Strain identifier
BacDive ID: 4320
Type strain:
Species: Cedecea davisae
Strain Designation: 005, 3278-77
Strain history: CIP <- 1980, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 15-79, Enterobacter agglomerans G1 <- CDC: strain 3278-77
NCBI tax ID(s): 566551 (strain), 158484 (species)
General
@ref: 1774
BacDive-ID: 4320
DSM-Number: 4568
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Cedecea davisae 005 is an aerobe, mesophilic, motile bacterium that was isolated from stool.
NCBI tax id
NCBI tax id | Matching level |
---|---|
566551 | strain |
158484 | species |
strain history
@ref | history |
---|---|
1774 | <- CIP <- P.A.D. Grimont; 005 |
67770 | Y. Kosako 82080 <-- R. Sakazaki 282 <-- CDC 3278-77 <-- P. A. D. Grimont 005. |
118859 | CIP <- 1980, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 15-79, Enterobacter agglomerans G1 <- CDC: strain 3278-77 |
doi: 10.13145/bacdive4320.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Enterobacteriaceae
- genus: Cedecea
- species: Cedecea davisae
- full scientific name: Cedecea davisae Grimont et al. 1981
@ref: 1774
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Enterobacteriaceae
genus: Cedecea
species: Cedecea davisae
full scientific name: Cedecea davisae Grimont et al. 1981
strain designation: 005, 3278-77
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 97.383 | |
69480 | 99.917 | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1774 | 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 |
38419 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
118859 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1774 | positive | growth | 30 | mesophilic |
38419 | positive | growth | 30 | mesophilic |
45680 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 45680
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.474 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
1774 | stool | New Jersey | USA | USA | North America | |
45680 | Human stool | New Jersey | USA | USA | North America | |
67770 | Stool | NJ | USA | USA | North America | |
118859 | Faeces | New Jersey | United States of America | USA | North America | 1977 |
isolation source categories
- Cat1: #Host Body Product
- Cat2: #Gastrointestinal tract
- Cat3: #Feces (Stool)
taxonmaps
- @ref: 69479
- File name: preview.99_575.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_411;98_470;99_575&stattab=map
- Last taxonomy: Enterobacteriaceae
- 16S sequence: AF493976
- Sequence Identity:
- Total samples: 11
- aquatic counts: 2
- animal counts: 9
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1774 | 2 | Risk group (German classification) |
118859 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Cedecea davisae DSM 4568 16S ribosomal RNA gene, partial sequence
- accession: AF493976
- length: 1403
- database: ena
- NCBI tax ID: 566551
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cedecea davisae DSM 4568 | 566551.4 | wgs | patric | 566551 |
66792 | Cedecea davisae strain NCTC13724 | 158484.3 | wgs | patric | 158484 |
66792 | Cedecea davisae 005, DSM 4568 | 2541046972 | draft | img | 566551 |
66792 | Cedecea davisae NCTC 13724 | 2808606631 | draft | img | 158484 |
67770 | Cedecea davisae DSM 4568 | GCA_000412335 | scaffold | ncbi | 566551 |
67770 | Cedecea davisae NCTC13724 | GCA_900446735 | contig | ncbi | 158484 |
GC content
- @ref: 67770
- GC-content: 48-49.6
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.194 | no |
anaerobic | no | 97.62 | yes |
halophile | no | 85.084 | no |
spore-forming | no | 94.136 | no |
glucose-util | yes | 94.69 | no |
thermophile | no | 99.343 | yes |
flagellated | no | 63.371 | no |
motile | yes | 91.985 | no |
aerobic | yes | 76.564 | no |
glucose-ferment | yes | 92.826 | no |
External links
@ref: 1774
culture collection no.: DSM 4568, ATCC 33431, CDC 3278-77, CIP 80.34, CCUG 12370, JCM 1685, BCRC 14815, CECT 842, LMG 7862, NBRC 105702, NCIMB 11889, NCTC 13724, NCTC 11465
straininfo link
- @ref: 73812
- straininfo: 1709
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16342775 | [Screening and identification of steroidal saponins-producing endophytes from Paris polyphylla var. chinensis Franch]. | Zhao M, He SR, Chen XJ, Huang CP, Wang YD, Zhang XJ, Feng DS | Wei Sheng Wu Xue Bao | 2005 | Bacillaceae/classification/*isolation & purification, Base Sequence, *Drugs, Chinese Herbal, Enterobacteriaceae/classification/*isolation & purification, Fermentation, Liliaceae/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Saponins/*biosynthesis, Steroids/*biosynthesis | Enzymology | |
Phylogeny | 36484840 | Cedecea sulfonylureivorans sp. nov., a novel chlorimuron-ethyldegrading bacterium isolated from an herbicides-degrading consortium. | Li Q, Wang J, Ma Q, Han X, Zhang W, Ruan Z | Arch Microbiol | 2022 | RNA, Ribosomal, 16S/genetics, *Ubiquinone, Phylogeny, *Herbicides, DNA, Bacterial/genetics, Base Composition, Bacterial Typing Techniques, Phospholipids, Sequence Analysis, DNA, Fatty Acids, Bacteria/genetics | Transcriptome | 10.1007/s00203-022-03362-2 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1774 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4568) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4568 | |||
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 | |
38419 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11128 | ||||
45680 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 12370) | https://www.ccug.se/strain?id=12370 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
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 | |||
73812 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1709.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118859 | Curators of the CIP | Collection of Institut Pasteur (CIP 80.34) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.34 |