Strain identifier
BacDive ID: 132628
Type strain: 
Species: Thiomicrorhabdus hydrogeniphila
Strain history: T. Watsuji; JAMSTEC, Japan; MAS2.
NCBI tax ID(s): 1572581 (species)
version 8.1 (current version)
General
@ref: 24417
BacDive-ID: 132628
DSM-Number: 100274
keywords: 16S sequence, Bacteria, obligate aerobe, chemolithoheterotroph, Gram-negative, motile, rod-shaped
description: Thiomicrorhabdus hydrogeniphila DSM 100274 is an obligate aerobe, chemolithoheterotroph, Gram-negative bacterium that was isolated from tank containing surface seawater and a block of beef tallow added as organic material.
NCBI tax id
- NCBI tax id: 1572581
- Matching level: species
strain history
| @ref | history |
|---|---|
| 24417 | <- T. Watsuji, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Yokosuka; MAS2 |
| 67770 | T. Watsuji; JAMSTEC, Japan; MAS2. |
doi: 10.13145/bacdive132628.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Piscirickettsiaceae
- genus: Thiomicrorhabdus
- species: Thiomicrorhabdus hydrogeniphila
- full scientific name: Thiomicrorhabdus hydrogeniphila (Watsuji et al. 2016) Boden et al. 2017
synonyms
- @ref: 20215
- synonym: Thiomicrospira hydrogeniphila
@ref: 24417
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Piscirickettsiaceae
genus: Thiomicrorhabdus
species: Thiomicrorhabdus hydrogeniphila
full scientific name: Thiomicrorhabdus hydrogeniphila (Watsuji et al. 2016) Boden et al. 2017
type strain: yes
Morphology
cell morphology
- @ref: 43576
- gram stain: negative
- cell length: 0.9-1.8 µm
- cell width: 0.3-0.5 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: monotrichous, polar
colony morphology
- @ref: 43576
- colony color: White cream
- medium used: Thiosulfate-agar
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 43576 | Thiosulfate-agar | yes | ||
| 24417 | THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142) | yes | https://mediadive.dsmz.de/medium/142 | Name: THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142) Composition: NaCl 24.8756 g/l Na2S2O3 x 5 H2O 4.97512 g/l MgSO4 x 7 H2O 1.49254 g/l (NH4)2SO4 0.995025 g/l K2HPO4 0.497512 g/l Na2-EDTA 0.00995025 g/l ZnSO4 x 7 H2O 0.00437811 g/l Bromothymol blue 0.0039801 g/l CaCl2 x 2 H2O 0.00110249 g/l MnCl2 x 4 H2O 0.00100697 g/l FeSO4 x 7 H2O 0.000995025 g/l CoCl2 x 6 H2O 0.000320398 g/l CuSO4 x 5 H2O 0.000312438 g/l Pyridoxine hydrochloride 0.000298507 g/l (NH4)6Mo7O24 x 4 H2O 0.000218905 g/l Nicotinic acid 0.000199005 g/l Thiamine-HCl x 2 H2O 0.000199005 g/l Vitamin B12 9.95025e-05 g/l Calcium pantothenate 9.95025e-05 g/l p-Aminobenzoic acid 7.9602e-05 g/l D-(+)-biotin 1.99005e-05 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 43576 | positive | growth | 2-40 | |
| 43576 | positive | optimum | 30 | mesophilic |
| 24417 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 43576 | positive | growth | 5-8 |
| 43576 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
- @ref: 43576
- oxygen tolerance: obligate aerobe
nutrition type
- @ref: 43576
- type: chemolithoheterotroph
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 43576 | NaCl | positive | growth | 0.30-1.380 M |
| 43576 | NaCl | positive | optimum | 0.27 M |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43576 | 29034 | ferric iron | - | electron acceptor |
| 43576 | ferrihydrite | - | electron acceptor | |
| 43576 | 29806 | fumarate | - | electron acceptor |
| 43576 | 17632 | nitrate | - | electron acceptor |
| 43576 | 16301 | nitrite | - | electron acceptor |
| 43576 | 15075 | selenate | - | electron acceptor |
| 43576 | 15379 | dioxygen | - | nitrogen source |
| 43576 | 17632 | nitrate | - | nitrogen source |
| 43576 | 16301 | nitrite | - | nitrogen source |
| 43576 | 15379 | dioxygen | + | electron acceptor |
| 43576 | 28938 | ammonium | + | nitrogen source |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
|---|---|---|---|---|---|---|---|
| 43576 | 28971 | ampicillin | yes | yes | 50 µg/mL | ||
| 43576 | 17698 | chloramphenicol | yes | yes | 50 µg/mL | ||
| 43576 | 6104 | kanamycin | yes | yes | 50 µg/mL | ||
| 43576 | 28077 | rifampicin | yes | yes | 50 µg/mL | ||
| 43576 | 17076 | streptomycin | yes | yes | 50 µg/mL | ||
| 43576 | 28001 | vancomycin | yes | yes | 50 µg/mL |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 24417 | tank containing surface seawater and a block of beef tallow added as organic material | Tokyo Bay | Japan | JPN | Asia | 35.3196 | 139.651 |
| 43576 | enrichment cultures, inoculated with slurry obtained from a silfidic tank containing surface seawater from Tokyo Bay, supplemented with a block of beef tallow (350 g/L) | ||||||
| 67770 | Surface seawater of Tokyo Bay | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Built environment | #Container (Reservoir) |
| #Engineered | #Food production | #Meat |
| #Engineered | #Laboratory | #Lab enrichment |
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Surface water |
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
taxonmaps
- @ref: 69479
- File name: preview.99_82276.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_118;96_339;97_378;98_2338;99_82276&stattab=map
- Last taxonomy: Thiomicrorhabdus hydrogeniphila
- 16S sequence: LC010781
- Sequence Identity:
- Total samples: 94
- aquatic counts: 91
- animal counts: 3
Safety information
risk assessment
- @ref: 24417
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24417
- description: Thiomicrorhabdus hydrogeniphila gene for 16S ribosomal RNA, partial sequence
- accession: LC010781
- length: 1470
- database: ena
- NCBI tax ID: 1572581
GC content
- @ref: 24417
- GC-content: 39.6
- method: high performance liquid chromatography (HPLC)
External links
@ref: 24417
culture collection no.: DSM 100274, JCM 30760, MAS 2
straininfo link
- @ref: 90942
- straininfo: 408286
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 27334912 | Thiomicrospira hydrogeniphila sp. nov., an aerobic, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a seawater tank containing a block of beef tallow. | Watsuji TO, Hada E, Miyazaki M, Ichimura M, Takai K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001250 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fats, Fatty Acids/chemistry, Hydrogen/metabolism, Oxidation-Reduction, *Phylogeny, Piscirickettsiaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur/metabolism, Thiosulfates/metabolism, Tokyo | Metabolism |
| Phylogeny | 28920830 | Reclassification of Thiomicrospira hydrogeniphila (Watsuji et al. 2016) to Thiomicrorhabdus hydrogeniphila comb. nov., with emended description of Thiomicrorhabdus (Boden et al., 2017). | Boden R, Scott KM, Rae AW, Hutt LP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002279 | 2017 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Hydrogen/metabolism, Oxidation-Reduction, *Phylogeny, Piscirickettsiaceae/*classification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/metabolism, Thiosulfates/metabolism | Metabolism |
| Phylogeny | 31613743 | Thiomicrorhabdus indica sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a deep-sea hydrothermal vent environment. | Liu X, Jiang L, Hu Q, Lyu J, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003744 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Indian Ocean, Oxidation-Reduction, *Phylogeny, Piscirickettsiaceae/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur, Thiosulfates | Transcriptome |
| Phylogeny | 33502307 | Thiomicrorhabdus sediminis sp. nov. and Thiomicrorhabdus xiamenensis sp. nov., novel sulfur-oxidizing bacteria isolated from coastal sediments and an emended description of the genus Thiomicrorhabdus. | Liu X, Chen B, Lai Q, Shao Z, Jiang L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004660 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Oxidation-Reduction, Phospholipids/chemistry, *Phylogeny, Piscirickettsiaceae/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur, Sulfur-Reducing Bacteria/*classification/isolation & purification | Enzymology |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 24417 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100274 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100274) | |||
| 43576 | Rich Boden, Kathleen M. Scott, Alexander W. Rae, Lee P. Hutt | Reclassification of Thiomicrospira hydrogeniphila (Watsuji et al. 2016) to Thiomicrorhabdus hydrogenophila comb. nov., with emended description of Thiomicrorhabdus (Boden et al., 2017) | 10.1099/ijsem.0.002279 | IJSEM 67: 4205-4209 2017 | 28920830 | |
| 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/ | |||
| 90942 | 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-ID408286.1 |