Strain identifier

BacDive ID: 17159

Type strain: Yes

Species: Selenomonas sputigena

Strain history: <- ATCC <- W.E.C. Moore, VPI D19B-28

NCBI tax ID(s): 546271 (strain), 69823 (species)

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

@ref: 9065

BacDive-ID: 17159

DSM-Number: 20758

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

description: Selenomonas sputigena DSM 20758 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from subgingival sulcus.

NCBI tax id

NCBI tax idMatching level
69823species
546271strain

strain history

  • @ref: 9065
  • history: <- ATCC <- W.E.C. Moore, VPI D19B-28

doi: 10.13145/bacdive17159.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Selenomonadales
  • family: Selenomonadaceae
  • genus: Selenomonas
  • species: Selenomonas sputigena
  • full scientific name: Selenomonas sputigena (Flügge 1886) Boskamp 1922 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Spirillum sputigenum

@ref: 9065

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Selenomonadaceae

genus: Selenomonas

species: Selenomonas sputigena

full scientific name: Selenomonas sputigena (Flügge 1886) Boskamp 1922 emend. Judicial Commission 1992

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.993

colony morphology

@refincubation period
90652-3 days
565532-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20758_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9065CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
9065PYG 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

culture temp

@refgrowthtypetemperaturerange
9065positivegrowth37mesophilic
56553positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
9065anaerobe
56553anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481no100
69480no99.706

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-
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
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
9065--++-+/-----------+/-------------

Isolation, sampling and environmental information

isolation

@refsample type
9065subgingival sulcus
56553Subgingival sulcus

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Gingiva

taxonmaps

  • @ref: 69479
  • File name: preview.99_160.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_55;96_119;97_126;98_141;99_160&stattab=map
  • Last taxonomy: Selenomonas sputigena subclade
  • 16S sequence: CP002637
  • Sequence Identity:
  • Total samples: 987
  • soil counts: 21
  • aquatic counts: 28
  • animal counts: 923
  • plant counts: 15

Safety information

risk assessment

  • @ref: 9065
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Selenomonas sputigena 16S ribosomal RNA gene, partial sequenceAF2877931497ena546271
20218Selenomonas sputigena strain ATCC35185 16S ribosomal RNA gene, partial sequenceAF3730231499ena546271
9065Selenomonas sputigena ATCC 35185, complete genomeCP0026372568361ena546271

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Selenomonas sputigena ATCC 35185GCA_000208405completencbi546271
66792Selenomonas sputigena ATCC 35185GCA_000160495scaffoldncbi546271
66792Selenomonas sputigena ATCC 35185546271.3wgspatric546271
66792Selenomonas sputigena ATCC 35185546271.5completepatric546271
66792Selenomonas sputigena DSM 207582504557006completeimg546271
66792Selenomonas sputigena ATCC 35185645951802draftimg546271

GC content

  • @ref: 9065
  • GC-content: 57.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes75.626no
flagellatedno78.212no
gram-positiveno98.192no
anaerobicyes99.999yes
aerobicno99.338yes
halophileno92.8no
spore-formingno83.179no
glucose-utilyes66.373no
glucose-fermentyes55.799no
thermophileno78.286no

External links

@ref: 9065

culture collection no.: DSM 20758, ATCC 35185, CCUG 44933, VPI D 19B-28, VPI D19B-28

straininfo link

  • @ref: 86158
  • straininfo: 46379

literature

  • topic: Phylogeny
  • Pubmed-ID: 30508628
  • title: Microbial biomarkers of common tongue coatings in patients with gastric cancer.
  • authors: Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J, Zhan Z
  • journal: Microb Pathog
  • DOI: 10.1016/j.micpath.2018.11.051
  • year: 2018
  • mesh: Aged, Bacteria/*classification/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Fungal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Female, Fungi/*classification/genetics, Humans, Male, *Microbiota, Middle Aged, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 18S/genetics, ROC Curve, Sequence Analysis, DNA, Stomach Neoplasms/*microbiology/*pathology, Tongue/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9065Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20758)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20758
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
56553Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44933)https://www.ccug.se/strain?id=44933
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
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
86158Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46379.1StrainInfo: A central database for resolving microbial strain identifiers