Strain identifier

BacDive ID: 5630

Type strain: Yes

Species: Psychroflexus halocasei

Strain Designation: WS 4520, G 5209

Strain history: <- H. Seiler, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC 4520 <- J. Hüfner, Milchwirtschaftliches Institut Dr. Hüfner, Hergatz, Germany

NCBI tax ID(s): 908615 (species)

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General

@ref: 17232

BacDive-ID: 5630

DSM-Number: 23581

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

description: Psychroflexus halocasei WS 4520 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sticky surface of a semi-hard, Raclette-type cheese.

NCBI tax id

  • NCBI tax id: 908615
  • Matching level: species

strain history

  • @ref: 17232
  • history: <- H. Seiler, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC 4520 <- J. Hüfner, Milchwirtschaftliches Institut Dr. Hüfner, Hergatz, Germany

doi: 10.13145/bacdive5630.20230509.8.1

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 halocasei
  • full scientific name: Psychroflexus halocasei Seiler et al. 2012

@ref: 17232

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Psychroflexus

species: Psychroflexus halocasei

full scientific name: Psychroflexus halocasei Seiler et al. 2012

strain designation: WS 4520, G 5209

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30385negative3 µm0.55 µmrod-shapedno
69480negative99.997

colony morphology

  • @ref: 62082
  • incubation period: 2 days

pigmentation

  • @ref: 30385
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17232
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17232positivegrowth28mesophilic
30385positivegrowth08-35
30385positiveoptimum28.5mesophilic
62082positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30385positivegrowth6-9.5alkaliphile
30385positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30385aerobe
62082aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
30385NaClpositivegrowth2.5-16 %
30385NaClpositiveoptimum7 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3038516449alanine+carbon source
3038522653asparagine+carbon source
3038523652dextrin+carbon source
3038524996lactate+carbon source
3038517306maltose+carbon source
3038518257ornithine+carbon source
3038517272propionate+carbon source
3038553426tween 80+carbon source

enzymes

@refvalueactivityec
30385acid phosphatase+3.1.3.2
30385alkaline phosphatase+3.1.3.1
30385catalase+1.11.1.6
30385gelatinase+
30385cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17232sticky surface of a semi-hard, Raclette-type cheeseSalzburgAustriaAUTEurope
62082Cheese rindSalzburgAustriaAUTEurope2007

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_158719.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_423;96_44914;97_57552;98_76291;99_158719&stattab=map
  • Last taxonomy: Psychroflexus halocasei subclade
  • 16S sequence: FR714910
  • Sequence Identity:
  • Total samples: 227
  • soil counts: 12
  • aquatic counts: 148
  • animal counts: 63
  • plant counts: 4

Safety information

risk assessment

  • @ref: 17232
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17232
  • description: Psychroflexus halocasei partial 16S rRNA gene, type strain WCC 4520T
  • accession: FR714910
  • length: 1488
  • database: ena
  • NCBI tax ID: 908615

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychroflexus halocasei DSM 23581GCA_900107595scaffoldncbi908615
66792Psychroflexus halocasei strain DSM 23581908615.3wgspatric908615
66792Psychroflexus halocasei DSM 235812675903162draftimg908615

GC content

@refGC-contentmethod
1723233.6high performance liquid chromatography (HPLC)
3038533.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.664no
glucose-fermentno86.393no
flagellatedno94.35no
gram-positiveno97.771yes
anaerobicno99.031no
aerobicyes88.229yes
halophileyes91.691yes
spore-formingno95.378no
thermophileno99.168yes
glucose-utilyes83.033no

External links

@ref: 17232

culture collection no.: DSM 23581, CCUG 59705, LMG 25857, WCC 4520

straininfo link

  • @ref: 75113
  • straininfo: 370034

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21984670Psychroflexus halocasei sp. nov., isolated from a microbial consortium on a cheese.Seiler H, Bleicher A, Busse HJ, Hufner J, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.034801-02011Bacterial Typing Techniques, Base Composition, Cheese/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, *Food Microbiology, *Microbial Consortia, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisBiotechnology
Phylogeny25048209Psychroflexus salarius sp. nov., isolated from Gomso salt pan.Chun J, Kang JY, Jahng KYInt J Syst Evol Microbiol10.1099/ijs.0.065219-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17232Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23581)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23581
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
30385Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2672428776041
62082Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59705)https://www.ccug.se/strain?id=59705
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
75113Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370034.1StrainInfo: A central database for resolving microbial strain identifiers