Strain identifier

BacDive ID: 3064

Type strain: Yes

Species: Slackia exigua

Strain Designation: S-7

Strain history: CIP <- 2015, CCUG <- 2000, CIP <- 1997, E. Hoshino, Niigata School Dent., Niigata City, Japan: strain S-7 <- T. Sato

NCBI tax ID(s): 649764 (strain), 84109 (species)

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General

@ref: 6186

BacDive-ID: 3064

DSM-Number: 15923

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

description: Slackia exigua S-7 is an anaerobe, rod-shaped bacterium that was isolated from human necrotic pulp.

NCBI tax id

NCBI tax idMatching level
84109species
649764strain

strain history

@refhistory
6186<- JCM/RIKEN; JCM 11022 <- E. Hoshino, Niigata Univ.; S-7
67770CIP 105133 <-- E. Hoshino S-7 <-- T. Sato.
67771<- DSM <- JCM 11022 <- CIP 105133 <- E Hoshino, Niigata Univ., S-7 <- T Sato
119153CIP <- 2015, CCUG <- 2000, CIP <- 1997, E. Hoshino, Niigata School Dent., Niigata City, Japan: strain S-7 <- T. Sato

doi: 10.13145/bacdive3064.20240916.9.1

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 exigua
  • full scientific name: Slackia exigua (Poco et al. 1996) Wade et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Eubacterium exiguum

@ref: 6186

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Slackia

species: Slackia exigua

full scientific name: Slackia exigua (Poco et al. 1996) Wade et al. 1999 emend. Nouioui et al. 2018

strain designation: S-7

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771rod-shapedno
67771positive
119153rod-shapednopositive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6186PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) 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 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 Tween 80 Vitamin K1 NaOH Distilled water
119153CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20
119153CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6186positivegrowth37
56394positivegrowth37
67770positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6186anaerobe
56394anaerobe
67771anaerobe

spore formation

@refspore formationconfidence
67771no
69481no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
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
68380glutamyl-glutamate 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
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
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
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6186-+----------+-----+-++-+/-+-+-+/-
6186-+/-----------------+-++-------
6186-+---------------+/-+-++-+++/-+/--+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
6186human necrotic pulpJapanJPNAsia
56394Human necrotic pulp of tooth1991
67770Human oral lesion
67771From human necrotic pulpJapanJPNAsia
119153Human, Necrotic pulp of tooth1991

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Human
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_1887.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_264;96_1061;97_1239;98_1487;99_1887&stattab=map
  • Last taxonomy: Slackia exigua subclade
  • 16S sequence: NR_024952
  • Sequence Identity:
  • Total samples: 12040
  • soil counts: 198
  • aquatic counts: 124
  • animal counts: 11626
  • plant counts: 92

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61862Risk group (German classification)
1191531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Slackia exigua 16S ribosomal RNA gene, complete sequenceAF1012401465nuccore649764
67770Slackia exigua gene for 16S ribosomal RNA, partial sequence, strain: JCM 11022LC0071131474nuccore84109
67771Slackia exigua ATCC 700122 16S ribosomal RNA, partial sequenceNR_0249521465nuccore649764

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Slackia exigua ATCC 700122649764.3wgspatric649764
66792Slackia exigua strain NCTC1299484109.4wgspatric84109
66792Slackia exigua NCTC 129942833514366draftimg84109
66792Slackia exigua ATCC 700122645951837draftimg649764
67770Slackia exigua ATCC 700122GCA_000162875scaffoldncbi649764
67770Slackia exigua NCTC12994GCA_900450505contigncbi84109

GC content

  • @ref: 67770
  • GC-content: 60
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes81.294no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes85.435no
69480spore-formingspore-formingAbility to form endo- or exosporesno82.58yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no88.478no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.404yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.674no

External links

@ref: 6186

culture collection no.: DSM 15923, ATCC 700122, JCM 11022, KCTC 5966, CCUG 44588, CIP 105133, NCTC 12994

straininfo link

  • @ref: 72584
  • straininfo: 43783

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319481The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.Wade WG, Downes J, Dymock D, Hiom SJ, Weightman AJ, Dewhirst FE, Paster BJ, Tzellas N, Coleman BInt J Syst Bacteriol10.1099/00207713-49-2-5951999Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Eubacterium/*classification/cytology/genetics/physiology, Genes, rRNA, Gram-Positive Bacteria/*classification/cytology/genetics/physiology, Molecular Sequence Data, Peptostreptococcus/*classification/cytology/genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNAGenetics
Metabolism17064396Degradation of arginine by Slackia exigua ATCC 700122 and Cryptobacterium curtum ATCC 700683.Uematsu H, Sato N, Djais A, Hoshino EOral Microbiol Immunol10.1111/j.1399-302X.2006.00307.x2006Ammonia/metabolism, Arginine/*metabolism, Chromatography, High Pressure Liquid, Citrulline/metabolism, Dental Pulp Necrosis/microbiology, Eubacterium/*enzymology/*growth & development, Humans, Hydrolases/*metabolism, Ornithine/metabolism, Periodontal Pocket/microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6186Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15923)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15923
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
56394Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44588)https://www.ccug.se/strain?id=44588
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
72584Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43783.1StrainInfo: A central database for resolving microbial strain identifiers
119153Curators of the CIPCollection of Institut Pasteur (CIP 105133)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105133