Strain identifier

BacDive ID: 4338

Type strain: Yes

Species: Citrobacter braakii

Strain Designation: 167, 80-58

Strain history: CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 80-58 <- L. Le Minor, Inst. Pasteur, Paris, France: strain 167

NCBI tax ID(s): 57706 (species)

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General

@ref: 7079

BacDive-ID: 4338

DSM-Number: 17596

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

description: Citrobacter braakii 167 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from snake.

NCBI tax id

  • NCBI tax id: 57706
  • Matching level: species

strain history

@refhistory
7079<- CIP <- P. A. D. Grimont <- CDC <- L. Le Minor, Institut Pasteur, Paris; 167
116986CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 80-58 <- L. Le Minor, Inst. Pasteur, Paris, France: strain 167

doi: 10.13145/bacdive4338.20230509.8.1

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 braakii
  • full scientific name: Citrobacter braakii Brenner et al. 1993

@ref: 7079

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter braakii

full scientific name: Citrobacter braakii Brenner et al. 1993

strain designation: 167, 80-58

type strain: yes

Morphology

cell morphology

  • @ref: 116986
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7079TRYPTICASE 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
39041MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116986CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7079positivegrowth30mesophilic
39041positivegrowth30mesophilic
50272positivegrowth37mesophilic
116986positivegrowth10-41
116986nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7079aerobe
50272aerobe
116986facultative 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
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
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
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
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan+energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine+degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
116986mannitol+fermentation29864
116986citrate+carbon source16947
116986nitrate+reduction17632
116986nitrite+reduction16301
116986malonate-assimilation15792
116986sodium thiosulfate+builds gas from132112

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideyes
11698635581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole+
11698615688acetoin-
11698617234glucose+

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
116986oxidase-
116986beta-galactosidase+3.2.1.23
116986alcohol dehydrogenase-1.1.1.1
116986gelatinase-
116986catalase+1.11.1.6
116986lysine decarboxylase-4.1.1.18
116986ornithine decarboxylase+4.1.1.17
116986tryptophan deaminase-
116986urease-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
116986-++--+----++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7079+--+++--+--++-++-+-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116986+-++++---+++++/-++-++-+/-+----+/-+++/-+/-+---+/---+/--+/---+--+++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116986+++++-+--++++++++++++++++----+-+-++-+--+-++++-+++++-+++++++++----++-++--++-+---++-+---+-+++++++-+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7079snakeFranceFRAEurope
50272Snake
116986SnakeFranceFRAEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Reptilia

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70792Risk group (German classification)
1169861Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Citrobacter braakii partial 16S rRNA gene, strain DSM 17596HG7989041427ena57706
7079Citrobacter braakii strain CDC 80-58 16S ribosomal RNA gene, partial sequenceAF0253681530ena57706

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter braakii ATCC 51113GCA_002075345contigncbi57706
66792Citrobacter braakii strain ATCC 5111357706.20wgspatric57706
66792Citrobacter braakii strain FDAARGOS 142157706.144completepatric57706
66792Citrobacter braakii ATCC 511132878893965draftimg57706

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.044no
anaerobicno95.527no
halophileno92.342no
spore-formingno93.047no
glucose-utilyes94.443no
thermophileno99.383yes
motileyes88.052no
aerobicyes85.962no
flagellatedyes54.405no
glucose-fermentyes93.38yes

External links

@ref: 7079

culture collection no.: DSM 17596, ATCC 51113, CCUG 30792, CDC 80-58, CIP 104554

straininfo link

  • @ref: 73830
  • straininfo: 42809

literature

  • topic: Pathogenicity
  • Pubmed-ID: 23529729
  • title: Characterization of qnrB-like genes in Citrobacter species of the American Type Culture Collection.
  • authors: Saga T, Sabtcheva S, Mitsutake K, Ishii Y, Tateda K, Yamaguchi K, Kaku M
  • journal: Antimicrob Agents Chemother
  • DOI: 10.1128/AAC.02396-12
  • year: 2013
  • mesh: Anti-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, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7079Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17596)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17596
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
39041Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16475
50272Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30792)https://www.ccug.se/strain?id=30792
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)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
73830Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42809.1StrainInfo: A central database for resolving microbial strain identifiers
116986Curators of the CIPCollection of Institut Pasteur (CIP 104554)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104554