Strain identifier

BacDive ID: 5335

Type strain: Yes

Species: Enterococcus phoeniculicola

Strain Designation: JLB-1

Strain history: CIP <- 2004, DSMZ <- P. R. Meyers <- J. Law-Brown, Inst. African Ornithol., Cape Town, South Africa: strain JLB-1

NCBI tax ID(s): 154621 (species)

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General

@ref: 5511

BacDive-ID: 5335

DSM-Number: 14726

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, coccus-shaped

description: Enterococcus phoeniculicola JLB-1 is a microaerophile, mesophilic, coccus-shaped bacterium that was isolated from uropygial gland of red-billed woodhoopoe.

NCBI tax id

  • NCBI tax id: 154621
  • Matching level: species

strain history

@refhistory
5511<- P. R. Meyers; JLB-1 <- J. Law-Brown
67771<- PR Meyers, JLB-1 <- J Law-Brown
121806CIP <- 2004, DSMZ <- P. R. Meyers <- J. Law-Brown, Inst. African Ornithol., Cape Town, South Africa: strain JLB-1

doi: 10.13145/bacdive5335.20230509.8.1

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 phoeniculicola
  • full scientific name: Enterococcus phoeniculicola Law-Brown and Meyers 2003

@ref: 5511

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus phoeniculicola

full scientific name: Enterococcus phoeniculicola Law-Brown and Meyers 2003

strain designation: JLB-1

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771coccus-shapedno
67771positive
69480no93.908
69480positive100
121806coccus-shapednopositive

colony morphology

  • @ref: 121806

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5511COLUMBIA 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
5511TRYPTICASE 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
33951MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121806CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338
121806CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5511positivegrowth37mesophilic
33951positivegrowth37mesophilic
58394positivegrowth37mesophilic
67771positivegrowth37mesophilic
121806positivegrowth10-41
121806nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5511microaerophile
58394aerobe
67771microaerophile
121806facultative anaerobe

spore formation

@refspore formationconfidence
67771no
69481yes100
69480no99.966

halophily

  • @ref: 121806
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
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
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
121806esculin+hydrolysis4853
121806hippurate+hydrolysis606565
121806nitrate-reduction17632
121806nitrite-reduction16301
68381D-ribose+builds acid from16988
68381D-mannitol-builds acid from16899
68381sorbitol-builds acid from30911
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+
12180615688acetoin-

enzymes

@refvalueactivityec
5511catalase-1.11.1.6
5511cytochrome-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
68381glycyl tryptophan arylamidase+
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
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
121806oxidase-
121806beta-galactosidase+3.2.1.23
121806alcohol dehydrogenase-1.1.1.1
121806gelatinase-
121806amylase-
121806catalase-1.11.1.6
121806gamma-glutamyltransferase-2.3.2.2
121806lysine decarboxylase-4.1.1.18
121806ornithine 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
121806--++-+---+++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121806---+++---++++---+/----++++++++++++--++--++-+------+

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
5511-++-+-+--++--+-+++++++---+--+++-
5511+++-+-+---+--+-++-++++---+--+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121806++-++----++----+-++-----------+----------------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
5511uropygial (preening) gland of red-billed woodhoopoeMorgan BaySouth AfricaZAFAfrica
58394Uropygial gland of a red-billed WoodhoopoeMorgan BaySouth AfricaZAFAfrica
67771From uropygial(preen) gland, Red-billed Woodhoopoe, `Phoeniculus purpureus`captured in the Morgan Bay regionEastern Cape provinceSouth AfricaZAFAfrica-32.716728.7833
121806Uropygial (preening) gland of red-billed woodhoopoeSouth AfricaZAFAfrica

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_3701.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_19;97_19;98_2828;99_3701&stattab=map
  • Last taxonomy: Enterococcus
  • 16S sequence: AB681238
  • Sequence Identity:
  • Total samples: 747
  • soil counts: 16
  • aquatic counts: 54
  • animal counts: 640
  • plant counts: 37

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55111Risk group (German classification)
1218062Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5511Enterococcus phoeniculicola 16S ribosomal RNA gene, partial sequenceAY0284371479ena154621
5511Enterococcus phoeniculicola strain DSM 14726, whole genome shotgun sequencing projectJXKY0000000078ena154621
67771Enterococcus phoeniculicola gene for 16S rRNA, partial sequence, strain: NBRC 100711AB6812381484ena154621

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus phoeniculicola strain DSM 14726154621.3wgspatric154621
67771Enterococcus phoeniculicola DSM 14726GCA_001886115scaffoldncbi154621

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.062yes
gram-positiveyes93.918no
anaerobicno96.271yes
aerobicno96.355no
halophileyes77.868no
spore-formingno88.799yes
thermophileno99.18yes
glucose-utilyes89.582no
flagellatedno96.671no
glucose-fermentyes85.259no

External links

@ref: 5511

culture collection no.: CCUG 48923, KCTC 3818, DSM 14726, ATCC BAA 412, CIP 108361, NBRC 100711

straininfo link

  • @ref: 74824
  • straininfo: 99941

literature

  • topic: Phylogeny
  • Pubmed-ID: 12807187
  • title: Enterococcus phoeniculicola sp. nov., a novel member of the enterococci isolated from the uropygial gland of the Red-billed Woodhoopoe, Phoeniculus purpureus.
  • authors: Law-Brown J, Meyers PR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02334-0
  • year: 2003
  • mesh: Animals, Bacterial Typing Techniques, Birds/*microbiology, Buttocks, DNA, Ribosomal/analysis, Enterococcus/*classification/genetics/isolation & purification/physiology, Exocrine Glands/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5511Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14726)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14726
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
33951Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5975
58394Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48923)https://www.ccug.se/strain?id=48923
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
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
74824Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99941.1StrainInfo: A central database for resolving microbial strain identifiers
121806Curators of the CIPCollection of Institut Pasteur (CIP 108361)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108361