Strain identifier

BacDive ID: 4329

Type strain: Yes

Species: Citrobacter koseri

Strain history: CIP <- 1982, NCTC <- 1971, W. Frederiksen, Statens Serum Inst., Copenhagen, Denmark: strain 14804, Citrobacter diversus

NCBI tax ID(s): 545 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1786

BacDive-ID: 4329

DSM-Number: 4595

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

description: Citrobacter koseri DSM 4595 is a facultative anaerobe, mesophilic, motile bacterium of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 545
  • Matching level: species

strain history

@refhistory
1786<- CIP <- NCTC
67770R. Sakazaki <-- ATCC 27028 <-- W. Frederiksen 14804.
120496CIP <- 1982, NCTC <- 1971, W. Frederiksen, Statens Serum Inst., Copenhagen, Denmark: strain 14804, Citrobacter diversus

doi: 10.13145/bacdive4329.20230509.8.1

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 koseri
  • full scientific name: Citrobacter koseri Frederiksen 1970 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Levinea malonatica
    20215Aerobacter diversum
    20215Citrobacter diversum
    20215Citrobacter diversus

@ref: 1786

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter koseri

full scientific name: Citrobacter koseri Frederiksen 1970

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.003
6948099.998negative
120496yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1786NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33053MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
1786TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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 water
1786COLUMBIA 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
120496CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120496CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1786positivegrowth30mesophilic
33053positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120496
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.964

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis
12049617632nitrate+reduction
12049616301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
12049635581indoleyes

metabolite tests

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

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
120496oxidase-
120496catalase+1.11.1.6
120496urease+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
120496-++--++-+-++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1786++-++---+--++++++-++-
1786++-++---+--++-+++-++-

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typeisolation date
33053DenmarkDNKEurope
44798DenmarkDNKEuropeHuman blood
67770Blood culture
120496DenmarkDNKEuropeHuman, Blood1971

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17862Risk group (German classification)
1204961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Citrobacter koseri strain CIP 82.87 16S ribosomal RNA gene, partial sequenceKF0579451459ena545
20218Citrobacter koseri partial 16S rRNA gene, strain LMG 5519HG7989051427ena545
20218Citrobacter koseri strain LMG 5519 16S ribosomal RNA gene, partial sequenceHQ9929451494ena545
67770Citrobacter koseri partial 16S rRNA gene, strain CDC-8132-86HF5583641469ena545

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter koseri strain NCTC10786545.59wgspatric545
67770Citrobacter koseri NCTC10786GCA_900446925contigncbi545

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.833no
anaerobicno94.332no
halophileno90.376no
spore-formingno93.729no
glucose-utilyes95.15no
thermophileno99.058yes
aerobicyes68.903no
motileyes88.763no
flagellatedyes52no
glucose-fermentyes92.005yes

External links

@ref: 1786

culture collection no.: DSM 4595, ATCC 27028, CCM 2537, CIP 82.87, Frederiksen 14804, NCTC 10786, CCUG 4859, JCM 1658, BCRC 14804, CCUG 14559, CIP 105014, LMG 5519, NCCB 92008, VTT E-991040

straininfo link

  • @ref: 73821
  • straininfo: 1748

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity23529729Characterization of qnrB-like genes in Citrobacter species of the American Type Culture Collection.Saga T, Sabtcheva S, Mitsutake K, Ishii Y, Tateda K, Yamaguchi K, Kaku MAntimicrob Agents Chemother10.1128/AAC.02396-122013Anti-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, DNAGenetics
Metabolism31611274Dysregulation of Intestinal Microbiota Elicited by Food Allergy Induces IgA-Mediated Oral Dysbiosis.Matsui S, Kataoka H, Tanaka JI, Kikuchi M, Fukamachi H, Morisaki H, Matsushima H, Mishima K, Hironaka S, Takaki T, Okahashi N, Maruoka Y, Kuwata HInfect Immun10.1128/IAI.00741-192019Animals, Cytokines/metabolism, Disease Models, Animal, *Dysbiosis, Epithelial Cells/metabolism, Food Hypersensitivity/*complications, Gastrointestinal Tract/*microbiology, Immunoglobulin A/*metabolism, Immunologic Factors/*metabolism, Mice, Inbred BALB C, Microbiota/*drug effects, Mouth/*microbiologyPathogenicity
Phylogeny32744988Intestinirhabdus alba gen. nov., sp. nov., a novel genus of the family Enterobacteriaceae, isolated from the gut of plastic-eating larvae of the Coleoptera insect Zophobas atratus.Xu Z, Xia M, Huo YX, Yang YInt J Syst Evol Microbiol10.1099/ijsem.0.0043642020Animals, Bacterial Typing Techniques, Base Composition, China, Coleoptera/*microbiology, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/isolation & purification, Fatty Acids/chemistry, *Gastrointestinal Microbiome, Genes, Bacterial, Larva/microbiology, *Phylogeny, Plastics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Biotechnology33439115Citrobacter koseri stimulates dendritic cells to induce IL-33 expression via abundant ATP production.Kataoka H, Mori T, Into TJ Med Microbiol10.1099/jmm.0.0013032021Adenosine Triphosphate/*metabolism, Animals, Cell Line, Citrobacter koseri/*pathogenicity, Dendritic Cells/microbiology, *Enterobacteriaceae Infections/immunology/microbiology, *Food Hypersensitivity/immunology/microbiology, Interleukin-33/*immunology, Mice, Signal TransductionMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1786Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4595)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4595
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
33053Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11362
44798Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4859)https://www.ccug.se/strain?id=4859
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73821Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1748.1StrainInfo: A central database for resolving microbial strain identifiers
120496Curators of the CIPCollection of Institut Pasteur (CIP 82.87)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.87