Strain identifier
BacDive ID: 159755
Type strain:
Species: Pseudothauera hydrothermalis
Strain Designation: GD-2
NCBI tax ID(s): 2184083 (species)
version 8.1 (current version)
General
@ref: 66685
BacDive-ID: 159755
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped, colony-forming
description: Pseudothauera hydrothermalis GD-2 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sediment sample from a hot spring .
NCBI tax id
- NCBI tax id: 2184083
- Matching level: species
doi: 10.13145/bacdive159755.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Rhodocyclales
- family: Zoogloeaceae
- genus: Pseudothauera
- species: Pseudothauera hydrothermalis
- full scientific name: Pseudothauera hydrothermalis (Yang et al. 2018) Huang et al. 2022
synonyms
- @ref: 20215
- synonym: Thauera hydrothermalis
@ref: 66685
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Rhodocyclales
family: Zoogloeaceae
genus: Thauera
species: Thauera hydrothermalis
strain designation: GD-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
66685 | negative | 1-2.5 µm | 0.3-0.5 µm | rod-shaped | ||
69480 | yes | 97.151 | ||||
69480 | negative | 99.999 |
colony morphology
- @ref: 66685
- colony color: white
- colony shape: circular
- incubation period: 2 days
- medium used: Y7 agar
Culture and growth conditions
culture medium
- @ref: 66685
- name: Y7 agar
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
66685 | positive | growth | 37-55 | |
66685 | positive | optimum | 45-50 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
66685 | positive | growth | 5.5-11 | alkaliphile |
66685 | positive | optimum | 7-7.5 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
66685 | no | |
69480 | no | 99.956 |
69481 | no | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
66685 | NaCl | positive | growth | 0-4 %(w/v) |
66685 | NaCl | positive | optimum | 0 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
66685 | 17108 | D-arabinose | + | builds acid from |
66685 | 17268 | myo-inositol | + | builds acid from |
66685 | 29864 | mannitol | + | builds acid from |
66685 | 30911 | sorbitol | + | builds acid from |
66685 | 15361 | pyruvate | - | carbon source |
66685 | 15824 | D-fructose | - | carbon source |
66685 | 16449 | alanine | - | carbon source |
66685 | 16988 | D-ribose | - | carbon source |
66685 | 17634 | D-glucose | - | carbon source |
66685 | 17754 | glycerol | - | carbon source |
66685 | 17790 | methanol | - | carbon source |
66685 | 25115 | malate | - | carbon source |
66685 | 28831 | propanol | - | carbon source |
66685 | 65327 | D-xylose | - | carbon source |
66685 | butanol | - | carbon source | |
66685 | casamino acids | - | carbon source | |
66685 | 15740 | formate | + | carbon source |
66685 | 16024 | D-mannose | + | carbon source |
66685 | 16150 | benzoate | + | carbon source |
66685 | 16236 | ethanol | + | carbon source |
66685 | 16411 | acetic acid | + | carbon source |
66685 | 16899 | D-mannitol | + | carbon source |
66685 | 17295 | L-phenylalanine | + | carbon source |
66685 | 17859 | glutaric acid | + | carbon source |
66685 | 22653 | asparagine | + | carbon source |
66685 | 24996 | lactate | + | carbon source |
66685 | 28260 | galactose | + | carbon source |
66685 | 29987 | glutamate | + | carbon source |
66685 | 30031 | succinate | + | carbon source |
66685 | 31011 | valerate | + | carbon source |
66685 | 35391 | aspartate | + | carbon source |
66685 | 27897 | tryptophan | + | energy source |
66685 | 16199 | urea | - | hydrolysis |
66685 | 27689 | decanoate | - | hydrolysis |
66685 | 4853 | esculin | + | hydrolysis |
66685 | 5291 | gelatin | + | hydrolysis |
66685 | 18401 | phenylacetate | + | hydrolysis |
66685 | 28017 | starch | + | hydrolysis |
66685 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 66685
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 66685
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
66685 | alpha-galactosidase | + | 3.2.1.22 |
66685 | alpha-glucosidase | + | 3.2.1.20 |
66685 | beta-glucosidase | + | 3.2.1.21 |
66685 | catalase | + | 1.11.1.6 |
66685 | chymotrypsin | + | 3.4.4.5 |
66685 | cytochrome oxidase | + | 1.9.3.1 |
66685 | esterase Lipase (C 8) | + | |
66685 | tryptophan deaminase | + | 4.1.99.1 |
fatty acid profile
fatty acids
@ref fatty acid percentage 66685 C10:0 3OH 7 66685 C14:0 3.5 66685 C18:1 w6c and/or C18:1 w7c 3.6 66685 C16:1 w6c and/or C16:1 w7c 33.6 66685 C16:0 47.9 66685 C12:0 7.4 - type of FA analysis: whole cell analysis
- incubation medium: Y7 medium
- incubation temperature: 45
- incubation time: 3
- software version: Sherlock 6.0B
- library/peak naming table: TSBA6
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
- @ref: 66685
- sample type: sediment sample from a hot spring (pH 7.0)
- geographic location: Tibet Autonomous Region
- country: China
- origin.country: CHN
- continent: Asia
- enrichment culture: Y7 agar
- enrichment culture composition: (1 g YE, 1 g glucose, 0.3 g sodium pyruvate, 0.3 g succinic acid, 0.5 g casamino acid, 0.5 g tryptone, 1.3 g (NH4)2SO4, 0.5 g KH2PO4, 0.5 g K2HPO4, 0.5 g MgSO4 x 7H2O, 0.07 g CaCl2 x 2H2O, 0.02 g FeCl3 x 6H2O)
- enrichment culture duration: 3 days
- enrichment culture temperature: 45
- isolation procedure: 1 g sediment sample were incubated at 45°C in 100 ml Allen medium, supplemented with 1 g l-1 yeast extract (YE) for bacteria enrichment. After cultivation of 5 days, the enriched culture was serially diluted (10-fold) in tubes containing 0.9 ml Allen broth. Dilutions of 0.2 ml were spread on Y7 agar plates to cultivate separated colonies. The plates were incubated at 45°C for 3 days.
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Sediment |
#Environmental | #Aquatic | #Thermal spring |
taxonmaps
- @ref: 69479
- File name: preview.99_47666.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_8760;97_10537;98_12925;99_47666&stattab=map
- Last taxonomy: Thauera hydrothermalis subclade
- 16S sequence: MF033446
- Sequence Identity:
- Total samples: 273
- soil counts: 38
- aquatic counts: 210
- animal counts: 22
- plant counts: 3
Sequence information
16S sequences
- @ref: 66685
- description: Thauera sp. strain GD-2 16S ribosomal RNA gene, partial sequence
- accession: MF033446
- length: 1495
- database: ena
- NCBI tax ID: 2184083
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudothauera hydrothermalis GD-2 | GCA_003345255 | complete | ncbi | 2184083 |
66792 | Thauera hydrothermalis GD-2 | 2841165597 | complete | img | 2184083 |
GC content
- @ref: 66685
- GC-content: 63.6
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 93.372 | no |
flagellated | yes | 85.504 | no |
gram-positive | no | 99.178 | yes |
anaerobic | no | 81.698 | no |
aerobic | no | 74.409 | no |
halophile | no | 92.571 | yes |
spore-forming | no | 93.842 | yes |
glucose-util | no | 79.193 | no |
thermophile | no | 55.461 | no |
glucose-ferment | no | 87.968 | no |
External links
@ref: 66685
culture collection no.: NBRC 112472, CGMCC 1.15527
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 30113299 | Thauera hydrothermalis sp. nov., a thermophilic bacterium isolated from hot spring. | Yang L, Muhadesi JB, Wang MM, Wang BJ, Liu SJ, Jiang CY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002960 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thauera/*classification/genetics/isolation & purification, Tibet, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 35596013 | Thauera sedimentorum sp. nov., Isolated from Coastal Sediment. | Baek J, Jaikwang N, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W | Curr Microbiol | 10.1007/s00284-022-02890-w | 2022 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Thauera/genetics | Transcriptome |
Reference
@id | authors | title | doi/url | 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 | ||
66685 | Lan Yang, Jiang-Baota Muhadesi, Meng-Meng Wang, Bao-Jun Wang, Shuang-Jiang Liu, Cheng-Ying Jiang | Thauera hydrothermalis sp. nov., a thermophilic bacterium isolated from hot spring | 10.1099/ijsem.0.002960 | IJSEM 68: 3163-3168 2018 | 30113299 |
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 | ||
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/ | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |