Strain identifier

BacDive ID: 24000

Type strain: No

Species: Pseudocitrobacter faecalis

Strain Designation: C138

Strain history: CIP <- 2013, P. Kämpfer, Justus-Liebig Univ., Giessen, Germany: strain C138

NCBI tax ID(s): 1398493 (species)

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General

@ref: 21332

BacDive-ID: 24000

DSM-Number: 27454

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Pseudocitrobacter faecalis C138 is a mesophilic, motile bacterium that was isolated from stool from a hospitalized patient.

NCBI tax id

  • NCBI tax id: 1398493
  • Matching level: species

strain history

@refhistory
21332<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; 138A <- S.A. Abbassi, Armed Forces Institute of Pathology, Pakistan
116413CIP <- 2013, P. Kämpfer, Justus-Liebig Univ., Giessen, Germany: strain C138

doi: 10.13145/bacdive24000.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Pseudocitrobacter
  • species: Pseudocitrobacter faecalis
  • full scientific name: Pseudocitrobacter faecalis Kämpfer et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Pseudocitrobacter anthropi

@ref: 21332

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Pseudocitrobacter

species: Pseudocitrobacter faecalis

full scientific name: Pseudocitrobacter faecalis Kämpfer et al. 2014

strain designation: C138

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.946
6948099.967negative
116413yesnegativerod-shaped

multimedia

  • @ref: 21332
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27454.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21332CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
21332COLUMBIA 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
116413CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
21332positivegrowth30mesophilic
21332positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.964

compound production

  • @ref: 21332
  • compound: NDM-1 carbapenemase

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
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 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21332+---+------++--+--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21332stool from a hospitalized patientRawalpindi, Combined Military HospitalPakistanPAKAsia
116413HumanRawalpindi, PakistanPakistanPAKAsia

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 116413
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21332
  • description: Pseudocitrobacter anthropi strain C138 16S ribosomal RNA gene, partial sequence
  • accession: KF057944
  • length: 1419
  • database: ena
  • NCBI tax ID: 1398496

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudocitrobacter faecalis CCM 8478GCA_014653055scaffoldncbi1398493
66792Pseudocitrobacter faecalis strain CCM 84781398493.8wgspatric1398493

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes86.971no
flagellatedno68.298no
gram-positiveno97.814no
anaerobicno96.401no
aerobicyes86.451no
halophileno90.549no
spore-formingno94.575no
thermophileno99.358yes
glucose-utilyes93.715no
glucose-fermentyes92.298no

External links

@ref: 21332

culture collection no.: DSM 27454, CCM 8478, LMG 27750, CIP 110623

straininfo link

  • @ref: 87975
  • straininfo: 398107

literature

  • topic: Phylogeny
  • Pubmed-ID: 24182752
  • title: Pseudocitrobacter gen. nov., a novel genus of the Enterobacteriaceae with two new species Pseudocitrobacter faecalis sp. nov., and Pseudocitrobacter anthropi sp. nov, isolated from fecal samples from hospitalized patients in Pakistan.
  • authors: Kampfer P, Glaeser SP, Raza MW, Abbasi SA, Perry JD
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2013.08.003
  • year: 2013
  • mesh: Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enterobacteriaceae/*classification/genetics/*isolation & purification/physiology, Feces/*microbiology, Humans, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Pakistan, Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, beta-Lactamases/metabolism
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21332Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27454Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27454)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87975Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID398107.1
116413Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110623Collection of Institut Pasteur (CIP 110623)