Strain identifier

BacDive ID: 5056

Type strain: Yes

Species: Pragia fontium

Strain Designation: HG16, IHE, 20125, HG 16

Strain history: CIP <- 1993, J. Sourek, NIPH, Prague, Czech Republic: strain 20125 <- A. Brezinova, Hyg. Stat., Frydek-Mistek, Czechoslovakia: strain HG 16

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

@ref: 2220

BacDive-ID: 5056

DSM-Number: 5563

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Pragia fontium HG16 is a mesophilic bacterium that was isolated from well water "Dobré".

NCBI tax id

NCBI tax idMatching level
82985species
1122977strain

strain history

@refhistory
2220<- ATCC <- CNCTC <- E. Aldová, IHE
67770R. Sakazaki 560 <-- CNCTC Eb11/82 <-- E. Aldová <-- A. Brezinova.
119423CIP <- 1993, J. Sourek, NIPH, Prague, Czech Republic: strain 20125 <- A. Brezinova, Hyg. Stat., Frydek-Mistek, Czechoslovakia: strain HG 16

doi: 10.13145/bacdive5056.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Budviciaceae
  • genus: Pragia
  • species: Pragia fontium
  • full scientific name: Pragia fontium Aldová et al. 1988

@ref: 2220

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Budviciaceae

genus: Pragia

species: Pragia fontium

full scientific name: Pragia fontium Aldová et al. 1988

strain designation: HG16, IHE, 20125, HG 16

type strain: yes

Morphology

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_5563_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5563_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5563_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5563_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_5563_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2220TRYPTICASE 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
2220NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37153MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119423CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2220positivegrowth30mesophilic
37153positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46746C12:03.312
    46746C13:01.613
    46746C14:018.714
    46746C15:0615
    46746C16:016.716
    46746C17:00.717
    46746C14:0 3OH/C16:1 ISO I15.815.485
    46746C16:1 ω7c30.915.819
    46746C18:1 ω7c /12t/9t3.917.824
    46746C18:2 ω6,9c/C18:0 ANTE117.724
    46746Unidentified0.613.736
    46746Unidentified0.818.549
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
2220-----+-----+-+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentsampling dategeographic locationorigin.countryisolation date
2220well water "Dobré"CzechoslovakiaEurope
46746Well waterCzechoslovakiaEurope1976Frydek-Mistek
67770Well waterCzechoslovakiaEurope
119423Environment, Well waterCzech RepublicEuropeFrydek MistekCZE1976

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3428.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1794;97_2146;98_2630;99_3428&stattab=map
  • Last taxonomy: Pragia fontium subclade
  • 16S sequence: AJ233424
  • Sequence Identity:
  • Total samples: 989
  • soil counts: 103
  • aquatic counts: 113
  • animal counts: 616
  • plant counts: 157

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
22201Risk group (German classification)
1194231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pragia fontium 16S rRNA gene (strain DSM 5563)
  • accession: AJ233424
  • length: 1485
  • database: ena
  • NCBI tax ID: 82985

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pragia fontium DSM 5563 = ATCC 491001122977.4wgspatric1122977
66792Pragia fontium strain DSM 556382985.9wgspatric82985
66792Pragia fontium DSM 55632602042030draftimg1122977
67770Pragia fontium DSM 5563 = ATCC 49100GCA_900112475scaffoldncbi1122977
67770Pragia fontium DSM 5563GCA_004959795contigncbi82985
66792Pragia fontium JCM24417GCA_024342125contigncbi82985

GC content

@refGC-contentmethod
222046.0thermal denaturation, midpoint method (Tm)
6777046-47thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes83.614no
flagellatedno61.88no
gram-positiveno97.7no
anaerobicno90.58no
aerobicyes62.318no
halophileno95.036no
spore-formingno95.948no
thermophileno99.001yes
glucose-utilyes88.937no
glucose-fermentyes88.218yes

External links

@ref: 2220

culture collection no.: LMG 7875, DSM 5563, ATCC 49100, CCUG 18073, CDC 963-84, CNCTC Eb11/82, DRL 20125, JCM 24417, CIP 103791, NCTC 12283, NCIMB 12865

straininfo link

  • @ref: 74551
  • straininfo: 3861

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny10872281[The properties of Pragia fontium bacteria isolated on the territories of Ukraine and the Czech Republic].Pokhyl SIMikrobiol Z2000Amino Acid Sequence, Base Sequence, Chromosomes, Bacterial/genetics, Czech Republic, DNA, Bacterial/genetics, Enterobacteriaceae/classification/genetics/*isolation & purification/metabolism, Escherichia coli/genetics, Feces/microbiology, Food Microbiology, Humans, Phenotype, Sequence Homology, Nucleic Acid, Soil Microbiology, Ukraine, Water MicrobiologyBiotechnology
Phylogeny33480837Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii).Ge Y, Wang B, Yang J, Lai XH, Zhang G, Lu S, Jin D, Huang Y, Cheng Y, Zhang X, Xu JInt J Syst Evol Microbiol2021Animals, Bacterial Typing Techniques, Base Composition, China, Cloaca/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Finches/*microbiology, Gammaproteobacteria/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome10.1099/ijsem.0.004653

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2220Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5563)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5563
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
37153Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15627
46746Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18073)https://www.ccug.se/strain?id=18073
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
74551Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3861.1StrainInfo: A central database for resolving microbial strain identifiers
119423Curators of the CIPCollection of Institut Pasteur (CIP 103791)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103791