Strain identifier

BacDive ID: 4320

Type strain: Yes

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

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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 idMatching level
566551strain
158484species

strain history

@refhistory
1774<- CIP <- P.A.D. Grimont; 005
67770Y. Kosako 82080 <-- R. Sakazaki 282 <-- CDC 3278-77 <-- P. A. D. Grimont 005.
118859CIP <- 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

@refmotilityconfidencegram stain
69480yes97.383
6948099.917negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1774NUTRIENT 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
38419MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118859CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1774positivegrowth30mesophilic
38419positivegrowth30mesophilic
45680positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 45680
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.474

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
1774stoolNew JerseyUSAUSANorth America
45680Human stoolNew JerseyUSAUSANorth America
67770StoolNJUSAUSANorth America
118859FaecesNew JerseyUnited States of AmericaUSANorth America1977

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

@refbiosafety levelbiosafety level comment
17742Risk group (German classification)
1188591Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cedecea davisae DSM 4568566551.4wgspatric566551
66792Cedecea davisae strain NCTC13724158484.3wgspatric158484
66792Cedecea davisae 005, DSM 45682541046972draftimg566551
66792Cedecea davisae NCTC 137242808606631draftimg158484
67770Cedecea davisae DSM 4568GCA_000412335scaffoldncbi566551
67770Cedecea davisae NCTC13724GCA_900446735contigncbi158484

GC content

  • @ref: 67770
  • GC-content: 48-49.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.194no
anaerobicno97.62yes
halophileno85.084no
spore-formingno94.136no
glucose-utilyes94.69no
thermophileno99.343yes
flagellatedno63.371no
motileyes91.985no
aerobicyes76.564no
glucose-fermentyes92.826no

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

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny16342775[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 DSWei Sheng Wu Xue Bao2005Bacillaceae/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/*biosynthesisEnzymology
Phylogeny36484840Cedecea 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 ZArch Microbiol2022RNA, Ribosomal, 16S/genetics, *Ubiquinone, Phylogeny, *Herbicides, DNA, Bacterial/genetics, Base Composition, Bacterial Typing Techniques, Phospholipids, Sequence Analysis, DNA, Fatty Acids, Bacteria/geneticsTranscriptome10.1007/s00203-022-03362-2

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1774Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4568)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4568
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
38419Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11128
45680Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12370)https://www.ccug.se/strain?id=12370
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
73812Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1709.1StrainInfo: A central database for resolving microbial strain identifiers
118859Curators of the CIPCollection of Institut Pasteur (CIP 80.34)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.34