Strain identifier

BacDive ID: 4322

Type strain: Yes

Species: Cedecea neteri

Strain Designation: Grimont 002, 0621-75, 002

Strain history: CIP <- 1988, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 002 <- CDC: strain 0621-75 <- California State Hlth. Dept.

NCBI tax ID(s): 1216978 (strain), 158822 (species)

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General

@ref: 5117

BacDive-ID: 4322

DSM-Number: 13693

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

description: Cedecea neteri Grimont 002 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from human foot.

NCBI tax id

NCBI tax idMatching level
158822species
1216978strain

strain history

@refhistory
5117<- ATCC <- CDC <- California State Health Dept.
67770R. Sakazaki 281 <-- P. A. D. Grimont 002 <-- CDC 0621-75 <-- California State Health Dept., USA.
121276CIP <- 1988, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 002 <- CDC: strain 0621-75 <- California State Hlth. Dept.

doi: 10.13145/bacdive4322.20230509.8.1

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 neteri
  • full scientific name: Cedecea neteri Farmer et al. 1983

@ref: 5117

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Cedecea

species: Cedecea neteri

full scientific name: Cedecea neteri Farmer et al. 1983

strain designation: Grimont 002, 0621-75, 002

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.323
6948099.981negative
121276yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5117CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40578MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121276CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121276CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5117positivegrowth37mesophilic
40578positivegrowth30mesophilic
67770positivegrowth37mesophilic
121276positivegrowth5-37
121276nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121276
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.916

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
68371D-lyxose-builds acid from62318
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
68371N-acetylglucosamine+builds acid from59640
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
121276mannitol+fermentation29864
121276citrate+carbon source16947
121276glucose+fermentation17234
121276lactose-fermentation17716
121276nitrate+reduction17632
121276nitrite-reduction16301
121276malonate+assimilation15792
121276sodium 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: 121276
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12127635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836815688acetoin+
6836835581indole-
12127615688acetoin+
12127617234glucose-

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
121276oxidase-
121276beta-galactosidase+3.2.1.23
121276alcohol dehydrogenase+1.1.1.1
121276gelatinase-
121276catalase+1.11.1.6
121276lysine decarboxylase-4.1.1.18
121276ornithine decarboxylase-4.1.1.17
121276phenylalanine ammonia-lyase-4.3.1.24
121276tryptophan deaminase-
121276urease-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
121276-+++++----++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
46880++--+----+-++-+-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121276+---++---++++---+++-+/-++/-++++++-++------+-----+--+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
46880-+-----+++++-+-+-++++-+--+-+++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121276+++++--+-+++-+-+++++-++---+----++++++----------+-++--++++--+++----------++-+--+++-+---+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5117human footCaliforniaUSAUSANorth America
46880Human foot
67770Human footCAUSAUSANorth America
121276Human, Foot woundCaliforniaUnited States of AmericaUSANorth America1975

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Limb#Foot

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: LC504043
  • Sequence Identity:
  • Total samples: 11
  • aquatic counts: 2
  • animal counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51172Risk group (German classification)
1212761Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cedecea neteri gene for 16S rRNA, partial sequenceAB0862301399ena158822
67770Cedecea neteri JCM 7582 gene for 16S ribosomal RNA, partial sequenceLC5040431464ena158822

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cedecea neteri NBRC 105707 = ATCC 338551216978.4wgspatric1216978
66792Cedecea neteri strain NCTC12120158822.24wgspatric158822
66792Cedecea neteri NBRC 1057072731957623draftimg1216978
67770Cedecea neteri NBRC 105707 = ATCC 33855GCA_001571265contigncbi1216978
67770Cedecea neteri NCTC12120GCA_900461005contigncbi158822

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.924no
gram-positiveno97.941no
anaerobicno96.553no
aerobicyes67.93no
halophileno88.135no
spore-formingno93.91no
thermophileno99.235no
glucose-utilyes95.351no
flagellatedno57.588no
glucose-fermentyes90.748no

External links

@ref: 5117

culture collection no.: DSM 13693, ATCC 33855, CDC 0621-75, CCUG 18763, CECT 855, JCM 7582, CDC 621-75, CIP 103241, GTC 1717, LMG 7864, NBRC 105707, NCTC 12120

straininfo link

  • @ref: 73814
  • straininfo: 1710

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5117Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13693)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13693
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
40578Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15017
46880Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18763)https://www.ccug.se/strain?id=18763
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
73814Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1710.1StrainInfo: A central database for resolving microbial strain identifiers
121276Curators of the CIPCollection of Institut Pasteur (CIP 103241)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103241