Strain identifier

BacDive ID: 4336

Type strain: Yes

Species: Citrobacter gillenii

Strain Designation: 3-85, 4693-86

Strain history: CIP <- 2000, CCUG <- 1992, R.E. Weaver, CDC, Atlanta, Georgia, USA: strain 4693-86 <- 1986, P.A.D. Grimont, Institut Pasteur, Paris, France

NCBI tax ID(s): 67828 (species)

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General

@ref: 5118

BacDive-ID: 4336

DSM-Number: 13694

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

description: Citrobacter gillenii 3-85 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 67828
  • Matching level: species

strain history

@refhistory
5118<- ATCC <- C. F. Riddle <- P. Grimont; 3-85
119617CIP <- 2000, CCUG <- 1992, R.E. Weaver, CDC, Atlanta, Georgia, USA: strain 4693-86 <- 1986, P.A.D. Grimont, Institut Pasteur, Paris, France

doi: 10.13145/bacdive4336.20230509.8.1

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 gillenii
  • full scientific name: Citrobacter gillenii Brenner et al. 2000

@ref: 5118

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter gillenii

full scientific name: Citrobacter gillenii Brenner et al. 2000

strain designation: 3-85, 4693-86

type strain: yes

Morphology

cell morphology

  • @ref: 119617
  • gram stain: negative
  • cell shape: oval-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5118NUTRIENT 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
40596MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119617CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119617CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
5118positivegrowth37mesophilic
40596positivegrowth37mesophilic
50276positivegrowth37mesophilic
119617positivegrowth5-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50276aerobe
119617facultative 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
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
68371esculin-builds acid from4853
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
119617mannitol+fermentation29864
119617citrate+carbon source16947
119617glucose+fermentation17234
119617lactose+fermentation17716
119617nitrate+reduction17632
119617nitrite-reduction16301
119617malonate+assimilation15792
119617sodium thiosulfate-builds gas from132112
119617glucose+degradation17234

antibiotic resistance

  • @ref: 119617
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119617
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11961715688acetoin-
11961717234glucose+

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
119617oxidase-
119617beta-galactosidase+3.2.1.23
119617alcohol dehydrogenase-1.1.1.1
119617gelatinase-
119617catalase+1.11.1.6
119617lysine decarboxylase-4.1.1.18
119617ornithine decarboxylase-4.1.1.17
119617phenylalanine ammonia-lyase+4.3.1.24
119617tryptophan deaminase-
119617urease-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
119617-+++-++---++-+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119617+-++++---++++-+-+++--+-+/--+/-++++-+------+----+--+++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119617+++++-+--+++++++++-+++-++------+++--+--+---++----++--+++++-+++------++---+-+--+++--+--+-+++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5118human faecesFranceFRAEurope
50276Human fecesFranceFRAEurope
119617Human, FecesFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_37975.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_17;99_37975&stattab=map
  • Last taxonomy: Citrobacter
  • 16S sequence: AF025367
  • Sequence Identity:
  • Total samples: 2091
  • soil counts: 59
  • aquatic counts: 162
  • animal counts: 1658
  • plant counts: 212

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51182Risk group (German classification)
1196171Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Citrobacter sp. 'genomospecies 10' 16S ribosomal RNA gene, partial sequence
  • accession: AF025367
  • length: 1527
  • database: ena
  • NCBI tax ID: 67828

External links

@ref: 5118

culture collection no.: DSM 13694, ATCC 51117, CCUG 30796, CDC 4693-86, CIP 106783

straininfo link

  • @ref: 73828
  • straininfo: 42812

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5118Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13694)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13694
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
40596Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18951
50276Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30796)https://www.ccug.se/strain?id=30796
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
73828Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42812.1StrainInfo: A central database for resolving microbial strain identifiers
119617Curators of the CIPCollection of Institut Pasteur (CIP 106783)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106783