Strain identifier

BacDive ID: 4342

Type strain: Yes

Species: Citrobacter werkmanii

Strain Designation: 876-58, 83I

Strain history: CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 876-58 <- Ohio State Hlth. Dept.: strain 83I

NCBI tax ID(s): 67827 (species)

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General

@ref: 7066

BacDive-ID: 4342

DSM-Number: 17579

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

description: Citrobacter werkmanii 876-58 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human blood.

NCBI tax id

  • NCBI tax id: 67827
  • Matching level: species

strain history

@refhistory
7066<- CIP <- P. A. D. Grimont, Institut Pasteur, Paris <- CDC <- Ohio State Health Dept.
123945CIP <- 1995, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 876-58 <- Ohio State Hlth. Dept.: strain 83I

doi: 10.13145/bacdive4342.20230509.8.1

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

@ref: 7066

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter werkmanii

full scientific name: Citrobacter werkmanii Brenner et al. 1993

strain designation: 876-58, 83I

type strain: yes

Morphology

cell morphology

  • @ref: 123945
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7066TRYPTICASE 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
39042MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123945CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123945CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7066positivegrowth30mesophilic
39042positivegrowth30mesophilic
50273positivegrowth37mesophilic
123945positivegrowth30mesophilic
123945nogrowth5psychrophilic
123945nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7066aerobe
123945facultative 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
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
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
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
123945mannitol+fermentation29864
123945glucose+fermentation17234
123945lactose-fermentation17716
123945nitrate+reduction17632
123945nitrite+reduction16301
123945sodium thiosulfate+builds gas from132112
123945glucose+degradation17234

antibiotic resistance

  • @ref: 123945
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideyes
12394535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12394515688acetoin-
12394517234glucose+

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
123945oxidase-
123945beta-galactosidase+3.2.1.23
123945gelatinase-
123945catalase+1.11.1.6
123945tryptophan deaminase-
123945urease-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
123945-++--++++-++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7066++--++---+-++-++---+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123945+-++++---++++++--++--+-+/---+++--+------+-+/---+--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7066human bloodOhioUSAUSANorth America
50273Human blood
123945Human, Blood

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

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: AF025373
  • 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
70662Risk group (German classification)
1239451Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7066
  • description: Citrobacter werkmanii 16S ribosomal RNA gene, partial sequence
  • accession: AF025373
  • length: 1521
  • database: ena
  • NCBI tax ID: 67827

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter werkmanii strain FDAARGOS_152467827.86completepatric67827
66792Citrobacter werkmanii strain FDAARGOS_152467827.74completepatric67827
66792Citrobacter werkmanii strain FDAARGOS_152467827.80completepatric67827

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.37no
anaerobicno94.097yes
halophileno91.103no
spore-formingno93.259no
glucose-utilyes95.202no
thermophileno99.443no
flagellatedyes51.284no
motileyes89.184no
aerobicyes79.651yes
glucose-fermentyes94.713yes

External links

@ref: 7066

culture collection no.: DSM 17579, ATCC 51114, CDC 876-58, CIP 104555, CCUG 30793

straininfo link

  • @ref: 73834
  • straininfo: 42810

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism23996279Unraveling the dha cluster in Citrobacter werkmanii: comparative genomic analysis of bacterial 1,3-propanediol biosynthesis clusters.Maervoet VE, De Maeseneire SL, Soetaert WK, De Mey MBioprocess Biosyst Eng10.1007/s00449-013-1041-02013*Bacterial Proteins/genetics/metabolism, *Citrobacter/enzymology/genetics, Genes, Bacterial/*physiology, Multigene Family/*physiology, Open Reading Frames/*physiology, Propylene Glycols/*metabolismEnzymology
Metabolism248858491,3-propanediol production with Citrobacter werkmanii DSM17579: effect of a dhaD knock-out.Maervoet VE, De Maeseneire SL, Avci FG, Beauprez J, Soetaert WK, De Mey MMicrob Cell Fact10.1186/1475-2859-13-702014Alcohol Dehydrogenase/metabolism, Bacterial Proteins/genetics/metabolism, Citrobacter/drug effects/*genetics/growth & development/*metabolism, Gene Knockout Techniques, Glucose/metabolism/pharmacology, Glycerol/metabolism/pharmacology, Hydrogen-Ion Concentration, Propylene Glycols/chemistry/*metabolism, Substrate Specificity, Sugar Alcohol Dehydrogenases/deficiency/*genetics/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitle
7066Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17579)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17579
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
39042Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16476
50273Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30793)https://www.ccug.se/strain?id=30793
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
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
73834Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42810.1StrainInfo: A central database for resolving microbial strain identifiers
123945Curators of the CIPCollection of Institut Pasteur (CIP 104555)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104555