: 30178
- observation: aggregates in clumps
metabolite utilization
- @ref: 30178
- Chebi-ID: 17632
- metabolite: nitrate
- utilization activity: +
- kind of utilization tested: reduction
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6383 | coastal hot spring | Kagoshima Prefecture, Ibusuki | Japan | JPN | Asia |
| 67770 | Coastal hot spring in Ibusuki | Kagoshima | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) | |
| #Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_147662.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16076;96_3100;97_72666;98_97704;99_147662&stattab=map
- Last taxonomy: Hydrogenivirga caldilitoris subclade
- 16S sequence: AB120294
- Sequence Identity:
- Total samples: 16
- soil counts: 1
- aquatic counts: 15
Safety information
risk assessment
- @ref: 6383
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6383
- description: Hydrogenivirga caldilitoris gene for 16S rRNA, partial sequence
- accession: AB120294
- length: 1492
- database: ena
- NCBI tax ID: 246264
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hydrogenivirga caldilitoris strain DSM 16510 | 246264.3 | wgs | patric | 246264 |
| 66792 | Hydrogenivirga caldilitoris DSM 16510 | 2681812961 | draft | img | 246264 |
| 67770 | Hydrogenivirga caldilitoris DSM 16510 | GCA_003664005 | contig | ncbi | 246264 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 30178 | 49.2 | |
| 67770 | 49.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 73 | no |
| motile | yes | 91.691 | yes |
| gram-positive | no | 99.619 | yes |
| anaerobic | yes | 73.983 | yes |
| aerobic | no | 96.331 | yes |
| halophile | no | 75.526 | no |
| spore-forming | no | 96.405 | no |
| glucose-util | yes | 53.731 | no |
| flagellated | no | 89.495 | no |
| thermophile | yes | 100 | no |
| glucose-ferment | no | 88.504 | no |
External links
@ref: 6383
culture collection no.: DSM 16510, ATCC BAA 821, JCM 12173
straininfo link
- @ref: 70188
- straininfo: 134430
literature
- topic: Phylogeny
- Pubmed-ID: 15545438
- title: Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field.
- authors: Nakagawa S, Nakamura S, Inagaki F, Takai K, Shirai N, Sako Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.03031-0
- year: 2004
- mesh: Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Gram-Negative Bacteria/*classification/cytology/*isolation & purification/metabolism, Hot Springs/*microbiology, Hot Temperature, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Inorganic Chemicals/metabolism, Japan, Molecular Sequence Data, Movement, Nitrates/metabolism, Nitrous Oxide/metabolism, Oxidation-Reduction, Oxygen/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Sequence Analysis, DNA, Sulfur/*metabolism
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6383 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16510) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16510 | ||||
| 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 | ||||
| 30178 | 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 | 26527 | 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) | ||||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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) | ||||
| 70188 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134430.1 | StrainInfo: A central database for resolving microbial strain identifiers |