Strain identifier

BacDive ID: 13170

Type strain: No

Species: Pseudomonas flexibilis

Strain Designation: 78-123

Strain history: Y.-H. Xin; CGMCC, China; 78-123.

NCBI tax ID(s): 1295129 (strain), 706570 (species)

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General

@ref: 18007

BacDive-ID: 13170

DSM-Number: 25351

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

description: Pseudomonas flexibilis 78-123 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sample of a bird's nest.

NCBI tax id

NCBI tax idMatching level
706570species
1295129strain

strain history

@refhistory
18007<- JCM <- Y.-G. Zhou, CGMCC; 78-123
67770Y.-H. Xin; CGMCC, China; 78-123.

doi: 10.13145/bacdive13170.20230509.8.1

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 flexibilis
  • full scientific name: Pseudomonas flexibilis (Hespell 1977) Shin et al. 2016

  • synonyms

    @refsynonym
    20215Serpens flexibilis
    20215Pseudomonas tuomuerensis

@ref: 18007

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas flexibilis

full scientific name: Pseudomonas flexibilis (Hespell 1977) Shin et al. 2016

strain designation: 78-123

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
28888negativerod-shapedyes
69480yes98.032
69480negative100

Culture and growth conditions

culture medium

  • @ref: 18007
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18007positivegrowth28mesophilic
28888positivegrowth15-42
62162positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28888aerobe
62162aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 28888
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2888830089acetate+carbon source
2888822599arabinose+carbon source
2888851850methyl pyruvate+carbon source
2888830031succinate+carbon source
2888853423tween 40+carbon source
2888853426tween 80+carbon source
2888817632nitrate+reduction

enzymes

@refvalueactivityec
28888catalase+1.11.1.6
28888cytochrome oxidase+1.9.3.1
28888urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18007sample of a bird's nestregion of Tuomuer Peak of Tianshan Mountain, bank of Qiongtailan RiverChinaCHNAsia
62162Bird's nest,riverside Qiongtailan RiverTianshan Mountain,Tuomuer PeakChinaCHNAsia
67770Bird's nest on the bank of the Qiongtailan River in the region of Tuomuer Peak of Tianshan MountainXin-jiang Uygur Autobomous Region, north-western ChinaChinaCHNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Birds

taxonmaps

  • @ref: 69479
  • File name: preview.99_5121.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_2491;97_3042;98_3820;99_5121&stattab=map
  • Last taxonomy: Pseudomonas flexibilis subclade
  • 16S sequence: DQ868767
  • Sequence Identity:
  • Total samples: 1259
  • soil counts: 688
  • aquatic counts: 223
  • animal counts: 229
  • plant counts: 119

Safety information

risk assessment

  • @ref: 18007
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18007
  • description: Pseudomonas tuomuerensis strain 78-123 16S ribosomal RNA gene, partial sequence
  • accession: DQ868767
  • length: 1411
  • database: ena
  • NCBI tax ID: 706570

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas flexibilis strain CGMCC 1.1365706570.4wgspatric706570
66792Pseudomonas tuomuerensis JCM 14085400095.4wgspatric706570
66792Pseudomonas tuomuerensis JCM 140851295129.3wgspatric1295129
66792Pseudomonas flexibilis JCM 140852728369709draftimg1295129
66792Pseudomonas flexibilis JCM 140852645728058draftimg1295129
66792Pseudomonas tuomuerensis CGMCC 1.13652596583557draftimg706570
67770Pseudomonas flexibilis JCM 14085GCA_001312105contigncbi1295129
67770Pseudomonas flexibilis CGMCC 1.1365GCA_900101515scaffoldncbi706570
67770Pseudomonas flexibilis JCM 14085GCA_000806415contigncbi706570

GC content

@refGC-contentmethod
1800760.4thermal denaturation, midpoint method (Tm)
2888860.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.306yes
gram-positiveno98.938yes
anaerobicno97.228yes
aerobicyes84.149yes
halophileno83.064no
spore-formingno96.395no
glucose-utilno65.699no
flagellatedyes82.177no
thermophileno99.307yes
glucose-fermentno90.612no

External links

@ref: 18007

culture collection no.: DSM 25351, CGMCC 1.1365, JCM 14085, CCUG 59930, CECT 7766

straininfo link

  • @ref: 82378
  • straininfo: 318381

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126738Pseudomonas tuomuerensis sp. nov., isolated from a bird's nest.Xin YH, Zhang DC, Liu HC, Zhou HL, Zhou YGInt J Syst Evol Microbiol10.1099/ijs.0.000547-02009Animals, Bacterial Typing Techniques, Base Composition, *Birds, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, *Housing, Animal, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPhenotype
Phylogeny22878554Pseudomonas linyingensis sp. nov.: a novel bacterium isolated from wheat soil subjected to long-term herbicides application.He WH, Wang YN, Du X, Zhou Y, Jia B, Bian J, Liu SJ, Chen GCCurr Microbiol10.1007/s00284-012-0187-32012China, Herbicides/*analysis, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, *Soil Microbiology, Soil Pollutants/*analysis, Triticum/*growth & developmentGenetics
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
Phylogeny26516088Reclassification of Serpens flexibilis Hespell 1977 as Pseudomonas flexibilis comb. nov., with Pseudomonas tuomuerensis Xin et al. 2009 as a later heterotypic synonym.Shin SK, Hwang CY, Cho YJ, Yi HSyst Appl Microbiol10.1016/j.syapm.2015.09.0072015Animals, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/analysis, Fatty Acids/analysis, Genome, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/*genetics/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18007Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25351)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25351
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
28888Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2532828776041
62162Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59930)https://www.ccug.se/strain?id=59930
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82378Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID318381.1StrainInfo: A central database for resolving microbial strain identifiers