Strain identifier

BacDive ID: 5321

Type strain: Yes

Species: Enterococcus cecorum

Strain Designation: A60, A 60

Strain history: CIP <- 1993, L.A. Devriese, Ghent Univ., Ghent, Belgium: strain A 60

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General

@ref: 9004

BacDive-ID: 5321

DSM-Number: 20682

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, human pathogen

description: Enterococcus cecorum A60 is a microaerophile, mesophilic human pathogen that was isolated from caecum of chicken.

NCBI tax id

NCBI tax idMatching level
44008species
1121864strain

strain history

@refhistory
9004<- NCDO <- L.A. Devriese, A60
407591993, L.A. Devriese, Gent Univ., Belgium: strain A 60
67770ATCC 43198 <-- NCDO 2674 <-- L. A. Devriese A60.
117227CIP <- 1993, L.A. Devriese, Ghent Univ., Ghent, Belgium: strain A 60

doi: 10.13145/bacdive5321.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Enterococcaceae
  • genus: Enterococcus
  • species: Enterococcus cecorum
  • full scientific name: Enterococcus cecorum (Devriese et al. 1983) Williams et al. 1989
  • synonyms

    • @ref: 20215
    • synonym: Streptococcus cecorum

@ref: 9004

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus cecorum

full scientific name: Enterococcus cecorum (Devriese et al. 1983) Williams et al. 1989

strain designation: A60, A 60

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.741
69480100positive
117227nopositivecoccus-shaped

colony morphology

  • @ref: 9004
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9004COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
9004TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
40759MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
117227CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
9004positivegrowth37mesophilic
40759positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
9004microaerophile
48706microaerophile
117227facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.576

murein

  • @ref: 9004
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11722717632nitrate-reduction
11722716301nitrite-reduction
6838129016arginine-hydrolysis
6838116988D-ribose+builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose+builds acid from
6838127082trehalose+builds acid from
6838116634raffinose+builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin+builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose+builds acid from
6838128053melibiose+builds acid from
683816731melezitose+builds acid from
68381320055methyl beta-D-glucopyranoside+builds acid from
6838116443D-tagatose+builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
11722735581indoleno
6838115688acetoinyes

metabolite tests

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
9004catalase-1.11.1.6
9004cytochrome-c oxidase-1.9.3.1
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
68381urease-3.5.1.5
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase+3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase+3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase+3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
117227oxidase-
117227catalase-1.11.1.6
117227urease-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
117227-+++-+----++++++++--

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
9004-++++++--++++--++-+-++---++++++/--
9004-++++++--++++--++-+-++---++++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
9004caecum of chicken
48706Chicken caecum
67770Chicken caecumBelgiumBELEurope
117227Animal, Chicken, cecaBelgiumBELEuropeGhent1980

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body-Site#Gastrointestinal tract#Large intestine

taxonmaps

  • @ref: 69479
  • File name: preview.99_2966.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1561;97_1865;98_2290;99_2966&stattab=map
  • Last taxonomy: Enterococcus cecorum subclade
  • 16S sequence: LC096213
  • Sequence Identity:
  • Total samples: 41215
  • soil counts: 1785
  • aquatic counts: 4501
  • animal counts: 34006
  • plant counts: 923

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
9004yes, in single cases1Risk group (German classification)
1172272Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterococcus cecorum strain ATCC 43198 16S-23S ribosomal RNA intergenic spacer, partial sequenceDQ217843190ena1121864
20218Enterococcus cecorum 16S rRNA geneY183551409ena1121864
9004Enterococcus cecorum 16S ribosomal RNA gene, partial sequenceAF0610091509ena1121864
67770Enterococcus cecorum 16S rRNA gene, strain LMG 12902AJ3018271667ena1121864
67770Enterococcus cecorum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8724LC0962131498ena44008

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus cecorum NCTC12421GCA_900474605completencbi44008
66792Enterococcus cecorum DSM 20682 = ATCC 43198GCA_000407565contigncbi1121864
66792Enterococcus cecorum DSM 20682 = ATCC 43198GCA_000492155scaffoldncbi1121864
66792Enterococcus cecorum DSM 20682 = ATCC 43198GCA_001885885contigncbi1121864
66792Enterococcus cecorum DSM 20682 = ATCC 43198GCA_000379745scaffoldncbi1121864
66792Enterococcus cecorum DSM 20682 = ATCC 431981121864.8wgspatric1121864
66792Enterococcus cecorum DSM 20682 = ATCC 431981121864.6wgspatric1121864
66792Enterococcus cecorum DSM 20682 = ATCC 43198 [PRJNA199185]1121864.3wgspatric1121864
66792Enterococcus cecorum DSM 20682 = ATCC 43198 [PRJNA206360]1121864.4wgspatric1121864
66792Enterococcus cecorum strain NCTC1242144008.68completepatric44008
66792Enterococcus cecorum DSM 206822515154031draftimg1121864
66792Enterococcus cecorum DSM 206822558860907draftimg1121864
66792Enterococcus cecorum DSM 206822541047997draftimg1121864
66792Enterococcus cecorum DSM 20682 = ATCC 43198 DSM 20682GCA_947055815contigncbi1121864

GC content

@refGC-content
900437.0
6777037

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno66no
flagellatedno96.605no
gram-positiveyes93.629no
anaerobicno89.053no
aerobicno98.279yes
halophileyes77.816no
spore-formingno91.401no
thermophileno98.267no
glucose-utilyes88.3no
motileno95.821no
glucose-fermentyes86.583no

External links

@ref: 9004

culture collection no.: DSM 20682, ATCC 43198, NCDO 2674, CCUG 27299, JCM 8724, CCM 3659, CECT 4088, CGMCC 1.2139, CIP 103676, KCTC 3642, LMG 12902, NBRC 100674, NCIMB 702674, NCTC 12421, NCFB 2674

straininfo link

  • @ref: 74810
  • straininfo: 10169

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9004Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20682)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20682
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
40759Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15499
48706Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27299)https://www.ccug.se/strain?id=27299
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/
68381Automatically annotated from API rID32STR
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)
74810Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10169.1StrainInfo: A central database for resolving microbial strain identifiers
117227Curators of the CIPCollection of Institut Pasteur (CIP 103676)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103676