Strain identifier
BacDive ID: 13183
Type strain:
Species: Pseudomonas toyotomiensis
Strain Designation: HT-3
Strain history: I. Yumoto HT-3.
NCBI tax ID(s): 554344 (species)
General
@ref: 18176
BacDive-ID: 13183
DSM-Number: 26169
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Pseudomonas toyotomiensis HT-3 is a mesophilic bacterium that was isolated from soil immersed in hot-spring water containing hydrocarbons.
NCBI tax id
- NCBI tax id: 554344
- Matching level: species
strain history
@ref | history |
---|---|
18176 | <- JCM <- I. Yumoto, Bioproduction Research Institute, Natl. Inst. Advanced Industrial Sci. and Technology (AIST), Sapporo, Japan; HT-3 |
67770 | I. Yumoto HT-3. |
doi: 10.13145/bacdive13183.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas toyotomiensis
- full scientific name: Pseudomonas toyotomiensis Hirota et al. 2011
@ref: 18176
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas toyotomiensis
full scientific name: Pseudomonas toyotomiensis Hirota et al. 2011
strain designation: HT-3
type strain: yes
Morphology
multimedia
- @ref: 18176
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26169.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 18176
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18176 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: Q-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18176 | - | - | - | - | - | - | - | - | + | - | - | + | - | - | + | + | - | + | + | - | + |
18176 | - | - | - | + | - | - | - | - | + | - | - | + | - | - | + | + | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
18176 | soil immersed in hot-spring water containing hydrocarbons | Hokkaido, Toyotomi | Japan | JPN | Asia |
67770 | Soil immersed in hot-spring water containing hydrocarbons in Toyotomi hot spring in northern Hokkaido | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Thermal spring |
#Environmental | #Terrestrial | #Soil |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_2828.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_1532;99_2828&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: AB453701
- Sequence Identity:
- Total samples: 7465
- soil counts: 769
- aquatic counts: 2670
- animal counts: 2451
- plant counts: 1575
Safety information
risk assessment
- @ref: 18176
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18176
- description: Pseudomonas toyotomiensis gene for 16S rRNA, partial sequence
- accession: AB453701
- length: 1490
- database: ena
- NCBI tax ID: 554344
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas toyotomiensis strain DSM 26169 | 554344.10 | wgs | patric | 554344 |
66792 | Pseudomonas toyotomiensis strain JCM 15604 | 554344.9 | wgs | patric | 554344 |
66792 | Pseudomonas toyotomiensis JCM 15604 | 2663762766 | draft | img | 554344 |
66792 | Pseudomonas toyotomiensis DSM 26169 | 2917185439 | draft | img | 554344 |
67770 | Pseudomonas toyotomiensis JCM 15604 | GCA_900115695 | scaffold | ncbi | 554344 |
67770 | Pseudomonas toyotomiensis DSM 26169 | GCA_002741095 | contig | ncbi | 554344 |
GC content
- @ref: 18176
- GC-content: 65.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.821 | no |
anaerobic | no | 97.874 | no |
halophile | no | 82.508 | no |
spore-forming | no | 96.092 | no |
glucose-util | yes | 92.611 | yes |
thermophile | no | 99.838 | yes |
aerobic | yes | 92.417 | no |
motile | yes | 88.694 | no |
flagellated | yes | 88.12 | no |
glucose-ferment | no | 90.878 | no |
External links
@ref: 18176
culture collection no.: DSM 26169, JCM 15604, NCIMB 14511
straininfo link
- @ref: 82391
- straininfo: 377459
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20817837 | Pseudomonas toyotomiensis sp. nov., a psychrotolerant facultative alkaliphile that utilizes hydrocarbons. | Hirota K, Yamahira K, Nakajima K, Nodasaka Y, Okuyama H, Yumoto I | Int J Syst Evol Microbiol | 10.1099/ijs.0.024612-0 | 2010 | Alkalies/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Hot Springs/*microbiology, Hydrocarbons/*metabolism, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 23178721 | Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil. | Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Chen WM, Shen FT, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.045567-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/analysis, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Taiwan, Ubiquinone/analysis | Genetics |
Phylogeny | 23918786 | Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring. | Liu YC, Young LS, Lin SY, Hameed A, Hsu YH, Lai WA, Shen FT, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.047712-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hot Springs/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Genetics |
Phylogeny | 24021726 | Pseudomonas chengduensis sp. nov., isolated from landfill leachate. | Tao Y, Zhou Y, He X, Hu X, Li D | Int J Syst Evol Microbiol | 10.1099/ijs.0.050294-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Solid Waste, Ubiquinone/chemistry, Waste Disposal Facilities, Water Microbiology, Water Pollutants, Chemical/*analysis | Genetics |
Phylogeny | 25574037 | Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils. | Zhang L, Pan Y, Wang K, Zhang X, Zhang C, Zhang S, Fu X, Jiang J | Int J Syst Evol Microbiol | 10.1099/ijs.0.000057 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
Phylogeny | 29239716 | Pseudomonas fluvialis sp. nov., a novel member of the genus Pseudomonas isolated from the river Ganges, India. | Sudan SK, Pal D, Bisht B, Kumar N, Chaudhry V, Patil P, Sahni G, Mayilraj S, Krishnamurthi S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002520 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, India, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, *Water Microbiology | Transcriptome |
Phylogeny | 29948825 | Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka. | Behera P, Mahapatra M, Seuylemezian A, Vaishampayan P, Ramana VV, Joseph N, Joshi A, Shouche Y, Suar M, Pattnaik AK, Rastogi G | J Microbiol | 10.1007/s12275-018-7549-x | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, *Genome, Bacterial, India, Lakes, Phospholipids/analysis, Phylogeny, Pseudomonas/chemistry/*classification/*genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Rhizosphere, Saline Waters, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 30024362 | Pseudomonas tianjinensis sp. nov., isolated from domestic sewage. | Chen P, Li S, Li QX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002799 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 33587227 | Pseudomonas lopnurensis sp. nov., an endophytic bacterium isolated from Populus euphratica at the ancient Ugan river. | Mamtimin T, Anwar N, Abdurahman M, Kurban M, Rozahon M, Mamtimin H, Hamood B, Rahman E, Wu M | Antonie Van Leeuwenhoek | 10.1007/s10482-021-01524-8 | 2021 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Phospholipids/analysis, Phylogeny, *Populus, Pseudomonas/genetics, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
18176 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26169) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26169 | |
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 | |
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) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68369 | Automatically annotated from API 20NE | |||
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 | |
82391 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID377459.1 | StrainInfo: A central database for resolving microbial strain identifiers |