Strain identifier
BacDive ID: 513
Type strain: 
Species: Hydrogenobaculum acidophilum
Strain Designation: 3H-1
Strain history: S. Shima 3H-1.
NCBI tax ID(s): 34092 (species)
version 9.2 (current version)
General
@ref: 4260
BacDive-ID: 513
DSM-Number: 11251
keywords: 16S sequence, Bacteria, thermophilic
description: Hydrogenobaculum acidophilum 3H-1 is a thermophilic bacterium that was isolated from mud sample from a solfataric field.
NCBI tax id
- NCBI tax id: 34092
- Matching level: species
strain history
| @ref | history |
|---|---|
| 4260 | <- JCM <- S. Shima, strain 3H-1 |
| 67770 | S. Shima 3H-1. |
doi: 10.13145/bacdive513.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/aquificota
- domain: Bacteria
- phylum: Aquificota
- class: Aquificia
- order: Aquificales
- family: Aquificaceae
- genus: Hydrogenobaculum
- species: Hydrogenobaculum acidophilum
- full scientific name: Hydrogenobaculum acidophilum (Shima and Suzuki 1993) Stöhr et al. 2001
synonyms
- @ref: 20215
- synonym: Hydrogenobacter acidophilus
@ref: 4260
domain: Bacteria
phylum: Aquificae
class: Aquificae
order: Aquificales
family: Aquificaceae
genus: Hydrogenobaculum
species: Hydrogenobaculum acidophilum
full scientific name: Hydrogenobaculum acidophilum (Shima and Suzuki 1993) Stöhr et al. 2001
strain designation: 3H-1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 4260
- name: HYDROGENOBACTER ACIDOPHILUS MEDIUM (DSMZ Medium 743)
- growth: yes
- link: https://mediadive.dsmz.de/medium/743
- composition: Name: HYDROGENOBACTER ACIDOPHILUS MEDIUM (DSMZ Medium 743) Composition: Sulfur 5.0 g/l (NH4)2SO4 1.0 g/l K2HPO4 1.0 g/l NaCl 1.0 g/l MgSO4 x 7 H2O 0.3 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 0.001 g/l ZnSO4 x 7 H2O 1.4e-05 g/l CoCl2 x 6 H2O 2e-06 g/l MnSO4 x 5 H2O 2e-06 g/l MoO3 2e-06 g/l H3BO3 2e-06 g/l CuSO4 x 5 H2O 1e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 4260 | positive | growth | 65 |
| 67770 | positive | growth | 65 |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: Methionaquinone (MTK)-7(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 4260 | mud sample from a solfataric field | Tsumagoi | Japan | JPN | Asia |
| 67770 | Mud sample from a solfataric field in Tsumagoi | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Terrestrial | #Volcanic |
Safety information
risk assessment
- @ref: 4260
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4260
- description: Hydrogenobaculum acidophilum gene for 16S rRNA
- accession: D16296
- length: 1436
- database: nuccore
- NCBI tax ID: 34092
GC content
| @ref | GC-content | method |
|---|---|---|
| 4260 | 35 | |
| 67770 | 35 | high performance liquid chromatography (HPLC) |
External links
@ref: 4260
culture collection no.: DSM 11251, JCM 8795, ATCC BAA-480
straininfo link
- @ref: 70192
- straininfo: 49057
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 8039650 | The phylogenetic position of Hydrogenobacter acidophilus based on 16S rRNA sequence analysis. | Shima S, Yanagi M, Saiki H | FEMS Microbiol Lett | 10.1111/j.1574-6968.1994.tb06877.x | 1994 | Archaea/classification/genetics, Base Sequence, Eubacterium/*classification/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*chemistry/genetics | Genetics |
| Phylogeny | 11594618 | Hydrogenothermus marinus gen. nov., sp. nov., a novel thermophilic hydrogen-oxidizing bacterium, recognition of Calderobacterium hydrogenophilum as a member of the genus Hydrogenobacter and proposal of the reclassification of Hydrogenobacter acidophilus as Hydrogenobaculum acidophilum gen. nov., comb. nov., in the phylum 'Hydrogenobacter/Aquifex'. | Stohr R, Waberski A, Volker H, Tindall BJ, Thomm M | Int J Syst Evol Microbiol | 10.1099/00207713-51-5-1853 | 2001 | Base Composition, Carbon/metabolism, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gram-Negative Bacteria/*classification/genetics/*growth & development/isolation & purification, Hydrogen/*metabolism, Lipids/analysis, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Quinones/metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Temperature | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4260 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11251) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11251 | |
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 70192 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49057.1 | StrainInfo: A central database for resolving microbial strain identifiers |