Strain identifier

BacDive ID: 4321

Type strain: Yes

Species: Cedecea lapagei

Strain Designation: 004, 0485-76

Strain history: CIP <- 1980, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 14-79, Enterobacter agglomerans G1 <- CDC: strain 0485-76

NCBI tax ID(s): 1354257 (strain), 158823 (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: 1782

BacDive-ID: 4321

DSM-Number: 4587

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped

description: Cedecea lapagei 004 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from human throat.

NCBI tax id

NCBI tax idMatching level
1354257strain
158823species

strain history

@refhistory
1782<- CIP <- P.A.D. Grimont; 004
67770Y. Kosako 82079 <-- R. Sakazaki 275 <-- CDC 485-76 <-- Canadian CDC.
120558CIP <- 1980, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 14-79, Enterobacter agglomerans G1 <- CDC: strain 0485-76

doi: 10.13145/bacdive4321.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Cedecea
  • species: Cedecea lapagei
  • full scientific name: Cedecea lapagei Grimont et al. 1981

@ref: 1782

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Cedecea

species: Cedecea lapagei

full scientific name: Cedecea lapagei Grimont et al. 1981

strain designation: 004, 0485-76

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120558negativerod-shapedyes
69480negative99

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1782NUTRIENT 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
38418MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120558CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120558CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
1782positivegrowth30
38418positivegrowth30
67770positivegrowth37
120558positivegrowth5-37
120558nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 120558
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate+builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose+builds acid from28847
68371D-tagatose-builds acid from16443
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine+hydrolysis29016
120558mannitol+fermentation29864
120558citrate+carbon source16947
120558glucose+fermentation17234
120558lactose+fermentation17716
120558nitrate+reduction17632
120558nitrite-reduction16301
120558malonate+assimilation15792
120558sodium thiosulfate-builds gas from132112
68374ornithine-degradation18257
68374arginine+hydrolysis29016
68374lysine-degradation25094
68374urea-hydrolysis16199
68374L-arabitol-builds acid from18403
68374D-galacturonic acid-builds acid from18024
68374Potassium 5-ketogluconate-builds acid from
68374D-mannitol+builds acid from16899
68374maltose+builds acid from17306
68374ribitol-builds acid from15963
68374palatinose-builds acid from18394
68374malonate+assimilation15792
68374tryptophan-energy source27897
68374D-glucose+builds acid from17634
68374sucrose-builds acid from17992
68374L-arabinose-builds acid from30849
68374D-arabitol+builds acid from18333
68374trehalose+builds acid from27082
68374L-rhamnose-builds acid from62345
68374myo-inositol-builds acid from17268
68374cellobiose+builds acid from17057
68374sorbitol-builds acid from30911

antibiotic resistance

  • @ref: 120558
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12055835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836815688acetoin-
6836835581indole-
12055815688acetoin+
12055817234glucose-

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
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase+3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase+
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase+3.5.3.6
68374ornithine decarboxylase-4.1.1.17
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
120558oxidase-
120558beta-galactosidase-3.2.1.23
120558alcohol dehydrogenase+1.1.1.1
120558gelatinase-
120558catalase+1.11.1.6
120558lysine decarboxylase-4.1.1.18
120558ornithine decarboxylase-4.1.1.17
120558tryptophan deaminase-
120558urease-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
120558-+++-+----++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
45681++--+------++----+++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120558+--+++---++++---++---+++++++++-+------+-+/--+-+--++/-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
45681-+-----+++++---+-+++--+--+--+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120558+++++----+++-+-+++++------+----+++--------+++--+-++--++++--++------------+-+--+++-+------++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
1782human throatCanadaCANNorth America
45681Human throatCanadaCANNorth America1976
67770ThroatCanadaCANNorth America
120558Human, ThroatCanadaCANNorth America1976

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Throat

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: LC036262
  • Sequence Identity:
  • Total samples: 11
  • aquatic counts: 2
  • animal counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17822Risk group (German classification)
1205581Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Cedecea lapagei gene for 16S ribosomal RNA, partial sequence, strain: JCM 1684, clone: 1LC0362601464nuccore158823
67770Cedecea lapagei gene for 16S ribosomal RNA, partial sequence, strain: JCM 1684, clone: 2LC0362611462nuccore158823
67770Cedecea lapagei gene for 16S ribosomal RNA, partial sequence, strain: JCM 1684, clone: 3LC0362621462nuccore158823
124043Cedecea lapagei partial 16S rRNA gene, type strain DSM 4587T, isolate Clone 1LM9997621532nuccore158823
124043Cedecea lapagei partial 16S rRNA gene, type strain DSM 4587T, isolate Clone 2LM9997631531nuccore158823
124043Cedecea lapagei partial 16S rRNA gene, type strain DSM 4587T, isolate Clone 3LM9997641531nuccore158823

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cedecea lapagei NCTC11466GCA_900635955completencbi158823
66792Cedecea lapagei strain NCTC11466158823.5completepatric158823
66792Cedecea lapagei NCTC114662836746200completeimg158823

GC content

  • @ref: 67770
  • GC-content: 47.2-49
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.328yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no62.122no
69480spore-formingspore-formingAbility to form endo- or exosporesno89.648no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.5yes
69480flagellatedmotile2+Ability to perform flagellated movementyes78.43no

External links

@ref: 1782

culture collection no.: CCUG 12371, NCTC 11466, LMG 7863, JCM 1684, DSM 4587, ATCC 33432, CDC 0485-76, CIP 80.35, BCRC 14816, CDC 485-76

straininfo link

  • @ref: 73813
  • straininfo: 13608

Reference

@idauthorscataloguedoi/urltitle
1782Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4587)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4587
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
38418Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11129
45681Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12371)https://www.ccug.se/strain?id=12371
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
68371Automatically annotated from API 50CH acid
68374Automatically annotated from API ID32E
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.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
73813Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13608.1StrainInfo: A central database for resolving microbial strain identifiers
120558Curators of the CIPCollection of Institut Pasteur (CIP 80.35)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.35
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy