Strain identifier

BacDive ID: 130292

Type strain: Yes

Species: Citrobacter pasteurii

Strain Designation: Na 1a

Strain history: CIP <- 1955, P.R. Edwards, Kentucky, USA: strain Na 1a, Citrobacter freundii

NCBI tax ID(s): 1563222 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.1 (current version)

General

@ref: 21549

BacDive-ID: 130292

DSM-Number: 28879

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, human pathogen

description: Citrobacter pasteurii Na 1a is a facultative anaerobe, Gram-negative human pathogen that was isolated from human diarrhoeal stool.

NCBI tax id

  • NCBI tax id: 1563222
  • Matching level: species

strain history

@refhistory
420541955, P.R. Edwards, Kentucky, USA: strain Na 1a, Citrobacter freundii
21549<- D. Clermont, CIP; Na 1a <- P. R. Edwards, Kentucky, USA
121621CIP <- 1955, P.R. Edwards, Kentucky, USA: strain Na 1a, Citrobacter freundii

doi: 10.13145/bacdive130292.20240916.9.1

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 pasteurii
  • full scientific name: Citrobacter pasteurii Clermont et al. 2015

@ref: 21549

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter pasteurii

full scientific name: Citrobacter pasteurii Clermont et al. 2015

strain designation: Na 1a

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121621negativerod-shapedyes
69480negative100

multimedia

  • @ref: 21549
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28879.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42054MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
21549CASO AGAR (MERCK 105458) (DSMZ Medium 220)yesName: 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 waterhttps://mediadive.dsmz.de/medium/220
21549TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92
21549COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
121621CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121621CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
42054positivegrowth30
21549positivegrowth28
21549positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 121621
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+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
12162117632nitrate+reduction
12162116301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes
12162135581indoleno

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
121621oxidase-
121621catalase-1.11.1.6
121621urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121621-+---+----++-+--+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21549++--++-----++-+++-+/-+
21549++--++-----++-+++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
21549human diarrhoeal stoolKentuckyUSAUSANorth America
121621Human, Stool, diarrhea, outbreakKentuckyUnited States of AmericaUSANorth America1955

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_141.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_17;99_141&stattab=map
  • Last taxonomy: Citrobacter
  • 16S sequence: KP057683
  • Sequence Identity:
  • Total samples: 10081
  • soil counts: 374
  • aquatic counts: 1036
  • animal counts: 8174
  • plant counts: 497

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
21549yes, in single cases1Risk group (German classification)
1216211Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
21549Citrobacter pasteurii strain CIP 55.13 16S ribosomal RNA gene, partial sequenceKP0576831492nuccore1563222
124043Citrobacter pasteurii strain CIP55.13 16S ribosomal RNA gene, partial sequence.OR6602601135nuccore1563222

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter pasteurii CIP 55.13GCA_000826205contigncbi1563222
66792Citrobacter pasteurii strain FDAARGOS 14241563222.16completepatric1563222
66792Citrobacter sp. CIP 55.131563222.3wgspatric1563222
66792Citrobacter pasteurii CIP 55.132648501483draftimg1563222

GC content

  • @ref: 21549
  • GC-content: 51.80
  • method: sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno100no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.637yes
69480spore-formingspore-formingAbility to form endo- or exosporesno88.627no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no76.895yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98no
69480flagellatedmotile2+Ability to perform flagellated movementyes78.664no

External links

@ref: 21549

culture collection no.: DSM 28879, CIP 55.13

straininfo link

  • @ref: 88827
  • straininfo: 67873

literature

  • topic: Phylogeny
  • Pubmed-ID: 25687346
  • title: Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.
  • authors: Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C, Brisse S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000122
  • year: 2015
  • mesh: Bacterial Typing Techniques, Citrobacter/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

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
21549Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28879Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28879)
42054Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4705
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
88827Reimer, 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-ID67873.1
121621Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2055.13Collection of Institut Pasteur (CIP 55.13)
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy