Strain identifier

BacDive ID: 158404

Type strain: Yes

Species: Ellagibacter isourolithinifaciens

Strain history: <- M. SELMA, CEBAS CSIC, ESPINARDO, MURCIA, SPAIN <-D. Beltran,CEBAS-CSIC; CEBAS 4A

NCBI tax ID(s): 2137581 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 65080

BacDive-ID: 158404

DSM-Number: 104140

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, Gram-positive, rod-shaped

description: Ellagibacter isourolithinifaciens DSM 104140 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from Human faeces from healthy volunteer.

NCBI tax id

  • NCBI tax id: 2137581
  • Matching level: species

strain history

  • @ref: 65080
  • history: <- M. SELMA, CEBAS CSIC, ESPINARDO, MURCIA, SPAIN <-D. Beltran,CEBAS-CSIC; CEBAS 4A

doi: 10.13145/bacdive158404.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Ellagibacter
  • species: Ellagibacter isourolithinifaciens
  • full scientific name: Ellagibacter isourolithinifaciens Beltrán et al. 2018

@ref: 65080

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Eggerthellales

family: Eggerthellaceae

genus: Ellagibacter

species: Ellagibacter isourolithinifaciens

full scientific name: Ellagibacter isourolithinifaciens Beltrán et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65569positive1.5 µm0.5 µmrod-shapedno
69480positive99.667

colony morphology

  • @ref: 65569
  • colony color: pale-white
  • incubation period: 5 days
  • medium used: ABB

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65080COLUMBIA 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
65569ABByes

culture temp

@refgrowthtypetemperaturerange
65569positivegrowth37mesophilic
65080positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
65569obligate anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
65569no
69480no99.982
69481no100

observation

  • @ref: 65569
  • observation: transforming ellagic acid into isourolithin A

metabolite utilization

  • @ref: 65569
  • Chebi-ID: 17632
  • metabolite: nitrate
  • utilization activity: -
  • kind of utilization tested: reduction

enzymes

@refvalueactivityec
65569catalase-1.11.1.6
65569urease-3.5.1.5
65569arginine arylamidase+
65569leucine arylamidase+3.4.11.1
65569arginine dihydrolase-3.5.3.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperatureisolation procedure
65080Human faeces from healthy volunteerMurcia (Latitude: 37.9439891, Longitude: -1.1636353)SpainESPEurope
65569human faeces of a healthy male volunteer (aged 41)nutrient brothsupplemented with 0.05 % L-cysteine hydrochloride37Diluted in ABB with propylene glycol containing 15 µM urolithin C. Anaerobic incubation

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_55911.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_627;96_14432;97_17609;98_21883;99_55911&stattab=map
  • Last taxonomy: Eggerthellaceae
  • 16S sequence: MF322780
  • Sequence Identity:
  • Total samples: 1973
  • soil counts: 20
  • aquatic counts: 49
  • animal counts: 1902
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 65080
  • description: Coriobacteriaceae bacterium strain CEBAS 4A 16S ribosomal RNA gene, partial sequence
  • accession: MF322780
  • length: 1596
  • database: ena
  • NCBI tax ID: 2137581

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ellagibacter isourolithinifaciens DSM 104140GCA_008831035contigncbi2137581
66792Ellagibacter isourolithinifaciens strain DSM 1041402137581.3wgspatric2137581
66792Ellagibacter isourolithinifaciens DSM 1041402887116418draftimg2137581

GC content

  • @ref: 65569
  • GC-content: 59.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.943yes
gram-positiveyes88.291yes
anaerobicyes99.724yes
aerobicno98.014no
halophileno85.994no
spore-formingno94.394no
glucose-utilyes69.358no
flagellatedno98.524no
thermophileno94.735yes
glucose-fermentyes60.334no

External links

@ref: 65080

culture collection no.: DSM 104140, CCUG 70284, CEBAS 4A

straininfo link

  • @ref: 111207
  • straininfo: 397603

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29583112Ellagibacter isourolithinifaciens gen. nov., sp. nov., a new member of the family Eggerthellaceae, isolated from human gut.Beltran D, Romo-Vaquero M, Espin JC, Tomas-Barberan FA, Selma MVInt J Syst Evol Microbiol10.1099/ijsem.0.0027352018Actinobacteria/*classification/genetics/isolation & purification, Adult, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid, Fatty Acids/chemistry, Feces/microbiology, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Humans, Male, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Metabolism32716447Metabolism of different dietary phenolic compounds by the urolithin-producing human-gut bacteria Gordonibacter urolithinfaciens and Ellagibacter isourolithinifaciens.Garcia-Villalba R, Beltran D, Frutos MD, Selma MV, Espin JC, Tomas-Barberan FAFood Funct10.1039/d0fo01649g2020Actinobacteria/*metabolism, Catechols/metabolism, Ellagic Acid/*metabolism, Gastrointestinal Microbiome/drug effects, Humans, Hydroxylation, Mixed Function Oxygenases/*metabolism, Phenols/*metabolismPathogenicity

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65080Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104140Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104140)
65569David Beltr an, María Romo-Vaquero, Juan C. Espín, Francisco A. Tom as-Barber an and Maria V. SelmaEllagibacter isourolithinifaciens gen. nov., sp. nov., a new member of the family Eggerthellaceae, isolated from human gut10.1099/ijsem.0.002735IJSEM 68: 1707-1712 201829583112
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111207Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397603.1