Strain identifier

BacDive ID: 12861

Type strain: Yes

Species: Pseudomonas fragi

Strain history: CIP <- 1955, NCIB <- 1952, ATCC <- B.W. Hammer, Iowa State Coll., USA

NCBI tax ID(s): 296 (species)

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General

@ref: 1314

BacDive-ID: 12861

DSM-Number: 3456

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

description: Pseudomonas fragi DSM 3456 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from Unknown source.

NCBI tax id

  • NCBI tax id: 296
  • Matching level: species

strain history

@refhistory
1314<- ATCC <- B.W. Hammer
119443CIP <- 1955, NCIB <- 1952, ATCC <- B.W. Hammer, Iowa State Coll., USA

doi: 10.13145/bacdive12861.20230509.8.1

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 fragi
  • full scientific name: Pseudomonas fragi (Eichholz 1902) Gruber 1905 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacterium fragi

@ref: 1314

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas fragi

full scientific name: Pseudomonas fragi (Eichholz 1902) Gruber 1905

type strain: yes

Morphology

cell morphology

  • @ref: 119443
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1314CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
1314NUTRIENT 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
36579MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119443CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119443CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1314positivegrowth26mesophilic
36579positivegrowth30mesophilic
119443positivegrowth5-30
119443nogrowth41thermophilic
119443nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119443
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11944316947citrate+carbon source
1194434853esculin-hydrolysis
11944317632nitrate-reduction
11944316301nitrite-reduction
11944315882phenol+degradation
11944317632nitrate-respiration

antibiotic resistance

  • @ref: 119443
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11944335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
11944315688acetoin-

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
119443oxidase+
119443beta-galactosidase-3.2.1.23
119443alcohol dehydrogenase+1.1.1.1
119443gelatinase-
119443amylase-
119443DNase-
119443caseinase-3.4.21.50
119443catalase+1.11.1.6
119443tween esterase-
119443lecithinase-
119443lysine decarboxylase-4.1.1.18
119443ornithine decarboxylase-4.1.1.17
119443phenylalanine ammonia-lyase+4.3.1.24
119443tryptophan deaminase-
119443urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119443--++-++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1314---+----++----++-++-+
1314---+----++----++-++-+
1314---+----++----++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119443++-++--+------------+++-+------+-----------+----+++--+--++--+-+-+--+---+++-+++-++++----++++++++-+++

Isolation, sampling and environmental information

isolation

  • @ref: 119443
  • sample type: Unknown source

taxonmaps

  • @ref: 69479
  • File name: preview.99_442.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_368;99_442&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB680088
  • Sequence Identity:
  • Total samples: 2942
  • soil counts: 460
  • aquatic counts: 830
  • animal counts: 1081
  • plant counts: 571

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13141Risk group (German classification)
1194431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas fragi strain ATCC 4973 16S ribosomal RNA gene, partial sequenceAF0947331458ena296
20218Pseudomonas fragi strain ATCC 4973 16S ribosomal RNA gene, partial sequenceFJ971871791ena296
20218Pseudomonas fragi 16S-23S intergenic spacer strain CECT 446AJ279241324ena296
20218Pseudomonas fragi gene for 16S rRNA, strain: IFO 3458AB0214131527ena296
20218Pseudomonas fragi gene for 16S rRNA, partial sequence, strain: NBRC 3458AB6800881462ena296

External links

@ref: 1314

culture collection no.: DSM 3456, ATCC 4973, NRRL B-25, WDCM 00116, CIP 55.4, CCM 1974, CCUG 556, IFO 3458, LMG 2191, NCDO 752, NRRL: B-25, NCIMB 8542, CECT 446, NCTC 10689

straininfo link

  • @ref: 82073
  • straininfo: 13764

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics1797390Structure of the glycocalyx polysaccharide of Pseudomonas fragi ATCC 4973.Parolis LA, Parolis H, Dutton GG, Wing PL, Skura BJCarbohydr Res10.1016/0008-6215(92)84184-t1991Carbohydrate Conformation, Carbohydrate Sequence, Glycoproteins/*chemistry, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Molecular Structure, Polysaccharides/*chemistry, Pseudomonas/*chemistry
Cultivation2292518Centroid search optimization of cultural conditions affecting the production of extracellular proteinase by Pseudomonas fragi ATCC 4973.Myhara RM, Skura BJ Appl Bacteriol10.1111/j.1365-2672.1990.tb01545.x1990Bacteriological Techniques, Culture Media, Endopeptidases/*biosynthesis, Glutamine/pharmacology, Hydrogen-Ion Concentration, Oxygen/pharmacology, Pseudomonas/*enzymology/growth & development, TemperatureBiotechnology
Enzymology3909961Ultrastructural localization of an extracellular protease in Pseudomonas fragi by using the peroxidase-antiperoxidase reaction.Thompson SS, Naidu YM, Pestka JJAppl Environ Microbiol10.1128/aem.50.4.1038-1042.19851985Cell Fractionation, Endopeptidases/*isolation & purification, Enzyme-Linked Immunosorbent Assay, Immunoenzyme Techniques, Microscopy, Electron, Molecular Weight, Neprilysin, Pseudomonas/*enzymology/ultrastructure, Reagent Kits, DiagnosticPhylogeny
7081988Scanning electron microscope study of Pseudomonas fragi on intact and sarcoplasm-depleted bovine longissimus dorsi muscle.Yada RY, Skura BJAppl Environ Microbiol10.1128/aem.43.4.905-915.19821982Animals, Cattle, Cell Adhesion, Microscopy, Electron, Scanning, Muscles/*microbiology/ultrastructure, Pseudomonas/*ultrastructure
Phylogeny7119735Numerical taxonomy of psychrotrophic pseudomonads.Molin G, Ternstrom AJ Gen Microbiol10.1099/00221287-128-6-12491982Food Microbiology, Meat, Pseudomonas/*classificationBiotechnology
Metabolism8704960Acquisition of iron by the non-siderophore-producing Pseudomonas fragi.Champomier-Verges MC, Stintzi A, Meyer JMMicrobiology (Reading)10.1099/13500872-142-5-11911996Animals, Bacterial Outer Membrane Proteins/biosynthesis/genetics, Ethylenediamines/pharmacology, Gene Expression Regulation, Bacterial/drug effects, Iron/*metabolism/pharmacology, Iron Chelating Agents/pharmacology, Meat/microbiology, Metalloproteins/metabolism, Oxyquinoline/pharmacology, Pseudomonas/growth & development/isolation & purification/*metabolism, Pseudomonas aeruginosa/metabolism, Pseudomonas fluorescens/metabolism, Pseudomonas putida/metabolism, Siderophores/pharmacology, Species SpecificityPhylogeny
Biotechnology11559409The differential adherence capabilities of two Listeria monocytogenes strains in monoculture and multispecies biofilms as a function of temperature.Norwood DE, Gilmour ALett Appl Microbiol10.1046/j.1472-765x.2001.01004.x2001Bacterial Adhesion/*physiology, Biofilms/*growth & development, Food Handling/instrumentation, Food Microbiology, Food-Processing Industry, Listeria monocytogenes/cytology/growth & development/*physiology, Microscopy, Fluorescence, Stainless Steel, Temperature
Metabolism12390485Control of pyrimidine synthesis in Pseudomonas fragi.West TPLett Appl Microbiol10.1046/j.1472-765x.2002.01203.x2002Aspartate Carbamoyltransferase/genetics/metabolism, Dihydroorotase/analysis/metabolism, Dihydroorotate Dehydrogenase, Enzyme Induction, Gene Expression Regulation, Bacterial, *Gene Expression Regulation, Enzymologic, Orotate Phosphoribosyltransferase/analysis/metabolism, Orotidine-5'-Phosphate Decarboxylase/analysis/metabolism, Oxidoreductases/analysis/metabolism, *Oxidoreductases Acting on CH-CH Group Donors, Pseudomonas/enzymology/*metabolism, Pyrimidines/*biosynthesisEnzymology
Biotechnology16013377Production of volatile compounds in cheese by Pseudomonas fragi strains of dairy origin.Morales P, Fernandez-Garcia E, Nunez MJ Food Prot10.4315/0362-028x-68.7.13992005Aldehydes/analysis, Cheese/*microbiology, Colony Count, Microbial, Esters/analysis, Fermentation, *Food Microbiology, Gas Chromatography-Mass Spectrometry/methods, Hydrogen-Ion Concentration, Ketones/analysis, Odorants/*analysis, Pseudomonas fragi/growth & development/*metabolism, Sulfur Compounds/analysis, Time Factors, VolatilizationMetabolism
Transcriptome27339315Cold stress promoting a psychrotolerant bacterium Pseudomonas fragi P121 producing trehaloase.Mei YZ, Huang PW, Liu Y, He W, Fang WWWorld J Microbiol Biotechnol10.1007/s11274-016-2097-12016Antarctic Regions, Cold Temperature, Fermentation, Pseudomonas fragi/*growth & development/*isolation & purification, Sequence Analysis, DNA, Soil Microbiology, Stress, Physiological, Trehalose/*metabolismStress
31018281Functional Characteristics of Extracellular Vesicles Produced by Pseudomonas fragi ATCC 4973.Myhara RM, Skura BJ, Patel T, Nakajima MJ Food Prot10.4315/0362-028X-53.10.8591990
31113117Biofilm Formation by Listeria monocytogenes Utilizes a Primary Colonizing Microorganism in Flowing Systems.Sasahara KC, Zottola EAJ Food Prot10.4315/0362-028X-56.12.10221993
31193311Efficacy of olive leaf extract (Olea europaea L. cv Gentile di Larino) in marinated anchovies (Engraulis encrasicolus, L.) process.Testa B, Lombardi SJ, Macciola E, Succi M, Tremonte P, Iorizzo MHeliyon10.1016/j.heliyon.2019.e017272019
Phylogeny31622235Pseudomonas bubulae sp. nov., isolated from beef.Lick S, Krockel L, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski JInt J Syst Evol Microbiol10.1099/ijsem.0.0037512020Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Red Meat/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny31730030Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate.Hofmann K, Huptas C, Doll EV, Scherer S, Wenning MInt J Syst Evol Microbiol10.1099/ijsem.0.0038512020Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, *Food Microbiology, Genes, Bacterial, Germany, Milk/*microbiology, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Phylogeny34097596Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef.Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Krockel LInt J Syst Evol Microbiol10.1099/ijsem.0.0048222021Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Genes, Bacterial, Germany, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Red Meat/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryBiotechnology
Enzymology34684733Phenolic Profile, Antioxidant Capacity and Antimicrobial Activity of Nettle Leaves Extracts Obtained by Advanced Extraction Techniques.Elez Garofulic I, Malin V, Repajic M, Zoric Z, Pedisic S, Sternisa M, Smole Mozina S, Dragovic-Uzelac VMolecules10.3390/molecules262061532021Anti-Bacterial Agents/isolation & purification, Anti-Infective Agents/pharmacology, Antioxidants/isolation & purification/pharmacology, Chromatography, High Pressure Liquid, Flavonoids/analysis, Microwaves, Phenols/*analysis/chemistry/*isolation & purification, Plant Extracts/chemistry/pharmacology, Plant Leaves/chemistry/metabolism, Urtica dioica/*metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1314Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3456)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3456
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
36579Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4605
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
82073Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13764.1StrainInfo: A central database for resolving microbial strain identifiers
119443Curators of the CIPCollection of Institut Pasteur (CIP 55.4)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2055.4