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): 1158610 (strain), 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 idMatching level
1158610strain
154621species

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/bacdive5335.20250331.9.3

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
121806coccus-shapednopositive
125438positive91.382

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

@refgrowthtypetemperature
5511positivegrowth37
33951positivegrowth37
58394positivegrowth37
67771positivegrowth37
121806positivegrowth10-41
121806nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5511microaerophile
58394aerobe
67771microaerophile
121806facultative anaerobe
125439obligate aerobe93.8

spore formation

  • @ref: 67771
  • spore formation: no

halophily

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838116199urea-hydrolysis
6838116443D-tagatose+builds acid from
683816731melezitose-builds acid from
6838128053melibiose-builds acid from
6838117306maltose+builds acid from
6838127941pullulan-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838118333D-arabitol-builds acid from
6838130849L-arabinose+builds acid from
6838116634raffinose-builds acid from
6838117992sucrose-builds acid from
6838127082trehalose+builds acid from
6838116988D-ribose+builds acid from
6838116899D-mannitol-builds acid from
1218064853esculin+hydrolysis
121806606565hippurate+hydrolysis
12180617632nitrate-reduction
12180616301nitrite-reduction
68371Potassium 5-ketogluconate+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837112936D-galactose+builds acid from
68381320055methyl beta-D-glucopyranoside+builds acid from
6838140585alpha-cyclodextrin+builds acid from
6838130911sorbitol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

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
68382N-acetyl-beta-glucosaminidase+3.2.1.52
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
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
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
68381alpha-galactosidase+3.2.1.22
68381alkaline phosphatase-3.1.3.1
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
68381beta-galactosidase+3.2.1.23
68381beta-glucuronidase-3.2.1.31
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21

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 sequenceAY0284371479nuccore154621
5511Enterococcus phoeniculicola strain DSM 14726, whole genome shotgun sequencing projectJXKY0000000078nuccore154621
67771Enterococcus phoeniculicola gene for 16S rRNA, partial sequence, strain: NBRC 100711AB6812381484nuccore154621

Genome sequences

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

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.382no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no88.845yes
125438spore-formingspore-formingAbility to form endo- or exosporesno78.039no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.078no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.327yes
125438motile2+flagellatedAbility to perform flagellated movementno87no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes78.2
125439BacteriaNetmotilityAbility to perform movementyes73.7
125439BacteriaNetgram_stainReaction to gram-stainingvariable74.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe93.8

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1