Strain identifier

BacDive ID: 3063

Type strain: Yes

Species: Slackia heliotrinireducens

Strain Designation: RHS 1

Strain history: CIP <- 2003, DSMZ <- ATCC <- G.W. Lanigan, RHS 1

NCBI tax ID(s): 471855 (strain), 84110 (species)

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General

@ref: 8845

BacDive-ID: 3063

DSM-Number: 20476

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, human pathogen

description: Slackia heliotrinireducens RHS 1 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from sheep rumen.

NCBI tax id

NCBI tax idMatching level
471855strain
84110species

strain history

@refhistory
8845<- ATCC <- G.W. Lanigan, RHS 1
67770CCUG 47954 <-- CIP 108017 <-- DSM 20476 <-- ATCC 29202 <-- G. W. Lanigan RHS 1.
119861CIP <- 2003, DSMZ <- ATCC <- G.W. Lanigan, RHS 1

doi: 10.13145/bacdive3063.20230509.8.1

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 heliotrinireducens
  • full scientific name: Slackia heliotrinireducens corrig. (Lanigan 1983) Wade et al. 1999

  • synonyms

    @refsynonym
    20215Slackia heliotrinreducens
    20215Peptostreptococcus heliotrinreducens
    20215Peptococcus helotrinreducens
    20215Peptococcus heliotrinreducans
    20215Peptococcus heliotrinreducens

@ref: 8845

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Slackia

species: Slackia heliotrinireducens

full scientific name: Slackia heliotrinireducens (Lanigan 1983) Wade et al. 1999 emend. Nouioui et al. 2018

strain designation: RHS 1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119861positivecoccus-shapedno

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20476_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8845PYG 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
39974MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
119861CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8845positivegrowth37mesophilic
39974positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8845anaerobe
69480anaerobe99.529

spore formation

@refspore formationconfidence
69481no100
69480no99.945

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-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
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8845-+/-----------------+-++-++++-+

Isolation, sampling and environmental information

isolation

@refsample type
8845sheep rumen
67770Rumen contents of sheep
119861Animal, Sheep rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_7247.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_264;96_3386;97_4157;98_5318;99_7247&stattab=map
  • Last taxonomy: Slackia heliotrinireducens subclade
  • 16S sequence: AF101241
  • Sequence Identity:
  • Total samples: 3277
  • soil counts: 48
  • aquatic counts: 41
  • animal counts: 3157
  • plant counts: 31

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8845yes, in single cases1Risk group (German classification)
1198611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Slackia heliotrinreducens 16S ribosomal RNA gene, complete sequenceAF1012411465ena471855
67770Slackia heliotrinireducens gene for 16S ribosomal RNA, partial sequence, strain: JCM 14554AB5598231424ena84110

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Slackia heliotrinireducens NCTC11029GCA_900637575completencbi84110
66792Slackia heliotrinireducens DSM 20476GCA_000023885completencbi471855
66792Slackia heliotrinireducens DSM 20476471855.5completepatric471855
66792Slackia heliotrinireducens strain NCTC1102984110.3completepatric84110
66792Slackia heliotrinireducens RHS 1, DSM 20476644736405completeimg471855

GC content

@refGC-contentmethod
6777036.1
6777061high performance liquid chromatography (HPLC)
6777034-36

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.802no
flagellatedno97.699no
gram-positiveyes86.203no
anaerobicyes98.559yes
aerobicno95.039yes
halophileno88.138no
spore-formingno91.661no
thermophileno97.107yes
glucose-utilyes65.966no
glucose-fermentno59.058no

External links

@ref: 8845

culture collection no.: DSM 20476, ATCC 29202, NCTC 11029, JCM 14554, CCUG 47954, CIP 108017

straininfo link

  • @ref: 72583
  • straininfo: 39401

literature

  • topic: Genetics
  • Pubmed-ID: 21304663
  • title: Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1).
  • authors: Pukall R, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Chertkov O, Bruce D, Goodwin L, Kuske C, Brettin T, Detter JC, Han C, Pitluck S, Pati A, Mavrommatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Schneider S, Rohde M, Chain P, D'haeseleer P, Goker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P
  • journal: Stand Genomic Sci
  • DOI: 10.4056/sigs.37633
  • year: 2009

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8845Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20476)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20476
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
39974Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5593
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
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
72583Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39401.1StrainInfo: A central database for resolving microbial strain identifiers
119861Curators of the CIPCollection of Institut Pasteur (CIP 108017)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108017