Strain identifier
BacDive ID: 5321
Type strain:
Species: Enterococcus cecorum
Strain Designation: A60, A 60
Strain history: CIP <- 1993, L.A. Devriese, Ghent Univ., Ghent, Belgium: strain A 60
NCBI tax ID(s): 1121864 (strain), 44008 (species)
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 id | Matching level |
---|---|
44008 | species |
1121864 | strain |
strain history
@ref | history |
---|---|
9004 | <- NCDO <- L.A. Devriese, A60 |
40759 | 1993, L.A. Devriese, Gent Univ., Belgium: strain A 60 |
67770 | ATCC 43198 <-- NCDO 2674 <-- L. A. Devriese A60. |
117227 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 92.741 | ||
69480 | 100 | positive | ||
117227 | no | positive | coccus-shaped |
colony morphology
- @ref: 9004
- incubation period: 1-2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9004 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
9004 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
40759 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
117227 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9004 | positive | growth | 37 | mesophilic |
40759 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
9004 | microaerophile |
48706 | microaerophile |
117227 | facultative 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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
117227 | 17632 | nitrate | - | reduction |
117227 | 16301 | nitrite | - | reduction |
68381 | 29016 | arginine | - | hydrolysis |
68381 | 16988 | D-ribose | + | builds acid from |
68381 | 16899 | D-mannitol | - | builds acid from |
68381 | 30911 | sorbitol | - | builds acid from |
68381 | 17716 | lactose | + | builds acid from |
68381 | 27082 | trehalose | + | builds acid from |
68381 | 16634 | raffinose | + | builds acid from |
68381 | 17992 | sucrose | + | builds acid from |
68381 | 30849 | L-arabinose | - | builds acid from |
68381 | 18333 | D-arabitol | - | builds acid from |
68381 | 40585 | alpha-cyclodextrin | + | builds acid from |
68381 | 606565 | hippurate | - | hydrolysis |
68381 | 28087 | glycogen | - | builds acid from |
68381 | 27941 | pullulan | - | builds acid from |
68381 | 17306 | maltose | + | builds acid from |
68381 | 28053 | melibiose | + | builds acid from |
68381 | 6731 | melezitose | + | builds acid from |
68381 | 320055 | methyl beta-D-glucopyranoside | + | builds acid from |
68381 | 16443 | D-tagatose | + | builds acid from |
68381 | 16199 | urea | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
117227 | 35581 | indole | no |
68381 | 15688 | acetoin | yes |
metabolite tests
- @ref: 68381
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
9004 | catalase | - | 1.11.1.6 |
9004 | cytochrome-c oxidase | - | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68381 | urease | - | 3.5.1.5 |
68381 | glycyl tryptophan arylamidase | + | |
68381 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68381 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68381 | beta-galactosidase | + | 3.2.1.23 |
68381 | Alanyl-Phenylalanyl-Proline arylamidase | - | |
68381 | alkaline phosphatase | + | 3.1.3.1 |
68381 | alpha-galactosidase | + | 3.2.1.22 |
68381 | beta-glucuronidase | + | 3.2.1.31 |
68381 | beta-glucosidase | + | 3.2.1.21 |
68381 | arginine dihydrolase | - | 3.5.3.6 |
117227 | oxidase | - | |
117227 | catalase | - | 1.11.1.6 |
117227 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
117227 | - | + | + | + | - | + | - | - | - | - | + | + | + | + | + | + | + | + | - | - |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9004 | - | + | + | + | + | + | + | - | - | + | + | + | + | - | - | + | + | - | + | - | + | + | - | - | - | + | + | + | + | + | +/- | - |
9004 | - | + | + | + | + | + | + | - | - | + | + | + | + | - | - | + | + | - | + | - | + | + | - | - | - | + | + | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location | isolation date |
---|---|---|---|---|---|---|
9004 | caecum of chicken | |||||
48706 | Chicken caecum | |||||
67770 | Chicken caecum | Belgium | BEL | Europe | ||
117227 | Animal, Chicken, ceca | Belgium | BEL | Europe | Ghent | 1980 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
9004 | yes, in single cases | 1 | Risk group (German classification) |
117227 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Enterococcus cecorum strain ATCC 43198 16S-23S ribosomal RNA intergenic spacer, partial sequence | DQ217843 | 190 | ena | 1121864 |
20218 | Enterococcus cecorum 16S rRNA gene | Y18355 | 1409 | ena | 1121864 |
9004 | Enterococcus cecorum 16S ribosomal RNA gene, partial sequence | AF061009 | 1509 | ena | 1121864 |
67770 | Enterococcus cecorum 16S rRNA gene, strain LMG 12902 | AJ301827 | 1667 | ena | 1121864 |
67770 | Enterococcus cecorum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8724 | LC096213 | 1498 | ena | 44008 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Enterococcus cecorum NCTC12421 | GCA_900474605 | complete | ncbi | 44008 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 | GCA_000407565 | contig | ncbi | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 | GCA_000492155 | scaffold | ncbi | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 | GCA_001885885 | contig | ncbi | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 | GCA_000379745 | scaffold | ncbi | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 | 1121864.8 | wgs | patric | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 | 1121864.6 | wgs | patric | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 [PRJNA199185] | 1121864.3 | wgs | patric | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 [PRJNA206360] | 1121864.4 | wgs | patric | 1121864 |
66792 | Enterococcus cecorum strain NCTC12421 | 44008.68 | complete | patric | 44008 |
66792 | Enterococcus cecorum DSM 20682 | 2515154031 | draft | img | 1121864 |
66792 | Enterococcus cecorum DSM 20682 | 2558860907 | draft | img | 1121864 |
66792 | Enterococcus cecorum DSM 20682 | 2541047997 | draft | img | 1121864 |
66792 | Enterococcus cecorum DSM 20682 = ATCC 43198 DSM 20682 | GCA_947055815 | contig | ncbi | 1121864 |
GC content
@ref | GC-content |
---|---|
9004 | 37.0 |
67770 | 37 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 66 | no |
flagellated | no | 96.605 | no |
gram-positive | yes | 93.629 | no |
anaerobic | no | 89.053 | no |
aerobic | no | 98.279 | yes |
halophile | yes | 77.816 | no |
spore-forming | no | 91.401 | no |
thermophile | no | 98.267 | no |
glucose-util | yes | 88.3 | no |
motile | no | 95.821 | no |
glucose-ferment | yes | 86.583 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9004 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20682) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20682 | |||
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 | |
40759 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15499 | ||||
48706 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 27299) | https://www.ccug.se/strain?id=27299 | |||
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/ | ||||
68381 | Automatically annotated from API rID32STR | |||||
68382 | Automatically annotated from API zym | |||||
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) | |||
74810 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10169.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
117227 | Curators of the CIP | Collection of Institut Pasteur (CIP 103676) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103676 |