Strain identifier

BacDive ID: 14790

Type strain: Yes

Species: Streptococcus gordonii

Strain Designation: SK3, SK 3

Strain history: CIP <- 1997, DSMZ <- ATCC <- J.M. Sherman, Streptococcus sanguis: strain SK 3

NCBI tax ID(s): 1302 (species)

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General

@ref: 2811

BacDive-ID: 14790

DSM-Number: 6777

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic

description: Streptococcus gordonii SK3 is a microaerophile, mesophilic bacterium that was isolated from subacute bacterial endocarditis, human.

NCBI tax id

  • NCBI tax id: 1302
  • Matching level: species

strain history

@refhistory
2811<- ATCC <- J.M. Sherman
67770CCUG 33482 <-- NCTC 7865 <-- ATCC 10558 <-- J. M. Sherman.
119711CIP <- 1997, DSMZ <- ATCC <- J.M. Sherman, Streptococcus sanguis: strain SK 3

doi: 10.13145/bacdive14790.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Streptococcaceae
  • genus: Streptococcus
  • species: Streptococcus gordonii
  • full scientific name: Streptococcus gordonii Kilian et al. 1989

@ref: 2811

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus gordonii

full scientific name: Streptococcus gordonii Kilian et al. 1989

strain designation: SK3, SK 3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.175
69480100positive
119711nopositivecoccus-shaped

colony morphology

@reftype of hemolysishemolysis abilityincubation period
2811alpha11-2 days
119711

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2811COLUMBIA 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
2811TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
42091MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119711CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119711CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
2811positivegrowth37mesophilic
42091positivegrowth37mesophilic
67770positivegrowth37mesophilic
119711positivegrowth25-41
119711nogrowth10psychrophilic
119711nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2811microaerophile
119711facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.95

halophily

  • @ref: 119711
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 2811
  • murein short key: A11.05
  • type: A3alpha L-Lys-L-Ala2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1197114853esculin+hydrolysis
119711606565hippurate-hydrolysis
11971117632nitrate-reduction
11971116301nitrite-reduction
6838129016arginine-hydrolysis
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose+builds acid from
6838127082trehalose+builds acid from
6838116634raffinose-builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose+builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
6838116199urea-hydrolysis

metabolite production

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin-
11971115688acetoin-

enzymes

@refvalueactivityec
2811catalase-1.11.1.6
2811cytochrome-c oxidase-1.9.3.1
68381urease-3.5.1.5
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
119711oxidase-
119711beta-galactosidase+3.2.1.23
119711alcohol dehydrogenase+1.1.1.1
119711catalase-1.11.1.6
119711gamma-glutamyltransferase-2.3.2.2
119711lysine decarboxylase-4.1.1.18
119711ornithine decarboxylase-4.1.1.17
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119711-+++++++--++-+-++---

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
2811-++-+/-+---++-+----++--+---+--+++-
2811-++--+---++-+----++--+---+--+++-
2811-++--+---++-+----++------+--+++/--
2811-+----+--++-+----+-------+---+--
2811-+---+---++-+----+----+--+---+/---
2811-++--++/---++-+----+-------+---++-

Isolation, sampling and environmental information

isolation

@refsample type
2811subacute bacterial endocarditis, human
67770Human subacute endocarditis
119711Subacute bacterial endocarditis

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Microbial#Bacteria
#Host Body-Site#Organ#Heart

taxonmaps

  • @ref: 69479
  • File name: preview.99_978.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4;96_4;97_490;98_763;99_978&stattab=map
  • Last taxonomy: Streptococcus
  • 16S sequence: LC258133
  • Sequence Identity:
  • Total samples: 151976
  • soil counts: 2729
  • aquatic counts: 4744
  • animal counts: 143458
  • plant counts: 1045

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
28112Risk group (German classification)
1197112Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptococcus gordonii DNA, 16S-23S rRNA intergenic spacer regionAB051019246ena1302
20218Streptococcus gordonii 16S ribosomal RNA gene, complete sequenceAF0039311512ena1302
20218Streptococcus gordonii strain ATCC 10558 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY353081246ena1302
20218Streptococcus gordonii strain ATCC 10558 16S small subunit ribosomal RNA gene, partial sequenceAY4856061479ena1302
20218Streptococcus gordonii strain ATCC 10558 16S ribosomal RNA gene, partial sequenceEU1567581329ena1302
20218Streptococcus gordonii strain ATCC 10558 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceJN181383511ena1302
20218Streptococcus gordonii strain KCTC 3286 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM241933458ena1302
20218Streptococcus gordonii 16S rRNA geneD384831413ena1302
20218Streptococcus gordonii strain NCTC 7865 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU860346323ena1302
67770Streptococcus gordonii gene for 16S ribosomal RNA, partial sequence, strain: JCM 12995LC2581331498ena1302

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus gordonii NCTC7865GCA_900475015completencbi1302
66792Streptococcus gordonii CCUG 33482GCA_001553855scaffoldncbi1302
66792Streptococcus gordonii ATCC 10558GCA_001469295scaffoldncbi1302
66792Streptococcus gordonii strain ATCC 105581302.19wgspatric1302
66792Streptococcus gordonii strain CCUG 334821302.20wgspatric1302
66792Streptococcus gordonii strain FDAARGOS 14541302.425completepatric1302
66792Streptococcus gordonii strain NCTC78651302.168completepatric1302
66792Streptococcus gordonii CCUG 334822728369123draftimg1302
66792Streptococcus gordonii ATCC 105582823469221draftimg1302

GC content

@refGC-contentmethod
281141.0thermal denaturation, midpoint method (Tm)
6777041

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.626no
gram-positiveyes94.754no
anaerobicno94.989yes
aerobicno96.727yes
halophileyes76.642no
spore-formingno91.05no
thermophileno99.377yes
glucose-utilyes83.879no
motileno95.807no
glucose-fermentyes78.997no

External links

@ref: 2811

culture collection no.: DSM 6777, ATCC 10558, CIP 105258, NCTC 7865, JCM 12995, CCUG 25608, CCUG 33482, CCUG 35801, LMG 14518

straininfo link

  • @ref: 83907
  • straininfo: 10362

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics8878047Identification of the streptococcal competence-pheromone receptor.Havarstein LS, Gaustad P, Nes IF, Morrison DAMol Microbiol10.1046/j.1365-2958.1996.521416.x1996Alleles, Amino Acid Sequence, Bacterial Proteins/*genetics, DNA-Binding Proteins/*genetics, Genes, Bacterial/*genetics, Histidine Kinase, Molecular Sequence Data, *Multienzyme Complexes, Multigene Family/genetics, Protein Kinases/*genetics, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Signal Transduction/genetics, Streptococcus/*genetics, Transformation, Bacterial/*geneticsTranscriptome
Pathogenicity9435058Anaerobic killing of oral streptococci by reduced, transition metal cations.Dunning JC, Ma Y, Marquis REAppl Environ Microbiol10.1128/AEM.64.1.27-33.19981998Actinomyces/drug effects, Adenosine Triphosphatases/drug effects, Anaerobiosis, Cations/*toxicity, Cell Membrane/metabolism, Copper/*toxicity, Enterococcus/drug effects, Escherichia coli/drug effects, *FMN Reductase, Ferricyanides/pharmacology, Ferrocyanides/pharmacology, Ferrous Compounds/*toxicity, Glycolysis/drug effects, Hydrogen Peroxide/metabolism/toxicity, Lactobacillus casei/drug effects, Mouth/microbiology, NADH, NADPH Oxidoreductases/metabolism, Oxygen/metabolism, Streptococcus/*drug effects/enzymology/metabolism, Thiocyanates/pharmacology, Uric Acid/pharmacologyMetabolism
Metabolism10030002Turning on and turning off the arginine deiminase system in oral streptococci.Curran TM, Ma Y, Rutherford GC, Marquis RECan J Microbiol10.1139/cjm-44-11-10781998Ammonia/metabolism, Arginine/metabolism, Biofilms, Enzyme Induction, Enzyme Repression, Esters, *Gene Expression Regulation, Bacterial, Humans, Hydrogen-Ion Concentration, Hydrolases/*biosynthesis/genetics/metabolism, Mouth/*microbiology, Streptococcus/*enzymology/genetics, Time FactorsPathogenicity
Pathogenicity21214874Invasion of human aortic endothelial cells by oral viridans group streptococci and induction of inflammatory cytokine production.Nagata E, de Toledo A, Oho TMol Oral Microbiol10.1111/j.2041-1014.2010.00597.x2010Aorta/cytology/*microbiology, Atherosclerosis/microbiology, Catalase/pharmacology, Cells, Cultured, Chemokine CCL2/biosynthesis, Coculture Techniques, Cytochalasin D/pharmacology, Cytokines/*biosynthesis, Endothelial Cells/immunology/*microbiology, Endothelium, Vascular/cytology/*microbiology, Humans, Inflammation Mediators/*metabolism, Interleukin-6/biosynthesis, Interleukin-8/biosynthesis, Microscopy, Confocal, Mouth/*microbiology, Streptococcus/physiology, Streptococcus anginosus/physiology, Streptococcus gordonii/physiology, Streptococcus intermedius/physiology, Streptococcus mitis/physiology, Streptococcus mutans/physiology, Streptococcus oralis/physiology, Viridans Streptococci/drug effects/immunology/*physiology, VirulenceBiotechnology
Pathogenicity22526889In vitro evaluation of surface roughness, adhesion of periodontal ligament fibroblasts, and Streptococcus gordonii following root instrumentation with Gracey curettes and subsequent polishing with diamond-coated curettes.Eick S, Bender P, Flury S, Lussi A, Sculean AClin Oral Investig10.1007/s00784-012-0719-z2012Bacterial Adhesion/*physiology, Cell Adhesion/physiology, Cell Count, Cell Culture Techniques, Coated Materials, Biocompatible/*chemistry, Curettage/instrumentation, Dental Materials/*chemistry, Dental Prophylaxis/instrumentation, Dental Scaling/instrumentation, Dentin/microbiology/pathology, Diamond/*chemistry, Equipment Design, Fibroblasts/*physiology, Humans, Materials Testing, Microscopy, Electron, Scanning, Periodontal Ligament/*cytology, Root Planing/*instrumentation, Smear Layer, Streptococcus gordonii/*physiology, Surface Properties, Tooth Root/microbiology/*pathology
Pathogenicity24603299Systematic screening of plant extracts from the Brazilian Pantanal with antimicrobial activity against bacteria with cariogenic relevance.Brighenti FL, Salvador MJ, Delbem AC, Delbem AC, Oliveira MA, Soares CP, Freitas LS, Koga-Ito CYCaries Res10.1159/0003572252014Actinomyces/drug effects, Annonaceae/chemistry, Anti-Bacterial Agents/*pharmacology, Arecaceae/chemistry, Brazil, Combretaceae/chemistry, Croton/chemistry, Dental Caries/*microbiology, Gram-Positive Bacteria/*drug effects, Humans, Jatropha/chemistry, Lactobacillus acidophilus/drug effects, Malpighiaceae/chemistry, Melastomataceae/chemistry, Microbial Sensitivity Tests, Phenols/analysis, Phytotherapy/*methods, Plant Extracts/chemistry/*pharmacology, Senna Extract/chemistry, Solvents/chemistry, Streptococcus gordonii/drug effects, Streptococcus mitis/drug effects, Streptococcus mutans/drug effects, Streptococcus sanguis/drug effects, Streptococcus sobrinus/drug effects, Temperature, Terpenes/analysis
Pathogenicity24621259Intensity and duration of in-vitro antibacterial activity of different adhesives used in orthodontics.Passariello C, Sannino G, Petti S, Gigola PEur J Oral Sci10.1111/eos.121202014Anti-Bacterial Agents/*pharmacology, Bacterial Load/drug effects, Benzalkonium Compounds/pharmacology, Biofilms/drug effects, Chlorhexidine/pharmacology, Dental Caries/microbiology/prevention & control, Dental Cements/*pharmacology, Dental Plaque/microbiology, Dentin-Bonding Agents/pharmacology, Fluorides/pharmacology, Glass Ionomer Cements/pharmacology, Humans, Lactobacillus acidophilus/drug effects, Materials Testing, *Orthodontic Appliances, Pyridinium Compounds/pharmacology, Resin Cements/pharmacology, Streptococcus gordonii/drug effects, Streptococcus mutans/drug effects, Streptococcus sanguis/drug effects, Time Factors
Genetics26893427Draft Genome Sequence of Type Strain Streptococcus gordonii ATCC 10558.Rasmussen LH, Dargis R, Christensen JJ, Skovgaard O, Nielsen XCGenome Announc10.1128/genomeA.01745-152016
Genetics27013051Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.Salva-Serra F, Jakobsson HE, Thorell K, Gonzales-Siles L, Hallback ET, Jaen-Luchoro D, Boulund F, Sikora P, Karlsson R, Svensson L, Bennasar A, Engstrand L, Kristiansson E, Moore ERGenome Announc10.1128/genomeA.00175-162016
Phylogeny27722787Bacterial invasion into radicular dentine-an in vitro study.Stauffacher S, Lussi A, Nietzsche S, Neuhaus KW, Eick SClin Oral Investig10.1007/s00784-016-1960-72016Actinomyces/isolation & purification, Bacterial Load, Coculture Techniques, Dental Pulp Cavity/*microbiology, Dentin/*microbiology, Fusobacterium nucleatum/isolation & purification, Humans, In Vitro Techniques, Microscopy, Electron, Scanning, Porphyromonas gingivalis/isolation & purification, Prevotella intermedia/isolation & purification, Species Specificity, Streptococcus gordonii/isolation & purification, Streptococcus sanguis/isolation & purificationEnzymology
Pathogenicity29355416Antimicrobial Activity of a Colloidal AgNP Suspension Demonstrated In Vitro against Monoculture Biofilms: Toward a Novel Tooth Disinfectant for Treating Dental Caries.Schwass DR, Lyons KM, Love R, Tompkins GR, Meledandri CJAdv Dent Res10.1177/00220345177364952018Biofilms/*drug effects, Chlorhexidine/pharmacology, Dental Caries/microbiology, Disinfectants/chemistry/*pharmacology, Electric Conductivity, Enterococcus faecalis/drug effects, Fluorides, Topical/pharmacology, Metal Nanoparticles/chemistry, Microbial Sensitivity Tests, Microscopy, Electron, Quaternary Ammonium Compounds/pharmacology, Silver Compounds/pharmacology, Silver Nitrate/*pharmacology, Spectrophotometry, Atomic, Streptococcus gordonii/drug effects, Streptococcus mitis/drug effects, Streptococcus mutans/drug effects
Metabolism29669961Aciduricity and acid tolerance mechanisms of Streptococcus anginosus.Sasaki M, Kodama Y, Shimoyama Y, Ishikawa T, Kimura SJ Gen Appl Microbiol10.2323/jgam.2017.11.0052018Acids/*metabolism/pharmacology, Arginine/metabolism, Culture Media, Dicyclohexylcarbodiimide/pharmacology, Gene Deletion, Hydrogen-Ion Concentration, Hydrolases/genetics/*metabolism, Microbial Viability/drug effects, Proton-Translocating ATPases/antagonists & inhibitors/genetics/*metabolism, Streptococcus anginosus/*drug effects/enzymology/genetics/*physiologyCultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2811Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6777)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6777
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
42091Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17258
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/
68381Automatically annotated from API rID32STR
68382Automatically annotated from API zym
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
83907Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10362.1StrainInfo: A central database for resolving microbial strain identifiers
119711Curators of the CIPCollection of Institut Pasteur (CIP 105258)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105258