Strain identifier

BacDive ID: 24609

Type strain: Yes

Species: Streptococcus rubneri

Strain Designation: beta 112/2b

Strain history: <- C. M. A. P. Franz, Max Rubner-Inst. (MRI), Federal Res. Inst. Nutrition and Food, Karlsruhe, Germany; LMG 27207 <- A. Bub and C. M. A. P. Franz

NCBI tax ID(s): 1234680 (species)

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

@ref: 21039

BacDive-ID: 24609

DSM-Number: 26920

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Streptococcus rubneri beta 112/2b is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from throat of a healthy human volunteer.

NCBI tax id

  • NCBI tax id: 1234680
  • Matching level: species

strain history

  • @ref: 21039
  • history: <- C. M. A. P. Franz, Max Rubner-Inst. (MRI), Federal Res. Inst. Nutrition and Food, Karlsruhe, Germany; LMG 27207 <- A. Bub and C. M. A. P. Franz

doi: 10.13145/bacdive24609.20230509.8.1

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 rubneri
  • full scientific name: Streptococcus rubneri Huch et al. 2013

@ref: 21039

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus rubneri

full scientific name: Streptococcus rubneri Huch et al. 2013

strain designation: beta 112/2b

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30961positivecoccus-shaped
69480no94.172
69480positive100

colony morphology

  • @ref: 21039
  • type of hemolysis: alpha
  • hemolysis ability: 1
  • incubation period: 1-2 days

pigmentation

  • @ref: 30961
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21039
  • name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/693
  • composition: Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
21039positivegrowth37mesophilic
30961positiveoptimum25-37mesophilic
63344positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
21039microaerophile
30961facultative anaerobe
63344microaerophile

spore formation

@refspore formationconfidence
30961no
69481no99
69480no99.96

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3096117057cellobiose+carbon source
3096128757fructose+carbon source
3096128260galactose+carbon source
3096117234glucose+carbon source
3096117716lactose+carbon source
3096117306maltose+carbon source
3096137684mannose+carbon source
3096128053melibiose+carbon source
30961506227N-acetylglucosamine+carbon source
3096116634raffinose+carbon source
3096117814salicin+carbon source
3096130911sorbitol+carbon source
3096117992sucrose+carbon source
6838116988D-ribose-builds acid from
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
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan+builds acid from
6838117306maltose+builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose+builds acid from
6838116199urea-hydrolysis

metabolite production

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

metabolite tests

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
21039catalase-1.11.1.6
21039cytochrome-c oxidase-1.9.3.1
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
21039++/-+-+----+-++--+/--+---+--+++/---+--
21039--+-+----+-++----+---+--+++/---+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21039throat of a healthy human volunteerKarlsruheGermanyDEUEurope
63344Throat,healthy human volunteerKarlsruheGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Throat

taxonmaps

  • @ref: 69479
  • File name: preview.99_646.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4;96_4;97_4;98_523;99_646&stattab=map
  • Last taxonomy: Streptococcus
  • 16S sequence: JX861483
  • Sequence Identity:
  • Total samples: 56184
  • soil counts: 635
  • aquatic counts: 678
  • animal counts: 54450
  • plant counts: 421

Safety information

risk assessment

  • @ref: 21039
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21039
  • description: Streptococcus rubneri strain LMG 27207 16S ribosomal RNA gene, partial sequence
  • accession: JX861483
  • length: 1457
  • database: ena
  • NCBI tax ID: 1234680

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus rubneri DSM 26920GCA_004785935contigncbi1234680
66792Streptococcus rubneri CCUG 66516GCA_016642415scaffoldncbi1234680
66792Streptococcus rubneri strain CCUG 665161234680.7wgspatric1234680
66792Streptococcus rubneri strain DSM 269201234680.3wgspatric1234680

GC content

  • @ref: 21039
  • GC-content: 40.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedno95.956no
gram-positiveyes95.421no
anaerobicno93.55yes
aerobicno97.181no
halophileyes67.327no
spore-formingno92.337yes
thermophileno99.346no
glucose-utilyes86.713yes
motileno94.236no
glucose-fermentyes84.473no

External links

@ref: 21039

culture collection no.: DSM 26920, LMG 27207, CCUG 66516

straininfo link

  • @ref: 88454
  • straininfo: 310322

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23749274Streptococcus rubneri sp. nov., isolated from the human throat.Huch M, De Bruyne K, Cleenwerck I, Bub A, Cho GS, Watzl B, Snauwaert I, Franz CMAP, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.048538-02013Amplified Fragment Length Polymorphism Analysis, Base Composition, DNA Fingerprinting, DNA, Bacterial/genetics, Electrophoresis, Gel, Pulsed-Field, Genes, Bacterial, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Pharynx/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptococcus/*classification/genetics/isolation & purificationEnzymology
Phylogeny31570960Streptococcus koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion.Lim YK, Park SN, Shin JH, Ji S, Jo E, Chang YH, Shin Y, Paek J, Kim H, Kook JKCurr Microbiol10.1007/s00284-019-01778-62019Base Composition, DNA, Bacterial/genetics, Dental Plaque/*microbiology, Fatty Acids/chemistry, Genome, Bacterial/genetics, Humans, Nucleic Acid Hybridization, Periodontitis/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Streptococcus/chemistry/*classification/cytology/geneticsGenetics
Phylogeny33133039Streptococcus xiaochunlingii sp. nov. E24 Isolated From the Oropharynx of Healthy Chinese Children.Zou Y, Sun Y, Qi H, Liu D, Tian H, Wang N, Li XFront Microbiol10.3389/fmicb.2020.5632132020

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21039Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26920Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26920)
30961Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172729128776041
63344Curators of the CCUGhttps://www.ccug.se/strain?id=66516Culture Collection University of Gothenburg (CCUG) (CCUG 66516)
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
68381Automatically annotated from API rID32STR
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
88454Reimer, 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-ID310322.1