Strain identifier

BacDive ID: 5278

Type strain: Yes

Species: Enterococcus durans

Strain Designation: 98 D, D3

Strain history: CIP <- 1955, R. Wahl, UK: strain D3 <- Public Hlth. Lab., London, UK: strain 98D, Streptococcus durans

NCBI tax ID(s): 1218088 (strain), 53345 (species)

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General

@ref: 8979

BacDive-ID: 5278

DSM-Number: 20633

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped, human pathogen

description: Enterococcus durans 98 D is a microaerophile, mesophilic, Gram-positive human pathogen that was isolated from dried milk.

NCBI tax id

NCBI tax idMatching level
1218088strain
53345species

strain history

@refhistory
8979<- K.H. Schleifer <- CCM <- P.M.F. Shattock <- (J.M. Sherman, 98 D)
67770ATCC 19432 <-- NCTC 8307 <-- Streptococcus Ref. Lab. London.
118979CIP <- 1955, R. Wahl, UK: strain D3 <- Public Hlth. Lab., London, UK: strain 98D, Streptococcus durans

doi: 10.13145/bacdive5278.20230509.8.1

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 durans
  • full scientific name: Enterococcus durans (ex Sherman and Wing 1937) Collins et al. 1984

  • synonyms

    • @ref: 20215
    • synonym: Streptococcus durans

@ref: 8979

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus durans

full scientific name: Enterococcus durans (ex Sherman and Wing 1937) Collins et al. 1984

strain designation: 98 D, D3

type strain: yes

Morphology

cell morphology

  • @ref: 118979
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@reftype of hemolysishemolysis abilityincubation period
8979beta11-2 days
1189791

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8979COLUMBIA 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
8979TRYPTICASE 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
37696MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118979CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
8979positivegrowth37mesophilic
37696positivegrowth37mesophilic
67770positivegrowth37mesophilic
118979positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8979microaerophile
118979facultative anaerobe

spore formation

  • @ref: 118979
  • spore formation: no

halophily

  • @ref: 118979
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 8979
  • 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
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
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
118979esculin+hydrolysis4853
118979hippurate-hydrolysis606565
118979nitrate-reduction17632
118979nitrite-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
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381melibiose-builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside+builds acid from320055
68381D-tagatose-builds acid from16443
68381urea-hydrolysis16199

metabolite production

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

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
11897915688acetoin+

enzymes

@refvalueactivityec
8979catalase+1.11.1.6
8979cytochrome-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
68381beta-mannosidase+3.2.1.25
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase+3.4.19.3
68381beta-galactosidase+3.2.1.23
68381alkaline phosphatase-3.1.3.1
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase+3.5.3.6
118979oxidase-
118979beta-galactosidase+3.2.1.23
118979alcohol dehydrogenase+1.1.1.1
118979catalase-1.11.1.6
118979gamma-glutamyltransferase-2.3.2.2
118979lysine decarboxylase-4.1.1.18
118979ornithine 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
118979--++-+-------+--++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118979+/----+----++++--------++++++++-----+/-+/---++/---------+/-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
8979+++---+--+------+-++-+---+--+-+-
8979+++/--+-+--+------+-++-----+--+-+-
8979+++-+-+--+------+-++-+---+--+-+-
8979+++-+-+--+------++/-++-+---+--+-+-

Isolation, sampling and environmental information

isolation

@refsample type
8979dried milk
67770Dried milk
118979Food, Dried milk

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_23.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_19;97_19;98_22;99_23&stattab=map
  • Last taxonomy: Enterococcus
  • 16S sequence: LC096214
  • Sequence Identity:
  • Total samples: 55544
  • soil counts: 1007
  • aquatic counts: 2532
  • animal counts: 51351
  • plant counts: 654

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8979yesyes2Risk group (German classification)
1189792Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterococcus durans strain ATCC 19432 16S ribosomal RNA gene, partial sequenceKC510230815ena53345
20218E.durans 16S-23S rRNA spacer DNA & tRNA-Ala geneX87177330ena53345
20218E.durans 16S-23S rRNA spacer DNAX87178277ena53345
20218E.durans 16S rRNA gene, partial (strain ATTC 19432 (CCUG 7972))Y12909366ena53345
8979Enterococcus durans 16S rRNA gene, strain DSM20633AJ2763541534ena53345
67770Enterococcus durans gene for 16S rRNA, partial sequence, strain: JCM 8725AB5969431482ena53345
67770Enterococcus durans 16S rRNA gene, strain CECT411TAJ4208011506ena53345
67770Enterococcus durans gene for 16S ribosomal RNA, partial sequence, strain: JCM 8725LC0962141502ena53345
67770Enterococcus durans 16S rRNA geneY183591434ena53345

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus durans NBRC 100479 = LMG 10746GCA_001544215contigncbi1218088
66792Enterococcus durans NBRC 1004791218088.3wgspatric1218088
66792Enterococcus durans strain FDAARGOS 143753345.186completepatric53345
66792Enterococcus durans NBRC 1004792731957564draftimg1218088

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes90.83no
anaerobicno94.929no
halophileyes89.547no
spore-formingno86.32no
glucose-utilyes86.731no
motileno94.452no
aerobicno96.802yes
thermophileno99.245yes
flagellatedno97.095no
glucose-fermentyes86.926no

External links

@ref: 8979

culture collection no.: DSM 20633, ATCC 19432, CCM 5612, NCDO 596, NCTC 8307, JCM 8725, BCRC 10790, CCUG 7972, CECT 411, CGMCC 1.2284, CIP 55.125, LMG 10746, LMG 12691, NBRC 100479, NCAIM B.02010, NCIMB 700596, VTT E-97805

straininfo link

  • @ref: 74768
  • straininfo: 2249

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism12200334Cholesterol assimilation by lactic acid bacteria and bifidobacteria isolated from the human gut.Pereira DI, Gibson GRAppl Environ Microbiol10.1128/AEM.68.9.4689-4693.20022002Bifidobacterium/drug effects/growth & development/isolation & purification/*metabolism, Bile/metabolism, Cholesterol/*metabolism, Culture Media, Digestive System/*microbiology, Humans, Hydrochloric Acid/pharmacology, Lactic Acid/metabolism, Lactobacillus/drug effects/growth & development/isolation & purification/*metabolismPathogenicity
Phylogeny18599707Enterococcus thailandicus sp. nov., isolated from fermented sausage ('mum') in Thailand.Tanasupawat S, Sukontasing S, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65535-02008Enterococcus/*classification/genetics/isolation & purification, Fermentation, *Food Microbiology, Meat Products/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, ThailandBiotechnology
Phylogeny22003038Enterococcus lactis sp. nov., from Italian raw milk cheeses.Morandi S, Cremonesi P, Povolo M, Brasca MInt J Syst Evol Microbiol10.1099/ijs.0.030825-02011Bacterial Typing Techniques, Cheese/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Enterococcus/*classification/genetics/isolation & purification, Fatty Acids/analysis, Genes, Bacterial, Italy, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny27260143Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.Ren X, Li M, Guo DCurr Microbiol10.1007/s00284-016-1065-12016Bacterial Proteins/genetics/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterococcus/classification/genetics/*isolation & purification/metabolism, Fermentation, Phylogeny, RNA, Ribosomal, 16S/genetics, Yogurt/*microbiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8979Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20633)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20633
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
37696Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8711
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/
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
74768Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2249.1StrainInfo: A central database for resolving microbial strain identifiers
118979Curators of the CIPCollection of Institut Pasteur (CIP 55.125)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2055.125