Strain identifier

BacDive ID: 13183

Type strain: Yes

Species: Pseudomonas toyotomiensis

Strain Designation: HT-3

Strain history: I. Yumoto HT-3.

NCBI tax ID(s): 554344 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
18176<- JCM <- I. Yumoto, Bioproduction Research Institute, Natl. Inst. Advanced Industrial Sci. and Technology (AIST), Sapporo, Japan; HT-3
67770I. 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

@refgrowthtypetemperaturerange
18176positivegrowth37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18176--------+--+--++-++-+
18176---+----+--+--++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18176soil immersed in hot-spring water containing hydrocarbonsHokkaido, ToyotomiJapanJPNAsia
67770Soil immersed in hot-spring water containing hydrocarbons in Toyotomi hot spring in northern HokkaidoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas toyotomiensis strain DSM 26169554344.10wgspatric554344
66792Pseudomonas toyotomiensis strain JCM 15604554344.9wgspatric554344
66792Pseudomonas toyotomiensis JCM 156042663762766draftimg554344
66792Pseudomonas toyotomiensis DSM 261692917185439draftimg554344
67770Pseudomonas toyotomiensis JCM 15604GCA_900115695scaffoldncbi554344
67770Pseudomonas toyotomiensis DSM 26169GCA_002741095contigncbi554344

GC content

  • @ref: 18176
  • GC-content: 65.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.821no
anaerobicno97.874no
halophileno82.508no
spore-formingno96.092no
glucose-utilyes92.611yes
thermophileno99.838yes
aerobicyes92.417no
motileyes88.694no
flagellatedyes88.12no
glucose-fermentno90.878no

External links

@ref: 18176

culture collection no.: DSM 26169, JCM 15604, NCIMB 14511

straininfo link

  • @ref: 82391
  • straininfo: 377459

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20817837Pseudomonas toyotomiensis sp. nov., a psychrotolerant facultative alkaliphile that utilizes hydrocarbons.Hirota K, Yamahira K, Nakajima K, Nodasaka Y, Okuyama H, Yumoto IInt J Syst Evol Microbiol10.1099/ijs.0.024612-02010Alkalies/*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/geneticsMetabolism
Phylogeny23178721Pseudomonas 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 CCInt J Syst Evol Microbiol10.1099/ijs.0.045567-02012Bacterial 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/analysisGenetics
Phylogeny23918786Pseudomonas 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 CCInt J Syst Evol Microbiol10.1099/ijs.0.047712-02013Bacterial 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/chemistryGenetics
Phylogeny24021726Pseudomonas chengduensis sp. nov., isolated from landfill leachate.Tao Y, Zhou Y, He X, Hu X, Li DInt J Syst Evol Microbiol10.1099/ijs.0.050294-02013Bacterial 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/*analysisGenetics
Phylogeny25574037Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils.Zhang L, Pan Y, Wang K, Zhang X, Zhang C, Zhang S, Fu X, Jiang JInt J Syst Evol Microbiol10.1099/ijs.0.0000572015Bacterial 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/chemistryGenetics
Phylogeny29239716Pseudomonas 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 SInt J Syst Evol Microbiol10.1099/ijsem.0.0025202017Bacterial 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 MicrobiologyTranscriptome
Phylogeny29948825Taxonomic 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 GJ Microbiol10.1007/s12275-018-7549-x2018Bacterial 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 MicrobiologyGenetics
Phylogeny30024362Pseudomonas tianjinensis sp. nov., isolated from domestic sewage.Chen P, Li S, Li QXInt J Syst Evol Microbiol10.1099/ijsem.0.0027992018Bacterial 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/chemistryTranscriptome
Phylogeny33587227Pseudomonas 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 MAntonie Van Leeuwenhoek10.1007/s10482-021-01524-82021Bacterial Typing Techniques, DNA, Bacterial/genetics, Phospholipids/analysis, Phylogeny, *Populus, Pseudomonas/genetics, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
18176Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26169)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26169
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69479João 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
82391Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377459.1StrainInfo: A central database for resolving microbial strain identifiers