Strain identifier

BacDive ID: 23019

Type strain: Yes

Species: Psychroflexus sediminis

Strain Designation: YIM-C238

Strain history: <- S.-K. Tang, YIM; YIM-C238

NCBI tax ID(s): 470826 (species)

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General

@ref: 19085

BacDive-ID: 23019

DSM-Number: 19803

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

description: Psychroflexus sediminis YIM-C238 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample, Dachaidamu salt lake in the Qaidam Basin.

NCBI tax id

  • NCBI tax id: 470826
  • Matching level: species

strain history

  • @ref: 19085
  • history: <- S.-K. Tang, YIM; YIM-C238

doi: 10.13145/bacdive23019.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Psychroflexus
  • species: Psychroflexus sediminis
  • full scientific name: Psychroflexus sediminis Chen et al. 2009

@ref: 19085

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Psychroflexus

species: Psychroflexus sediminis

full scientific name: Psychroflexus sediminis Chen et al. 2009

strain designation: YIM-C238

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28988negative3.0-6.0 µm0.4-1.0 µmrod-shapedno
69480no90.887
69480negative99.992

pigmentation

  • @ref: 28988
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19085
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19085positivegrowth25mesophilic
28988positivegrowth10-40
28988positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
28988positivegrowth06-10alkaliphile
28988positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 28988
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
28988no
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
28988NaClpositivegrowth0.5-6 %
28988NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2898835391aspartate+carbon source
2898823652dextrin+carbon source
2898828757fructose+carbon source
2898828087glycogen+carbon source
2898817306maltose+carbon source
2898829864mannitol+carbon source
2898837657methyl D-glucoside+carbon source
2898817822serine+carbon source
2898830031succinate+carbon source
2898817992sucrose+carbon source
2898827082trehalose+carbon source
2898853426tween 80+carbon source
289884853esculin+hydrolysis
2898817632nitrate+reduction

enzymes

@refvalueactivityec
28988acid phosphatase+3.1.3.2
28988alkaline phosphatase+3.1.3.1
28988catalase+1.11.1.6
28988gelatinase+
28988cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 19085
  • sample type: sediment sample, Dachaidamu salt lake in the Qaidam Basin
  • geographic location: Qinghai Province,
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_35527.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_423;96_1937;97_2329;98_26218;99_35527&stattab=map
  • Last taxonomy: Psychroflexus sediminis subclade
  • 16S sequence: EU135715
  • Sequence Identity:
  • Total samples: 21
  • aquatic counts: 21

Safety information

risk assessment

  • @ref: 19085
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19085
  • description: Psychroflexus sediminis strain YIM C238 16S ribosomal RNA gene, partial sequence
  • accession: EU135715
  • length: 1475
  • database: ena
  • NCBI tax ID: 470826

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychroflexus sediminis DSM 19803GCA_900099815scaffoldncbi470826
66792Psychroflexus sediminis strain DSM 19803470826.3wgspatric470826
66792Psychroflexus sediminis DSM 198032622736510draftimg470826

GC content

  • @ref: 28988
  • GC-content: 35.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.664yes
flagellatedno94.117yes
gram-positiveno97.991no
anaerobicno99.051yes
aerobicyes88.852yes
halophileyes83.02no
spore-formingno96.351yes
glucose-fermentno90.052no
thermophileno98.908no
glucose-utilyes81.269no

External links

@ref: 19085

culture collection no.: DSM 19803, CCTCC AA 207030, KCTC 22166

straininfo link

  • @ref: 87259
  • straininfo: 402816

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244443Psychroflexus sediminis sp. nov., a mesophilic bacterium isolated from salt lake sediment in China.Chen YG, Cui XL, Wang YX, Tang SK, Zhang YQ, Li WJ, Liu JH, Peng Q, Xu LHInt J Syst Evol Microbiol10.1099/ijs.0.003269-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Fresh Water/chemistry/*microbiology, Genes, rRNA, Geologic Sediments/chemistry/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityEnzymology
Phylogeny33118924Psychroflexus aurantiacus sp. nov., isolated from soil in the Yellow River Delta wetlands.Wu SG, Wang JJ, Wang JN, Chen Q, Sheng DH, Li YZInt J Syst Evol Microbiol10.1099/ijsem.0.0045272020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19085Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19803)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19803
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
28988Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2542128776041
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
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
87259Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402816.1StrainInfo: A central database for resolving microbial strain identifiers