Strain identifier

BacDive ID: 5328

Type strain: Yes

Species: Enterococcus columbae

Strain history: CIP <- 1993, L.A. Devriese, Ghent Univ., Ghent, Belgium: strain STR 345

NCBI tax ID(s): 1121865 (strain), 1355 (species)

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General

@ref: 3130

BacDive-ID: 5328

DSM-Number: 7374

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive

description: Enterococcus columbae DSM 7374 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from pigeon intestine.

NCBI tax id

NCBI tax idMatching level
1355species
1121865strain

strain history

@refhistory
3130<- NCIMB <- L.A. Devriese, STR 345
407581993, L.A. Devriese, Gent Univ., Belgium: strain STR 345
118707CIP <- 1993, L.A. Devriese, Ghent Univ., Ghent, Belgium: strain STR 345

doi: 10.13145/bacdive5328.20230509.8.1

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 columbae
  • full scientific name: Enterococcus columbae Devriese et al. 1993

@ref: 3130

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus columbae

full scientific name: Enterococcus columbae Devriese et al. 1993

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118707positivecoccus-shapedno

colony morphology

@reftype of hemolysishemolysis ability
3130gamma
1187071

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3130COLUMBIA 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
3130TRYPTICASE 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
40758MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118707CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
3130positivegrowth37mesophilic
40758positivegrowth37mesophilic
49006positivegrowth37mesophilic
118707positivegrowth25-45
118707nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3130microaerophile
49006aerobe
118707facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.25

halophily

  • @ref: 118707
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 3130
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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
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
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
118707esculin+hydrolysis4853
118707hippurate+hydrolysis606565
118707nitrate-reduction17632
118707nitrite-reduction16301
68381arginine-hydrolysis29016
68381D-ribose+builds acid from16988
68381D-mannitol+builds acid from16899
68381sorbitol+builds acid from30911
68381lactose+builds acid from17716
68381trehalose+builds acid from27082
68381raffinose+builds acid from16634
68381sucrose+builds acid from17992
68381L-arabinose+builds acid from30849
68381alpha-cyclodextrin+builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381maltose+builds acid from17306
68381melibiose+builds acid from28053
68381urea-hydrolysis16199

metabolite production

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
11870715688acetoin-

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
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
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-
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
118707oxidase-
118707beta-galactosidase+3.2.1.23
118707alcohol dehydrogenase-1.1.1.1
118707catalase-1.11.1.6
118707gamma-glutamyltransferase-2.3.2.2
118707lysine decarboxylase-4.1.1.18
118707ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118707-+++-+----+++--++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118707---+++---++++-+--++-++-++++++++++-+++-++-+-+----+/-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
3130-+--++/-+++++++++/-++----+--+/-+++/--+/---
3130-+--+++++++++++++----+--++++++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118707---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
3130pigeon intestineBelgiumBELEurope
49006Pigeon (Columba livia) intestineBelgiumBELEuropeGent
118707Animal, Pigeon, intestineBelgiumBELEuropeGhent1988

isolation source categories

Cat1Cat2
#Host#Birds
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_3741.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1561;97_1865;98_2855;99_3741&stattab=map
  • Last taxonomy: Enterococcus columbae subclade
  • 16S sequence: Y18275
  • Sequence Identity:
  • Total samples: 3630
  • soil counts: 163
  • aquatic counts: 442
  • animal counts: 2889
  • plant counts: 136

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31301Risk group (German classification)
1187072Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218E.columbae 16S rRNA geneX564221493ena1121865
20218Enterococcus columbae (strain NCIMB 13013T)16S rRNA geneY182751443ena1121865
3130Enterococcus columbae 16S ribosomal RNA gene, partial sequenceAF0610061480ena1121865
3130Enterococcus columbae DSM 7374 = ATCC 51263 strain DSM 7374, whole genome shotgun sequencing projectARDE0000000044ena1121865

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus columbae DSM 7374 = ATCC 51263GCA_000407225scaffoldncbi1121865
66792Enterococcus columbae DSM 7374 = ATCC 51263GCA_000406925scaffoldncbi1121865
66792Enterococcus columbae DSM 7374 = ATCC 51263GCA_000373065scaffoldncbi1121865
66792Enterococcus columbae DSM 7374 = ATCC 51263GCA_001885835contigncbi1121865
66792Enterococcus columbae DSM 7374 = ATCC 512631121865.7wgspatric1121865
66792Enterococcus columbae DSM 7374 = ATCC 51263 [PRJNA199225]1121865.4wgspatric1121865
66792Enterococcus columbae DSM 7374 = ATCC 51263 [PRJNA206271]1121865.3wgspatric1121865
66792Enterococcus columbae DSM 7374 = ATCC 51263 [PRJNA206361]1121865.5wgspatric1121865
66792Enterococcus columbae DSM 73742541047998draftimg1121865
66792Enterococcus columbae DSM 73742541047448draftimg1121865
66792Enterococcus columbae DSM 73742515154086draftimg1121865

GC content

  • @ref: 3130
  • GC-content: 38.0
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno58no
motileno51.546no
flagellatedno78.484no
gram-positiveyes90.991no
anaerobicno82.83no
aerobicno98.029no
halophileyes59.162no
spore-formingno78.738no
thermophileno94.992yes
glucose-utilyes90.884no
glucose-fermentyes85.992no

External links

@ref: 3130

culture collection no.: DSM 7374, ATCC 51263, NCIMB 13013, CCUG 27894, STR 345, CIP 103675, LMG 11740

straininfo link

  • @ref: 74817
  • straininfo: 2245

literature

  • topic: Genetics
  • Pubmed-ID: 2272492
  • title: Enterococcus columbae, a species from pigeon intestines.
  • authors: Devriese LA, Ceyssens K, Rodrigues UM, Collins MD
  • journal: FEMS Microbiol Lett
  • DOI: 10.1016/0378-1097(90)90228-i
  • year: 1990
  • mesh: Amino Acid Sequence, Animals, Columbidae/*microbiology, DNA/analysis, Enterobacteriaceae/*genetics, Intestines/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3130Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7374)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7374
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
40758Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15498
49006Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27894)https://www.ccug.se/strain?id=27894
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
68371Automatically annotated from API 50CH acid
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)
74817Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2245.1StrainInfo: A central database for resolving microbial strain identifiers
118707Curators of the CIPCollection of Institut Pasteur (CIP 103675)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103675