Strain identifier

BacDive ID: 5336

Type strain: Yes

Species: Enterococcus ratti

Strain Designation: DS 2705-87

Strain history: CIP <- 2001, CCUG <- 2000, CDC, Atlanta, USA <- Johns Hopkins Univ.

NCBI tax ID(s): 1158605 (strain), 150033 (species)

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General

@ref: 6054

BacDive-ID: 5336

DSM-Number: 15687

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, spore-forming, mesophilic, animal pathogen

description: Enterococcus ratti DS 2705-87 is a microaerophile, spore-forming, mesophilic animal pathogen of the family Enterococcaceae.

NCBI tax id

NCBI tax idMatching level
150033species
1158605strain

strain history

@refhistory
6054<- E. Falsen, CCUG <- R. R. Facklam, CDC <- M. E. Etheridge
122144CIP <- 2001, CCUG <- 2000, CDC, Atlanta, USA <- Johns Hopkins Univ.

doi: 10.13145/bacdive5336.20230509.8.1

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 ratti
  • full scientific name: Enterococcus ratti Teixeira et al. 2001

@ref: 6054

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus ratti

full scientific name: Enterococcus ratti Teixeira et al. 2001

strain designation: DS 2705-87

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.05
69480100positive
122144nopositivecoccus-shaped

colony morphology

@reftype of hemolysis
6054gamma
122144

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6054TRYPTICASE 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
6054COLUMBIA 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
33088MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122144CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6054positivegrowth37mesophilic
33088positivegrowth37mesophilic
55736positivegrowth37mesophilic
122144positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6054microaerophile
55736aerobe

spore formation

@refspore formationconfidence
69481yes99
69480no99.974

halophily

  • @ref: 122144
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

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
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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-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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122144esculin+hydrolysis4853
122144nitrate-reduction17632
122144nitrite-reduction16301
68381arginine+hydrolysis29016
68381D-ribose+builds acid from16988
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

metabolite production

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

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
12214415688acetoin-

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
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-
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
122144oxidase-
122144beta-galactosidase+3.2.1.23
122144alcohol dehydrogenase-1.1.1.1
122144gelatinase-
122144amylase-
122144catalase-1.11.1.6
122144gamma-glutamyltransferase+2.3.2.2
122144lysine decarboxylase-4.1.1.18
122144ornithine 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
122144-+++------------+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122144----+/------+/-+/-+/---------+/---+-+/-+/---------------------+/-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
6054++----++-++-----+--+-----+-----+
6054++----+--++-----+--+-----+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122144------------------+--------------------------------+----------+--+-------------+---+--+------------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typesampling dategeographic locationisolation date
6054USAUSANorth America
55736USAUSANorth AmericaNeonatel rat diarrhea1992Johns Hopkins University
122144United States of AmericaUSANorth AmericaNeonatal rat, diarrhea1992

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Infection#Disease
#Host Body-Site#Gastrointestinal tract
#Host#Juvenile

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6054yes2Risk group (German classification)
1221442Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterococcus ratti strain ATCC 700914 16S ribosomal RNA gene, partial sequenceAF5397051503ena150033
6054Enterococcus ratti 16S ribosomal RNA gene, partial sequenceAF3264721523ena150033

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus ratti DSM 15687GCA_001886195contigncbi150033
66792Enterococcus ratti strain DSM 15687150033.3wgspatric150033

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileno95.892no
gram-positiveyes93.857no
anaerobicno94.856yes
aerobicno95.661no
halophileyes90.242no
spore-formingno90.764no
glucose-utilyes90.389no
flagellatedno98.191no
thermophileno99.469yes
glucose-fermentyes86.258no

External links

@ref: 6054

culture collection no.: DSM 15687, ATCC 700914, CCUG 43228, CDC 2705-87, CIP 107173, NCIMB 13635

straininfo link

  • @ref: 74825
  • straininfo: 60946

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11594604Enterococcus porcinus sp. nov. and Enterococcus ratti sp. nov., associated with enteric disorders in animals.Teixeira LM, Carvalho MG, Espinola MM, Steigerwalt AG, Douglas MP, Brenner DJ, Facklam RRInt J Syst Evol Microbiol10.1099/00207713-51-5-17372001Animals, Bacterial Proteins/analysis, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Diarrhea/microbiology/*veterinary, Electrophoresis, Gel, Pulsed-Field, Enterococcus/*classification/genetics/isolation & purification/physiology, Gram-Positive Bacterial Infections/microbiology/*veterinary, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Rats, Sequence Analysis, DNA, Swine, Swine Diseases/*microbiology, Terminology as TopicEnzymology
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
6054Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15687)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15687
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
33088Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4579
55736Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43228)https://www.ccug.se/strain?id=43228
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
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
74825Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID60946.1StrainInfo: A central database for resolving microbial strain identifiers
122144Curators of the CIPCollection of Institut Pasteur (CIP 107173)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107173