Strain identifier

BacDive ID: 3068

Type strain: Yes

Species: Slackia piriformis

Strain history: Y. Watanabe A15 (=YIT 12062).

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

@ref: 16259

BacDive-ID: 3068

DSM-Number: 22477

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

description: Slackia piriformis DSM 22477 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces .

NCBI tax id

NCBI tax idMatching level
626934species
742818strain

strain history

@refhistory
16259<- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan <- F. Nagai and M. Morotomi
67770Y. Watanabe A15 (=YIT 12062).

doi: 10.13145/bacdive3068.20230509.8.1

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 piriformis
  • full scientific name: Slackia piriformis Nagai et al. 2010

@ref: 16259

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Slackia

species: Slackia piriformis

full scientific name: Slackia piriformis Nagai et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29633positive0.9-2.6 µm0.4-1.1 µmrod-shapedno
69480positive99.999

pigmentation

  • @ref: 29633
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16259COLUMBIA 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
16259PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l Arginine 3.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Vitamin K1 NaOH Tween 80 Distilled water

culture temp

@refgrowthtypetemperaturerange
16259positivegrowth37mesophilic
29633positivegrowth37mesophilic
29633positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29633positivegrowth7
29633positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16259obligate anaerobe
29633anaerobe
69480anaerobe99.465

spore formation

@refspore formationconfidence
29633no
69481no100
69480no99.941

observation

  • @ref: 29633
  • observation: aggregates in chains

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
29633acid phosphatase+3.1.3.2
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
16259-+----------+-----+-++-++++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16259human faeces (healthy Japanese adult)TokyoJapanJPNAsia
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5021.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_264;96_2455;97_2996;98_3754;99_5021&stattab=map
  • Last taxonomy: Slackia piriformis subclade
  • 16S sequence: AB601000
  • Sequence Identity:
  • Total samples: 20538
  • soil counts: 204
  • aquatic counts: 888
  • animal counts: 19381
  • plant counts: 65

Safety information

risk assessment

  • @ref: 16259
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Slackia piriformis gene for 16S ribosomal RNA, partial sequenceAB6010001472ena742818
16259Slackia piriformis gene for 16S rRNA, partial sequence, strain: YIT 12062AB4908061463ena742818

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Slackia piriformis YIT 12062742818.3wgspatric742818
66792Slackia piriformis YIT 120622529292933draftimg742818
67770Slackia piriformis YIT 12062GCA_000296445scaffoldncbi742818

GC content

@refGC-contentmethod
1625958.3
6777058.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.56yes
flagellatedno98.31yes
gram-positiveyes93.022no
anaerobicyes99.034yes
aerobicno97.248yes
halophileno89.025no
spore-formingno93.687no
thermophileno94.579yes
glucose-utilyes67.271no
glucose-fermentyes50.653no

External links

@ref: 16259

culture collection no.: DSM 22477, JCM 16070, YIT 12062, KCTC 15189

straininfo link

  • @ref: 72588
  • straininfo: 401197

literature

  • topic: Phylogeny
  • Pubmed-ID: 20023061
  • title: Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces.
  • authors: Nagai F, Watanabe Y, Morotomi M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.017533-0
  • year: 2009
  • mesh: Actinobacteria/*classification/enzymology/genetics/*isolation & purification, Adult, Bacterial Proteins/metabolism, Base Composition, Catalase/metabolism, DNA, Bacterial/genetics, Feces/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Urease/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16259Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22477)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22477
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
29633Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126023
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
72588Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401197.1StrainInfo: A central database for resolving microbial strain identifiers