Strain identifier

BacDive ID: 4325

Type strain: Yes

Species: Citrobacter freundii

Strain history: CIP <- 1957, NCTC <- 1953, ATCC <- C.H. Werkman, strain Br (Braak)

NCBI tax ID(s): 1006003 (strain), 546 (species)

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

@ref: 9097

BacDive-ID: 4325

DSM-Number: 30039

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, antibiotic resistance

description: Citrobacter freundii DSM 30039 is an aerobe, mesophilic, motile bacterium that has multiple antibiotic resistances and was isolated from water of a canal.

NCBI tax id

NCBI tax idMatching level
546species
1006003strain

strain history

@refhistory
9097<- ATCC; ATCC 8090 <- C. H. Werkman;
67770R. Sakazaki 96 <-- ATCC 8090 <-- C. H. Werkman.
119459CIP <- 1957, NCTC <- 1953, ATCC <- C.H. Werkman, strain Br (Braak)

doi: 10.13145/bacdive4325.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Citrobacter
  • species: Citrobacter freundii
  • full scientific name: Citrobacter freundii (Braak 1928) Werkman and Gillen 1932 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Bethesda ballerupensis
    20215Bacterium freundii

@ref: 9097

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter freundii

full scientific name: Citrobacter freundii (Braak 1928) Werkman and Gillen 1932

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.498
6948099.979negative
119459yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9097COLUMBIA 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
9097TRYPTICASE 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
42192MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119459CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
9097positivegrowth30mesophilic
42192positivegrowth30mesophilic
44198positivegrowth37mesophilic
67770positivegrowth37mesophilic
119459positivegrowth10-41
119459nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44198aerobe
119459facultative anaerobe

antibiogram

@refmediumPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactamincubation temperatureoxygen condition
9097Mueller-Hinton Agar001636261420-2238423428-303024260803840143022-24014-163620223603834000032
9097M 9200163826142038423232322426-281080344014-163026016262022-243610-12403200003237aerob
9097M 9200163826142038423232322426-281080344014-163026016262022-243610-12403200003237aerob

spore formation

@refspore formationconfidence
69481no100
69480no99.852
119459no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836818257ornithine-degradation
6836825094lysine-degradation
11945929864mannitol+fermentation
11945916947citrate+carbon source
11945917234glucose+fermentation
11945917716lactose+fermentation
11945917632nitrate+reduction
11945916301nitrite+reduction
11945915792malonate-assimilation
119459132112sodium thiosulfate+builds gas from
11945917234glucose+degradation

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideyes
11945935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole-
11945915688acetoin-
11945917234glucose+

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
68368beta-galactosidase+3.2.1.23
119459oxidase-
119459beta-galactosidase+3.2.1.23
119459alcohol dehydrogenase-1.1.1.1
119459gelatinase-
119459catalase+1.11.1.6
119459lysine decarboxylase-4.1.1.18
119459ornithine decarboxylase-4.1.1.17
119459tryptophan deaminase-
119459urease-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
119459-++--+----++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
9097++--++---+/--++++++-++-
9097++--++-----+++++++++-
9097++--++-----+++++++++-
9097+----+-----++-+++-++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119459++++++++++++-+-+++-++++++------++++-+--+-+++++--+++-++++++-++----++-++-----+---++-+++-+-+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample type
9097water of a canal
119459Environment, Water (channel)

taxonmaps

  • @ref: 69479
  • File name: preview.99_644.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_17;99_644&stattab=map
  • Last taxonomy: Citrobacter
  • 16S sequence: AB626119
  • Sequence Identity:
  • Total samples: 66090
  • soil counts: 3252
  • aquatic counts: 7413
  • animal counts: 52478
  • plant counts: 2947

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
90972Risk group (German classification)
1194591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Citrobacter freundii strain ATCC 8090 16S ribosomal RNA gene, partial sequenceFJ971857797ena1006003
20218Citrobacter freundii partial 16S rRNA gene, strain ATCC 8090FM207096390ena1006003
20218Citrobacter freundii gene for 16S rRNA, partial sequence, strain: JCM 1657AB6261191464ena546
20218Citrobacter freundii partial 16S rRNA gene, strain LMG 3246HG7989061427ena546
20218Citrobacter freundii gene for 16S rRNA, partial sequence, strain: NBRC 12681AB6803141467ena546
20218Citrobacter freundii gene for 16S ribosomal RNA, partial sequence, strain: NBRC 12681AB7416881324ena546
9097Citrobacter freundii 16S rRNA gene (strain DSM 30039)AJ2334081505ena1006003

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 12681GCA_011064845completencbi1006003
66792Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 12681GCA_000759735contigncbi1006003
66792Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 12681GCA_000734905contigncbi1006003
66792Citrobacter freundii NCTC9750GCA_900635425completencbi546
66792Citrobacter freundii ATCC 8090 = MTCC 16581006003.7wgspatric1006003
66792Citrobacter freundii ATCC 8090 = MTCC 16581006003.3wgspatric1006003
66792Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 126811006003.13completepatric1006003
66792Citrobacter freundii NBRC 126811114920.3wgspatric1006003
66792Citrobacter freundii strain NCTC9750546.494completepatric546
66792Citrobacter freundii NBRC 126812600255012draftimg1114920
66792Citrobacter freundii ATCC 80902519899575draftimg1006003
66792Citrobacter freundii ATCC 80902588253794draftimg1006003
67770Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 12681GCA_000312465contigncbi1006003

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.345no
flagellatedyes53.315no
gram-positiveno98.421no
anaerobicno95.228yes
aerobicyes81.906no
halophileno91.889no
spore-formingno93.051no
thermophileno99.48no
glucose-utilyes93.687no
glucose-fermentyes93.838yes

External links

@ref: 9097

culture collection no.: DSM 30039, ATCC 8090, IFO 12681, NBRC 12681, NCTC 9750, CCUG 418, ATCC 13316, JCM 1657, CECT 401, CIP 57.32, IAM 12471, KCTC 2509, LMG 3246, LMG 3247, MTCC 1658, NCIMB 11490, NRRL B-2643, Br (Braak)

straininfo link

  • @ref: 73817
  • straininfo: 1750

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1369091Characterization of membrane-bound spermidine dehydrogenase of Citrobacter freundii.Hisano T, Murata K, Kimura A, Matsushita K, Toyama H, Adachi OBiosci Biotechnol Biochem10.1271/bbb.56.19161992Amino Acids/analysis, Cell Fractionation/methods, Cell Membrane/enzymology, Chromatography, DEAE-Cellulose/methods, Chromatography, Gel/methods, Citrobacter freundii/*enzymology, Cytosol/enzymology, Detergents, Electrophoresis, Polyacrylamide Gel/methods, Isoenzymes/isolation & purification/*metabolism, Kinetics, Octoxynol, Oxidoreductases Acting on CH-NH Group Donors/isolation & purification/*metabolism, Polyethylene GlycolsPhylogeny
Metabolism3941048Conservation of DNA sequences for plasmid-mediated citrate utilization within the enterobacteria.Hirato T, Ishiguro N, Shinagawa M, Sato GJ Bacteriol10.1128/jb.165.1.324-327.19861986*Base Sequence, Citrates/*metabolism, Citric Acid, DNA, Bacterial/*analysis, Enterobacteriaceae/*genetics/metabolism, Plasmids, *Sequence Homology, Nucleic Acid
Pathogenicity18708273Synthesis, characterization and antibacterial activity of some triazole Mannich bases carrying diphenylsulfone moieties.Almajan GL, Barbuceanu SF, Almajan ER, Draghici C, Saramet GEur J Med Chem10.1016/j.ejmech.2008.07.0032008Anti-Bacterial Agents/*chemical synthesis/chemistry/*pharmacology, Bacteria/*drug effects, Mannich Bases/*chemistry, Microbial Sensitivity Tests, Sulfones/*chemistry, Triazoles/*chemical synthesis/chemistry/*pharmacology
Pathogenicity19616347Synthesis, characterization and evaluation of antibacterial activity of some thiazolo[3,2-b][1,2,4]triazole incorporating diphenylsulfone moieties.Barbuceanu SF, Almajan GL, Saramet I, Draghici C, Tarcomnicu AI, Bancescu GEur J Med Chem10.1016/j.ejmech.2009.06.0212009Anti-Bacterial Agents/*chemistry/*pharmacology, Bacteria/drug effects, Biphenyl Compounds/chemistry/pharmacology, Microbial Sensitivity Tests, Molecular Structure, Structure-Activity Relationship, Sulfones/*chemistry/*pharmacology, Triazoles/*chemistry/*pharmacology
19702172Comparative study of anthocyanin composition, antimicrobial and antioxidant activity in bilberry (Vaccinium myrtillus L.) and blueberry (Vaccinium corymbosum L.) fruits.Burdulis D, Sarkinas A, Jasutiene I, Stackevicene E, Nikolajevas L, Janulis VActa Pol Pharm2009Anthocyanins/*analysis, Anti-Infective Agents/*pharmacology, Antioxidants/*pharmacology, Blueberry Plants/*chemistry, Chromatography, High Pressure Liquid, Fruit/*chemistry, Microbial Sensitivity Tests
Genetics23405287Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658.Kumar S, Kaur C, Kimura K, Takeo M, Raghava GP, Mayilraj SGenome Announc10.1128/genomeA.00120-122013
Pathogenicity23529729Characterization of qnrB-like genes in Citrobacter species of the American Type Culture Collection.Saga T, Sabtcheva S, Mitsutake K, Ishii Y, Tateda K, Yamaguchi K, Kaku MAntimicrob Agents Chemother10.1128/AAC.02396-122013Anti-Bacterial Agents/*pharmacology, Bacterial Proteins/genetics, Citrobacter/*classification/*drug effects/genetics, Drug Resistance, Bacterial/*genetics, *Genes, Bacterial, Humans, Molecular Sequence Data, Plasmids/genetics, Quinolones/*pharmacology, Sequence Analysis, DNAGenetics
Metabolism256449461,3-Propanediol production by new recombinant Escherichia coli containing genes from pathogenic bacteria.Przystalowska H, Zeyland J, Szymanowska-Powalowska D, Szalata M, Slomski R, Lipinski DMicrobiol Res10.1016/j.micres.2014.12.0072014Bioreactors, Catalysis, Escherichia coli/*genetics/*metabolism, Fermentation, Gene Expression, *Genes, Bacterial, Hydro-Lyases/genetics/metabolism, Metabolic Networks and Pathways, Plasmids/genetics, Propylene Glycols/*metabolism, Recombinant Proteins/genetics/isolation & purification/metabolismBiotechnology
Phylogeny28857032Citrobacter portucalensis sp. nov., isolated from an aquatic sample.Ribeiro TG, Goncalves BR, da Silva MS, Novais A, Machado E, Carrico JA, Peixe LInt J Syst Evol Microbiol10.1099/ijsem.0.0021542017Bacterial Typing Techniques, Base Composition, Citrobacter/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, Multilocus Sequence Typing, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *Water WellsTranscriptome
340369793D printed imaging platform for portable cell counting.Awate DM, Pola CC, Shumaker E, Gomes CL, Juarez JJAnalyst10.1039/d1an00778e2021*Algorithms, Flow Cytometry, Microscopy, Fluorescence, *Printing, Three-Dimensional
Phylogeny34037857Generation of electrical energy in a microbial fuel cell coupling acetate oxidation to Fe(3+) reduction and isolation of the involved bacteria.Becerril-Varela K, Serment-Guerrero JH, Manzanares-Leal GL, Ramirez-Duran N, Guerrero-Barajas CWorld J Microbiol Biotechnol10.1007/s11274-021-03077-42021Acetates/metabolism, Bacteria/*classification/genetics/isolation & purification, Biodegradation, Environmental, Bioelectric Energy Sources/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Iron/*chemistry, Oxidation-Reduction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNA/*methods, Sewage/microbiologyTranscriptome
Genetics35779647Engineering Citrobacter freundii using CRISPR/Cas9 system.Alfaro T, Elmore JR, Stromberg ZR, Hutchison JR, Hess BMJ Microbiol Methods10.1016/j.mimet.2022.1065332022*CRISPR-Cas Systems, *Citrobacter freundii/genetics, Gene Editing/methods, Genome, BacterialBiotechnology
36121562Iron reducing sludge as a source of electroactive bacteria: assessing iron reduction in biofilm bacteria, planktonic cells and isolates from a microbial fuel cell.Gonzalez-Paz JR, Becerril-Varela K, Guerrero-Barajas CArch Microbiol10.1007/s00203-022-03253-62022*Bioelectric Energy Sources/microbiology, Biofilms, Carbon, Electricity, Iron, Plankton, Sewage
36263957LC-MS profile, in vitro acetylcholinesterase inhibitory, antibacterial and hemostatic properties of Ranunculus bullatus extract.Lemoui R, Cheriet T, Kahlouche F, Noman L, Seghiri R, Abudunia ANat Prod Res10.1080/14786419.2022.21366612022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9097Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30039)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30039
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
42192Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9617
44198Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 418)https://www.ccug.se/strain?id=418
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
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
73817Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1750.1StrainInfo: A central database for resolving microbial strain identifiers
119459Curators of the CIPCollection of Institut Pasteur (CIP 57.32)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2057.32