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/bacdive4338.20250331.9.3

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

@refgram staincell shapemotilityconfidence
116986negativerod-shapedyes
125438negative99.5
125439negative90

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

@refgrowthtypetemperature
7079positivegrowth30
39041positivegrowth30
50272positivegrowth37
116986positivegrowth10-41
116986nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7079aerobe
50272aerobe
116986facultative anaerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 91.7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11698629864mannitol+fermentation
11698616947citrate+carbon source
11698617632nitrate+reduction
11698616301nitrite+reduction
11698615792malonate-assimilation
116986132112sodium thiosulfate+builds gas from
68371Potassium 5-ketogluconate+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate+builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol+builds acid from
6837162345L-rhamnose+builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
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-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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
68382alpha-glucosidase+3.2.1.20
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 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 17596HG7989041427nuccore57706
7079Citrobacter braakii strain CDC 80-58 16S ribosomal RNA gene, partial sequenceAF0253681530nuccore57706

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.268yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.553no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no72.4no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98yes
125438motile2+flagellatedAbility to perform flagellated movementyes75.033no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91.7
125439BacteriaNetmotilityAbility to perform movementyes65.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative90
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe84.4

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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1