Strain identifier

BacDive ID: 4367

Type strain: Yes

Species: Pluralibacter gergoviae

Strain Designation: 16-74

Strain history: CIP <- 1976, C. Richard, Inst. Pasteur, Paris, France: strain 16-74, Enterobacter gergoviae

NCBI tax ID(s): 1354260 (strain), 61647 (species)

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General

@ref: 3523

BacDive-ID: 4367

DSM-Number: 9245

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Pluralibacter gergoviae 16-74 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from urine.

NCBI tax id

NCBI tax idMatching level
61647species
1354260strain

strain history

@refhistory
3523<- CIP; CIP 76.01 <- C. Richard; 16-74
67770Y. Kosako 221 <-- R. Sakazaki 221 <-- CDC 604-77 <-- CIP 76.1 <-- C. Richard 16-74.
119607CIP <- 1976, C. Richard, Inst. Pasteur, Paris, France: strain 16-74, Enterobacter gergoviae

doi: 10.13145/bacdive4367.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Pluralibacter
  • species: Pluralibacter gergoviae
  • full scientific name: Pluralibacter gergoviae (Brenner et al. 1980) Brady et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Enterobacter gergoviae

@ref: 3523

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Pluralibacter

species: Pluralibacter gergoviae

full scientific name: Pluralibacter gergoviae (Brenner et al. 1980) Brady et al. 2013

strain designation: 16-74

type strain: yes

Morphology

cell morphology

  • @ref: 119607
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 119607
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3523TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
3523COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
3523TRYPTICASE 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
38473MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119607CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3523positivegrowth30mesophilic
38473positivegrowth30mesophilic
67770positivegrowth37mesophilic
119607positivegrowth10-41
119607nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119607
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate+builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol-fermentation30911
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea+hydrolysis16199
68368ornithine+degradation18257
68368lysine+degradation25094
68368arginine-hydrolysis29016
119607mannitol+fermentation29864
119607citrate+carbon source16947
119607glucose+fermentation17234
119607lactose-fermentation17716
119607nitrate+reduction17632
119607nitrite+reduction16301
119607malonate+assimilation15792
119607sodium thiosulfate-builds gas from132112
119607glucose+degradation17234

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11960735581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
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
119607oxidase-
119607beta-galactosidase+3.2.1.23
119607alcohol dehydrogenase-1.1.1.1
119607catalase+1.11.1.6
119607lysine decarboxylase+4.1.1.18
119607ornithine decarboxylase+4.1.1.17
119607tryptophan deaminase-
119607urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119607-+----+---++----++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
3523+-++--+--+-+++-+++++-
3523+-+++-+--+-+++-+++++-
3523+-+++-+--+-++--+++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119607+--+++---++++-+-++---+-++++++/-+++--++/---+-----+-+++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119607+++++-++++++--++++++++-+--+----+++-------------+-++-++--++-+++++++++-+-+++++---++-++--+-++++++-++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3523urineClermont-FerrandFranceFRAEurope
67770Urine
119607UrineClermont FerrandFranceFRAEurope1974

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_927.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_632;98_730;99_927&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: AB004748
  • Sequence Identity:
  • Total samples: 2113
  • soil counts: 76
  • aquatic counts: 191
  • animal counts: 1487
  • plant counts: 359

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
35232Risk group (German classification)
1196072Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3523
  • description: Enterobacter gergoviae gene for 16S ribosomal RNA, partial sequence
  • accession: AB004748
  • length: 1450
  • database: ena
  • NCBI tax ID: 1354260

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pluralibacter gergoviae ATCC 33028 = NBRC 1057061354260.8wgspatric1354260
66792Pluralibacter gergoviae strain NCTC1143461647.66wgspatric61647
66792Pluralibacter gergoviae NBRC 1057062681812978draftimg1354260
67770Pluralibacter gergoviae ATCC 33028 = NBRC 105706GCA_001598855contigncbi1354260
67770Pluralibacter gergoviae NCTC11434GCA_900454925contigncbi61647

GC content

  • @ref: 67770
  • GC-content: 60
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.61no
gram-positiveno97.968no
anaerobicno96.313no
halophileno92.134no
spore-formingno92.516no
thermophileno99.203no
glucose-utilyes95.881no
flagellatedno52.889no
aerobicyes73.145no
glucose-fermentyes90.283yes

External links

@ref: 3523

culture collection no.: DSM 9245, ATCC 33028, CDC 604-77, CIP 76.01, JCM 1234, LMG 5739, NCTC 11434, CCUG 14557, CECT 857, CIP 76.1, HUT 8110, NBRC 105706, NCIMB 13304

straininfo link

  • @ref: 73858
  • straininfo: 13641

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism25355161Enterobacter gergoviae membrane modifications are involved in the adaptive response to preservatives used in cosmetic industry.Periame M, Pages JM, Davin-Regli AJ Appl Microbiol10.1111/jam.126762014Adaptation, Physiological, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/metabolism, Cell Membrane Permeability/drug effects, Cosmetics, Disinfectants/pharmacology, Enterobacter/*drug effects/metabolism, Flagellin/analysis, Membrane Proteins/metabolism, Peroxiredoxins/analysis, Preservatives, Pharmaceutical/*pharmacology, ThiazolesPathogenicity
Pathogenicity25919899Phenotypic changes contributing to Enterobacter gergoviae biocide resistance.Periame M, Philippe N, Condell O, Fanning S, Pages JM, Davin-Regli ALett Appl Microbiol10.1111/lam.124352015Biofilms/drug effects, Cosmetics, Disinfectants/*pharmacology, Drug Resistance, Bacterial/*physiology, Enterobacter/*drug effects/genetics, Fimbriae, Bacterial, Flagella/physiology, Microbial Sensitivity Tests, Preservatives, Pharmaceutical/*pharmacology, Thiazoles/*pharmacology, Triclosan/*pharmacology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3523Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9245)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9245
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
38473Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10769
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
73858Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13641.1StrainInfo: A central database for resolving microbial strain identifiers
119607Curators of the CIPCollection of Institut Pasteur (CIP 76.1)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2076.1