Strain identifier
BacDive ID: 4329
Type strain:
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)
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
@ref | history |
---|---|
1786 | <- CIP <- NCTC |
67770 | R. Sakazaki <-- ATCC 27028 <-- W. Frederiksen 14804. |
120496 | CIP <- 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
@ref synonym 20215 Levinea malonatica 20215 Aerobacter diversum 20215 Citrobacter diversum 20215 Citrobacter 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 96.003 | ||
69480 | 99.998 | negative | ||
120496 | yes | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1786 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
33053 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
1786 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
1786 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
120496 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
120496 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1786 | positive | growth | 30 | mesophilic |
33053 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 120496
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.964 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | + | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | + | fermentation |
68368 | 62345 | L-rhamnose | + | fermentation |
68368 | 30911 | sorbitol | + | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | + | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | + | hydrolysis |
120496 | 17632 | nitrate | + | reduction |
120496 | 16301 | nitrite | + | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | yes |
68368 | 16136 | hydrogen sulfide | no |
120496 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | + | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
120496 | oxidase | - | |
120496 | catalase | + | 1.11.1.6 |
120496 | urease | + | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120496 | - | + | + | - | - | + | + | - | + | - | + | + | - | + | - | + | + | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1786 | + | + | - | + | + | - | - | - | + | - | - | + | + | + | + | + | + | - | + | + | - |
1786 | + | + | - | + | + | - | - | - | + | - | - | + | + | - | + | + | + | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | country | origin.country | continent | sample type | isolation date |
---|---|---|---|---|---|
33053 | Denmark | DNK | Europe | ||
44798 | Denmark | DNK | Europe | Human blood | |
67770 | Blood culture | ||||
120496 | Denmark | DNK | Europe | Human, Blood | 1971 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Fluids | #Blood |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1786 | 2 | Risk group (German classification) |
120496 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Citrobacter koseri strain CIP 82.87 16S ribosomal RNA gene, partial sequence | KF057945 | 1459 | ena | 545 |
20218 | Citrobacter koseri partial 16S rRNA gene, strain LMG 5519 | HG798905 | 1427 | ena | 545 |
20218 | Citrobacter koseri strain LMG 5519 16S ribosomal RNA gene, partial sequence | HQ992945 | 1494 | ena | 545 |
67770 | Citrobacter koseri partial 16S rRNA gene, strain CDC-8132-86 | HF558364 | 1469 | ena | 545 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Citrobacter koseri strain NCTC10786 | 545.59 | wgs | patric | 545 |
67770 | Citrobacter koseri NCTC10786 | GCA_900446925 | contig | ncbi | 545 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.833 | no |
anaerobic | no | 94.332 | no |
halophile | no | 90.376 | no |
spore-forming | no | 93.729 | no |
glucose-util | yes | 95.15 | no |
thermophile | no | 99.058 | yes |
aerobic | yes | 68.903 | no |
motile | yes | 88.763 | no |
flagellated | yes | 52 | no |
glucose-ferment | yes | 92.005 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Pathogenicity | 23529729 | Characterization 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 M | Antimicrob Agents Chemother | 10.1128/AAC.02396-12 | 2013 | 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 | Genetics |
Metabolism | 31611274 | Dysregulation 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 H | Infect Immun | 10.1128/IAI.00741-19 | 2019 | Animals, 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/*microbiology | Pathogenicity |
Phylogeny | 32744988 | Intestinirhabdus 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 Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004364 | 2020 | Animals, 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, DNA | Transcriptome |
Biotechnology | 33439115 | Citrobacter koseri stimulates dendritic cells to induce IL-33 expression via abundant ATP production. | Kataoka H, Mori T, Into T | J Med Microbiol | 10.1099/jmm.0.001303 | 2021 | Adenosine Triphosphate/*metabolism, Animals, Cell Line, Citrobacter koseri/*pathogenicity, Dendritic Cells/microbiology, *Enterobacteriaceae Infections/immunology/microbiology, *Food Hypersensitivity/immunology/microbiology, Interleukin-33/*immunology, Mice, Signal Transduction | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1786 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4595) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4595 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
33053 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11362 | ||||
44798 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 4859) | https://www.ccug.se/strain?id=4859 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73821 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1748.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120496 | Curators of the CIP | Collection of Institut Pasteur (CIP 82.87) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.87 |