Strain identifier

BacDive ID: 2952

Type strain: Yes

Species: Delftia tsuruhatensis

Strain Designation: T7

Strain history: <- T. Shigematsu, Kumamoto University; T7

NCBI tax ID(s): 1220577 (strain), 180282 (species)

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General

@ref: 7068

BacDive-ID: 2952

DSM-Number: 17581

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped

description: Delftia tsuruhatensis T7 is a mesophilic, Gram-negative, motile bacterium that was isolated from activated sludge at a domestic wastewater treatment plant.

NCBI tax id

NCBI tax idMatching level
1220577strain
180282species

strain history

  • @ref: 7068
  • history: <- T. Shigematsu, Kumamoto University; T7

doi: 10.13145/bacdive2952.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Delftia
  • species: Delftia tsuruhatensis
  • full scientific name: Delftia tsuruhatensis Shigematsu et al. 2003

@ref: 7068

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Delftia

species: Delftia tsuruhatensis

full scientific name: Delftia tsuruhatensis Shigematsu et al. 2003 emend. Jørgensen et al. 2009

strain designation: T7

type strain: yes

Morphology

cell morphology

  • @ref: 23084
  • gram stain: negative
  • cell length: 2.4-4.0 µm
  • cell width: 0.7-1.2 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 23084
  • colony color: white
  • medium used: nutrient broth plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7068TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23084nutrient broth platesyes

culture temp

@refgrowthtypetemperaturerange
7068positivegrowth35mesophilic
23084positivegrowth10.0-40.0
23084positiveoptimum35.0mesophilic

culture pH

@refabilitytypepHPH range
23084positivegrowth5.0-9.0alkaliphile
23084positiveoptimum7.0

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23084879973-aminobutyrate-carbon source
2308417563phthalate-carbon source
23084879973-aminobutyrate-growth
2308417563phthalate-growth
2308428017starch-hydrolysis
2308416958beta-alanine+carbon source
2308417754glycerol+carbon source
2308430803isophthalate+carbon source
2308436241protocatechuate+carbon source
2308430043terephthalate+carbon source
2308416958beta-alanine+growth
2308417754glycerol+growth
2308430803isophthalate+growth
2308436241protocatechuate+growth
2308430043terephthalate+growth
2308417632nitrate+reduction
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
6836929016arginine-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
23084arginine dihydrolase+3.5.3.6
23084catalase+1.11.1.6
23084cytochrome oxidase+1.9.3.1
23084lipase (Tween 80)+
23084urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7068+-------------++++-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture
7068activated sludge at a domestic wastewater treatment plantKumamotoJapanJPNAsia
23084Tsuruhata, Kumamoto Prefecturebasal salt medium

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_701.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_431;97_492;98_563;99_701&stattab=map
  • Last taxonomy: Delftia
  • 16S sequence: AB681119
  • Sequence Identity:
  • Total samples: 58111
  • soil counts: 6069
  • aquatic counts: 15249
  • animal counts: 31574
  • plant counts: 5219

Safety information

risk assessment

  • @ref: 7068
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Delftia tsuruhatensis gene for 16S rRNA, partial sequence, strain: NBRC 16741AB6811191458ena180282
7068Delftia tsuruhatensis gene for 16S rRNA, partial sequenceAB0750171456ena180282

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Delftia tsuruhatensis NBRC 16741GCA_001571325contigncbi1220577
66792Delftia tsuruhatensis NBRC 167411220577.3wgspatric1220577
66792Delftia tsuruhatensis NBRC 167412839144908draftimg1220577

GC content

  • @ref: 23084
  • GC-content: 66.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.335yes
gram-positiveno98.465yes
anaerobicno98.606no
aerobicyes93.279no
halophileno94.28no
spore-formingno93.926no
glucose-utilno58.839no
flagellatedyes64.694no
thermophileno99.62no
glucose-fermentno88.668yes

External links

@ref: 7068

culture collection no.: DSM 17581, ATCC BAA 554, NBRC 16741

straininfo link

  • @ref: 72474
  • straininfo: 127988

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19605727Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium.Jorgensen NO, Brandt KK, Nybroe O, Hansen MInt J Syst Evol Microbiol10.1099/ijs.0.008375-02009Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, Chitinases/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Delftia/*classification/genetics/*isolation & purification/metabolism, Denmark, Fatty Acids/analysis, Fresh Water/*microbiology, Locomotion, Molecular Sequence Data, Muramidase/metabolism, Nucleic Acid Hybridization, Peptidoglycan/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny25842037Delftia deserti sp. nov., isolated from a desert soil sample.Li CT, Yan ZF, Chu X, Hussain F, Xian WD, Yunus Z, Hozzein WN, Abaydulla G, Li WJAntonie Van Leeuwenhoek10.1007/s10482-015-0440-42015Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Delftia/*classification/genetics/*isolation & purification/physiology, Desert Climate, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7068Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17581)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17581
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23084Toru Shigematsu,Kazuyo Yumihara,Yutaka Ueda,Masaki Numaguchi,Shigeru Morimura,Kenji Kida10.1099/ijs.0.02285-0Delftia tsuruhatensis sp. nov., a terephthalate-assimilating bacterium isolated from activated sludgeIJSEM 53: 1479-1483 200313130036
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)
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
72474Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127988.1StrainInfo: A central database for resolving microbial strain identifiers