Strain identifier

BacDive ID: 5132

Type strain: Yes

Species: Serratia ficaria

Strain Designation: 4024

Strain history: CIP <- 1979, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 4024

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

@ref: 1775

BacDive-ID: 5132

DSM-Number: 4569

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

description: Serratia ficaria 4024 is a mesophilic, motile bacterium that was isolated from fig.

NCBI tax id

NCBI tax idMatching level
61651species
1411141strain

strain history

@refhistory
1775<- CIP <- P.A.D. Grimont; 4024
330571979, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 4024
67770Y. Kosako 316 <-- R. Sakazaki 316 <-- ATCC 33105 <-- M. P. Starr <-- P. A. D. Grimont 4024.
119342CIP <- 1979, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 4024

doi: 10.13145/bacdive5132.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Serratia
  • species: Serratia ficaria
  • full scientific name: Serratia ficaria Grimont et al. 1981

@ref: 1775

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Serratia

species: Serratia ficaria

full scientific name: Serratia ficaria Grimont et al. 1981

strain designation: 4024

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.6
6948099.93negative
119342yesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1775REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33057MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119342CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
119342CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1775positivegrowth30mesophilic
33057positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.464

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
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
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
68368nitrate+reduction17632
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol+fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
68372glycerol+assimilation17754
68372erythritol+assimilation17113
68372D-arabinose-assimilation17108
68372L-arabinose+assimilation30849
68372D-ribose+assimilation16988
68372D-xylose+assimilation65327
68372L-xylose-assimilation65328
68372ribitol-assimilation15963
68372methyl beta-D-xylopyranoside-assimilation74863
68372D-galactose+assimilation12936
68372D-glucose+assimilation17634
68372D-fructose+assimilation15824
68372D-mannose+assimilation16024
68372L-sorbose-assimilation17266
68372L-rhamnose+assimilation62345
68372galactitol-assimilation16813
68372myo-inositol+assimilation17268
68372D-mannitol+assimilation16899
68372sorbitol+assimilation30911
68372methyl alpha-D-mannoside-assimilation43943
68372methyl alpha-D-glucopyranoside-assimilation320061
68372N-acetylglucosamine+assimilation59640
68372amygdalin-assimilation27613
68372arbutin+assimilation18305
68372esculin+assimilation4853
68372salicin+assimilation17814
68372cellobiose+assimilation17057
68372maltose+assimilation17306
68372lactose-assimilation17716
68372melibiose+assimilation28053
68372sucrose+assimilation17992
68372trehalose+assimilation27082
68372inulin-assimilation15443
68372melezitose+assimilation6731
68372raffinose+assimilation16634
68372starch-assimilation28017
68372glycogen-assimilation28087
68372xylitol-assimilation17151
68372gentiobiose+assimilation28066
68372turanose+assimilation32528
68372D-lyxose-assimilation62318
68372D-tagatose-assimilation16443
68372D-fucose-assimilation28847
68372L-fucose+assimilation18287
68372D-arabitol+assimilation18333
68372L-arabitol+assimilation18403
68372gluconate+assimilation24265
68372Potassium 2-ketogluconate+assimilation
68372Potassium 5-ketogluconate+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
1775+---+----+++++++++++-+-
1775+---+----+++++++++++-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
1775-++++++-+-++++-+-+++-++++++++++++-++---+++-++++--+

API 50CHas

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
1775-++-+++---++++-+-+++--+-+++++-+++-++---++---++++++

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
1775fig
46119Calimyrna fig,Winters1977
67770Smyrna figs
119342Calimyrna figWinters, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Fruit (Seed)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17751Risk group (German classification)
1193421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Serratia ficaria gene for 16S ribosomal RNA, partial sequenceAB0047451449ena61651
20218Serratia ficaria gene for 16S rRNA, partial sequence, strain: NBRC 102596AB6818731467ena61651
20218Serratia ficaria partial 16S rRNA gene, strain NCTC 12148AJ2790541362ena61651
1775Serratia ficaria 16S rRNA gene (strain DSM 4569)AJ2334281495ena61651

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serratia ficaria NCTC12148GCA_900187015completencbi61651
66792Serratia ficaria NBRC 1025961411141.3wgspatric1411141
66792Serratia ficaria strain NCTC1214861651.3completepatric61651
66792Serratia ficaria NBRC 1025962731957628draftimg1411141
66792Serratia ficaria NCTC 121482773857830completeimg61651
67770Serratia ficaria NBRC 102596GCA_001590885contigncbi1411141

GC content

  • @ref: 67770
  • GC-content: 59.4-59.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.262no
flagellatedno54.998no
gram-positiveno97.906no
anaerobicno98.404no
aerobicyes86.332no
halophileno93.31no
spore-formingno95.564no
thermophileno99.733no
glucose-utilyes94.84yes
glucose-fermentyes91.175no

External links

@ref: 1775

culture collection no.: DSM 4569, ATCC 33105, CIP 79.23, ICPB 4050, CCUG 14507, NCTC 12148, LMG 7881, JCM 1241, BCRC 14809, CCM 3418, IAM 13540, NBRC 102596

straininfo link

  • @ref: 74624
  • straininfo: 389412

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25281728Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves.Garcia-Fraile P, Chudickova M, Benada O, Pikula J, Kolarik MInt J Syst Evol Microbiol10.1099/ijs.0.066407-02014Animals, Bacterial Typing Techniques, Base Composition, Caves, Chiroptera/*microbiology, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/isolation & purificationGenetics
Phylogeny31089912Serratia microhaemolytica sp. nov., isolated from an artificial lake in Southern China.Wang J, Zheng ML, Jiao JY, Wang WJ, Li S, Xiao M, Chen C, Qu PH, Li WJAntonie Van Leeuwenhoek10.1007/s10482-019-01273-92019Anaerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Hydrogen-Ion Concentration, Lakes/*microbiology, Locomotion, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification/genetics/*isolation & purification/physiology, Sodium Chloride/metabolism, TemperatureTranscriptome
Phylogeny31971498Serratia vespertilionis (Garcia-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981).Garcia-Fraile P, Sproer C, Chesneau O, Criscuolo A, Lang E, Clermont DInt J Syst Evol Microbiol10.1099/ijsem.0.0039962020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serratia/*classification, Whole Genome SequencingTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1775Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4569)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4569
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
33057Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11049
46119Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14507)https://www.ccug.se/strain?id=14507
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
68372Automatically annotated from API 50CH assim
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
74624Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389412.1StrainInfo: A central database for resolving microbial strain identifiers
119342Curators of the CIPCollection of Institut Pasteur (CIP 79.23)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2079.23