Strain identifier

BacDive ID: 136390

Type strain: No

Species: Streptococcus pneumoniae

Strain Designation: D 39

Strain history: CIP <- 1997, NCTC <- 1948, S.D. Elliot: strain D 39 <- Rockfeller Inst. Med. Res., USA

NCBI tax ID(s): 1313 (species)

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General

@ref: 35786

BacDive-ID: 136390

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic

description: Streptococcus pneumoniae D 39 is a facultative anaerobe, mesophilic bacterium of the family Streptococcaceae.

NCBI tax id

  • NCBI tax id: 1313
  • Matching level: species

strain history

  • @ref: 35786
  • history: CIP <- 1997, NCTC <- 1948, S.D. Elliot: strain D 39 <- Rockfeller Inst. Med. Res., USA

doi: 10.13145/bacdive136390.20230509.8.1

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 pneumoniae
  • full scientific name: Streptococcus pneumoniae (Klein 1884) Chester 1901 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Staphylococcus pneumoniae
    20215Micrococcus pneumoniae

@ref: 35786

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus pneumoniae

strain designation: D 39

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.946
69480100positive
35786nopositivecoccus-shaped

colony morphology

  • @ref: 35786
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35786MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
35786CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
35786positivegrowth37mesophilic
35786positivegrowth25-41
35786nogrowth10psychrophilic
35786nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 35786
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

  • @ref: 35786
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
35786esculin+hydrolysis4853
35786hippurate-hydrolysis606565
35786nitrate-reduction17632
35786nitrite-reduction16301

antibiotic resistance

@refmetaboliteis antibioticis sensitiveis resistantChEBI
357860129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno
35786optochinyesyesno86455

metabolite tests

  • @ref: 35786
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
35786oxidase-
35786beta-galactosidase+3.2.1.23
35786alcohol dehydrogenase-1.1.1.1
35786catalase-1.11.1.6
35786gamma-glutamyltransferase-2.3.2.2
35786lysine decarboxylase-4.1.1.18
35786ornithine 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
35786-----++--+-----+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
35786+/---------+/-+++/----------+/-----++/--+---+/-----+/---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
35786------------------+--------------------------------------------------------------------------------

Safety information

risk assessment

  • @ref: 35786
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus pneumoniae NCTC7466GCA_900475305completencbi1313
66792Streptococcus pneumoniae strain NCTC74661313.15900completepatric1313
66792Streptococcus pneumoniae NCTC 74662860972970completeimg1313

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.217no
gram-positiveyes93.959no
anaerobicno96.697no
aerobicno95.771no
halophileyes76.487no
spore-formingno92.675no
thermophileno98.457yes
glucose-utilyes86.978no
motileno93.993no
glucose-fermentyes84.602no

External links

@ref: 35786

culture collection no.: CIP 105179, NCTC 7466

straininfo link

  • @ref: 93556
  • straininfo: 70345

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity28945368A Streptococcus pneumoniae Type 2 Oligosaccharide Glycoconjugate Elicits Opsonic Antibodies and Is Protective in an Animal Model of Invasive Pneumococcal Disease.Emmadi M, Khan N, Lykke L, Reppe K, G Parameswarappa S, Lisboa MP, Wienhold SM, Witzenrath M, Pereira CL, Seeberger PHJ Am Chem Soc10.1021/jacs.7b078362017Administration, Intranasal, Animals, Antibodies, Bacterial/*immunology, B-Lymphocytes/immunology, Bacterial Load, Blood/microbiology, Disease Models, Animal, Female, Glycoconjugates/chemical synthesis/*immunology, Humans, Lung/microbiology, Mice, Mice, Inbred C57BL, Oligosaccharides/chemical synthesis/*immunology, Phagocytosis, Pneumococcal Infections/*immunology/*microbiology/prevention & control, Pneumococcal Vaccines/chemistry/immunology, Polysaccharides, Bacterial/chemistry/immunology, Rabbits, Streptococcus pneumoniae/*chemistry/classification/*immunology/pathogenicity, T-Lymphocytes/immunology, Vaccination, Vaccines, Conjugate/chemistry/immunologyPhylogeny
32002605The roles of genes associated with regulation, transportation, and macrocyclization in desotamide biosynthesis in Streptomyces scopuliridis SCSIO ZJ46.Ding W, Dong Y, Ju J, Li QAppl Microbiol Biotechnol10.1007/s00253-020-10414-42020Bacterial Proteins/genetics, Biosynthetic Pathways, *Gene Expression Regulation, Bacterial, *Genes, Regulator, Multigene Family, Peptides, Cyclic/*biosynthesis, Streptomyces/*genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
35786Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105179Collection of Institut Pasteur (CIP 105179)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
93556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID70345.1