Strain identifier
BacDive ID: 5056
Type strain:
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
NCBI tax ID(s): 1122977 (strain), 82985 (species)
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 id | Matching level |
---|---|
82985 | species |
1122977 | strain |
strain history
@ref | history |
---|---|
2220 | <- ATCC <- CNCTC <- E. Aldová, IHE |
67770 | R. Sakazaki 560 <-- CNCTC Eb11/82 <-- E. Aldová <-- A. Brezinova. |
119423 | CIP <- 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
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_5563_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_5563_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_5563_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_5563_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_5563_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2220 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
2220 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
37153 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
119423 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2220 | positive | growth | 30 | mesophilic |
37153 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 17632 | nitrate | + | reduction |
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | + | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 17997 | dinitrogen | no |
68368 | 16301 | nitrite | yes |
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 46746 C12:0 3.3 12 46746 C13:0 1.6 13 46746 C14:0 18.7 14 46746 C15:0 6 15 46746 C16:0 16.7 16 46746 C17:0 0.7 17 46746 C14:0 3OH/C16:1 ISO I 15.8 15.485 46746 C16:1 ω7c 30.9 15.819 46746 C18:1 ω7c /12t/9t 3.9 17.824 46746 C18:2 ω6,9c/C18:0 ANTE 1 17.724 46746 Unidentified 0.6 13.736 46746 Unidentified 0.8 18.549 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX | NO2 | N2 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2220 | - | - | - | - | - | + | - | - | - | - | - | + | - | + | - | - | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | continent | sampling date | geographic location | origin.country | isolation date |
---|---|---|---|---|---|---|---|
2220 | well water "Dobré" | Czechoslovakia | Europe | ||||
46746 | Well water | Czechoslovakia | Europe | 1976 | Frydek-Mistek | ||
67770 | Well water | Czechoslovakia | Europe | ||||
119423 | Environment, Well water | Czech Republic | Europe | Frydek Mistek | CZE | 1976 |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
2220 | 1 | Risk group (German classification) |
119423 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pragia fontium DSM 5563 = ATCC 49100 | 1122977.4 | wgs | patric | 1122977 |
66792 | Pragia fontium strain DSM 5563 | 82985.9 | wgs | patric | 82985 |
66792 | Pragia fontium DSM 5563 | 2602042030 | draft | img | 1122977 |
67770 | Pragia fontium DSM 5563 = ATCC 49100 | GCA_900112475 | scaffold | ncbi | 1122977 |
67770 | Pragia fontium DSM 5563 | GCA_004959795 | contig | ncbi | 82985 |
66792 | Pragia fontium JCM24417 | GCA_024342125 | contig | ncbi | 82985 |
GC content
@ref | GC-content | method |
---|---|---|
2220 | 46.0 | thermal denaturation, midpoint method (Tm) |
67770 | 46-47 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 83.614 | no |
flagellated | no | 61.88 | no |
gram-positive | no | 97.7 | no |
anaerobic | no | 90.58 | no |
aerobic | yes | 62.318 | no |
halophile | no | 95.036 | no |
spore-forming | no | 95.948 | no |
thermophile | no | 99.001 | yes |
glucose-util | yes | 88.937 | no |
glucose-ferment | yes | 88.218 | yes |
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
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10872281 | [The properties of Pragia fontium bacteria isolated on the territories of Ukraine and the Czech Republic]. | Pokhyl SI | Mikrobiol Z | 2000 | Amino 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 Microbiology | Biotechnology | |
Phylogeny | 33480837 | Jinshanibacter, 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 J | Int J Syst Evol Microbiol | 2021 | Animals, 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/chemistry | Transcriptome | 10.1099/ijsem.0.004653 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2220 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5563) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5563 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
37153 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15627 | ||||
46746 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 18073) | https://www.ccug.se/strain?id=18073 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
69479 | João 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 | |||
74551 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3861.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119423 | Curators of the CIP | Collection of Institut Pasteur (CIP 103791) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103791 |