Strain identifier

BacDive ID: 3067

Type strain: Yes

Species: Slackia equolifaciens

Strain Designation: DZE

Strain history: M. Hattori strain DZE.

NCBI tax ID(s): 498718 (species)

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General

@ref: 17787

BacDive-ID: 3067

DSM-Number: 24851

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

description: Slackia equolifaciens DZE is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from faeces of a healthy human female.

NCBI tax id

  • NCBI tax id: 498718
  • Matching level: species

strain history

@refhistory
17787<- JCM <- M. Hattori, Univ. Toyama, Japan; DZE
67770M. Hattori strain DZE.

doi: 10.13145/bacdive3067.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Slackia
  • species: Slackia equolifaciens
  • full scientific name: Slackia equolifaciens Jin et al. 2010

@ref: 17787

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Slackia

species: Slackia equolifaciens

full scientific name: Slackia equolifaciens Jin et al. 2010

strain designation: DZE

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29599positive0.9 µm0.5 µmrod-shapedno
69480positive99.999

colony morphology

  • @ref: 61635
  • incubation period: 3-5 days

pigmentation

  • @ref: 29599
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17787
  • name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/339
  • composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17787positivegrowth37mesophilic
29599positivegrowth37mesophilic
61635positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17787anaerobe
29599anaerobe
61635anaerobe
69480anaerobe99.676

spore formation

@refspore formationconfidence
29599no
69481no100
69480no99.995

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
17787-----------------++-++-++++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
17787faeces of a healthy human femaleJapanJPNAsia
61635Human fecesJapanJPNAsia2006-07-31
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_21916.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_264;96_11086;97_13426;98_16527;99_21916&stattab=map
  • Last taxonomy: Slackia equolifaciens subclade
  • 16S sequence: AB910741
  • Sequence Identity:
  • Total samples: 8827
  • soil counts: 190
  • aquatic counts: 373
  • animal counts: 8198
  • plant counts: 66

Safety information

risk assessment

  • @ref: 17787
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Slackia equolifaciens gene for 16S ribosomal RNA, partial sequenceAB9107411474ena498718
17787Slackia equolifaciens strain DZE 16S ribosomal RNA gene, partial sequenceEU3776631474ena498718

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Slackia equolifaciens strain DSM 24851498718.3wgspatric498718
66792Slackia equolifaciens DSM 248512866335328draftimg498718
67770Slackia equolifaciens DSM 24851GCA_003725995contigncbi498718

GC content

@refGC-contentmethod
1778760.8high performance liquid chromatography (HPLC)
2959960.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes92.345yes
anaerobicyes99.247yes
halophileno89.178no
spore-formingno92.904yes
glucose-utilyes63.5no
aerobicno97.915no
thermophileno97.603yes
motileno94.418no
glucose-fermentno52.62no
flagellatedno98.824no

External links

@ref: 17787

culture collection no.: DSM 24851, CCUG 58231, JCM 16059

straininfo link

  • @ref: 72587
  • straininfo: 406586

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19734283Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol.Jin JS, Kitahara M, Sakamoto M, Hattori M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.016774-02009Actinobacteria/classification/genetics/*isolation & purification/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Equol, Fatty Acids/metabolism, Humans, Intestines/*microbiology, Isoflavones/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Metabolism25747993Biotransformation of (-)-epigallocatechin and (-)-gallocatechin by intestinal bacteria involved in isoflavone metabolism.Takagaki A, Nanjo FBiol Pharm Bull10.1248/bpb.b14-006462015Actinobacteria/*metabolism, Biotransformation, Catechin/*analogs & derivatives/metabolism, Intestines/microbiology, Isoflavones/metabolism
27242689Quantification of Slackia and Eggerthella spp. in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells.Cho GS, Ritzmann F, Eckstein M, Huch M, Briviba K, Behsnilian D, Neve H, Franz CMFront Microbiol10.3389/fmicb.2016.006582016
Genetics30643901Draft Genome Sequences of Type Strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis, Parvibacter caecicola,Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens.Danylec N, Stoll DA, Dotsch A, Huch MMicrobiol Resour Announc10.1128/MRA.01532-182019

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
17787Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24851)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24851
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
29599Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125990
61635Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58231)https://www.ccug.se/strain?id=58231
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/
68380Automatically annotated from API rID32A
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
72587Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406586.1StrainInfo: A central database for resolving microbial strain identifiers