Strain identifier

BacDive ID: 140138

Type strain: Yes

Species: Streptococcus oricebi

Strain Designation: M8

Strain history: M. Saito; Nihon Univ. Sch. of Dent. at Matsudo, Japan; M8.

NCBI tax ID(s): 1547447 (species)

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General

@ref: 42745

BacDive-ID: 140138

DSM-Number: 100101

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped, colony-forming

description: Streptococcus oricebi M8 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from oral cavity of tufted capuchin .

NCBI tax id

  • NCBI tax id: 1547447
  • Matching level: species

strain history

@refhistory
42745<- M. Saito, Nihon Univ., School of Dentistry, Matsudo; M8
67770M. Saito; Nihon Univ. Sch. of Dent. at Matsudo, Japan; M8.

doi: 10.13145/bacdive140138.20230509.8.1

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 oricebi
  • full scientific name: Streptococcus oricebi Saito et al. 2016

@ref: 42745

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus oricebi

full scientific name: Streptococcus oricebi Saito et al. 2016

strain designation: M8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43819positive0.8-1 µmcoccus-shapedno
69480no95.352
69480positive100

colony morphology

@reftype of hemolysishemolysis abilitycolony sizecolony colorcolony shapeincubation periodmedium used
43819alpha10.6-0.9 mmWhitecircular2 daysBlood agar
43819Dark blueMS agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43819Blood agaryes
43819MS agaryes
42745COLUMBIA 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
42745TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
63760positivegrowth37mesophilic
42745positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43819facultative anaerobe
63760microaerophile

spore formation

@refspore formationconfidence
43819no
69481no100
69480no99.987

observation

@refobservation
43819Colonies on MS agar are small and have a crinkled appearance
43819Cells react with Lancefield group A antisera.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43819168082-dehydro-D-gluconate-builds acid from
43819581435-dehydro-D-gluconate-builds acid from
4381927613amygdalin-builds acid from
4381918305arbutin-builds acid from
4381917057cellobiose-builds acid from
4381923456cyclodextrin-builds acid from
4381915963ribitol-builds acid from
4381917108D-arabinose-builds acid from
4381918333D-arabitol-builds acid from
4381928847D-fucose-builds acid from
4381912936D-galactose-builds acid from
4381962318D-lyxose-builds acid from
4381916899D-mannitol-builds acid from
4381916988D-ribose-builds acid from
4381917924D-sorbitol-builds acid from
4381916443D-tagatose-builds acid from
4381965327D-xylose-builds acid from
4381916813galactitol-builds acid from
4381917113erythritol-builds acid from
4381928066gentiobiose-builds acid from
4381924265gluconate-builds acid from
4381917754glycerol-builds acid from
4381928087glycogen-builds acid from
4381917268myo-inositol-builds acid from
4381915443inulin-builds acid from
4381918403L-arabitol-builds acid from
4381918287L-fucose-builds acid from
4381962345L-rhamnose-builds acid from
4381917266L-sorbose-builds acid from
4381965328L-xylose-builds acid from
438196731melezitose-builds acid from
4381928053melibiose-builds acid from
43819320061methyl alpha-D-glucopyranoside-builds acid from
4381943943methyl alpha-D-mannoside-builds acid from
4381974863methyl beta-D-xylopyranoside-builds acid from
4381927941pullulan-builds acid from
4381928017starch-builds acid from
4381932528turanose-builds acid from
4381917151xylitol-builds acid from
43819606565hippurate-hydrolysis
4381916199urea-hydrolysis
4381915824D-fructose+builds acid from
4381917634D-glucose+builds acid from
4381916024D-mannose+builds acid from
4381917716lactose+builds acid from
4381917306maltose+builds acid from
43819320055methyl beta-D-glucopyranoside+builds acid from
43819506227N-acetylglucosamine+builds acid from
4381916634raffinose+builds acid from
4381917814salicin+builds acid from
4381917992sucrose+builds acid from
4381927082trehalose+builds acid from
4381929016arginine+hydrolysis
438194853esculin+hydrolysis
6838129016arginine+hydrolysis
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
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose+builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside+builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4381915688acetoinyes
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
4381915688acetoin+
6838115688acetoin-

enzymes

@refvalueactivityec
43819catalase-1.11.1.6
43819beta-glucosidase+3.2.1.21
43819leucine arylamidase+3.4.11.1
43819valine arylamidase+
43819acid phosphatase+3.1.3.2
43819naphthol-AS-BI-phosphohydrolase+
43819arginine dihydrolase+3.5.3.6
43819alanine arylamidase+3.4.11.2
43819phenylalanine arylamidase+
43819proline-arylamidase+3.4.11.5
43819alkaline phosphatase-3.1.3.1
43819esterase (C 4)-
43819esterase Lipase (C 8)-
43819lipase (C 14)-
43819cystine arylamidase-3.4.11.3
43819trypsin-3.4.21.4
43819alpha-chymotrypsin-3.4.21.1
43819alpha-galactosidase-3.2.1.22
43819beta-galactosidase-3.2.1.23
43819beta-glucuronidase-3.2.1.31
43819alpha-glucosidase-3.2.1.20
43819N-acetyl-beta-glucosaminidase-3.2.1.52
43819alpha-fucosidase-3.2.1.51
43819pyroglutamic acid arylamidase-
43819glycyl tryptophan arylamidase-
43819alpha-mannosidase-3.2.1.24
43819urease-3.5.1.5
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381pyrrolidonyl arylamidase-3.4.19.3
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase+3.5.3.6

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
42745+++-+/-----++++----++/--+/-----+--+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
42745oral cavity of tufted capuchin (Cebus apella)Cebus apellaNasu World Monkey Park, TochigiJapanJPNAsia
43819The oral cavity of a tufted capuchin (Nasu World Monkey Park)TochigiJapanJPNAsia
63760Oral cavity,tufted capuchin
67770Oral cavity of tufted capuchin (Cebus apella)Cebus apella

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Primates
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_88178.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4;96_33593;97_46473;98_60903;99_88178&stattab=map
  • Last taxonomy: Streptococcus oricebi subclade
  • 16S sequence: LC002970
  • Sequence Identity:
  • Total samples: 549
  • soil counts: 1
  • aquatic counts: 8
  • animal counts: 523
  • plant counts: 17

Sequence information

16S sequences

  • @ref: 42745
  • description: Streptococcus oricebi gene for 16S ribosomal RNA, partial sequence
  • accession: LC002970
  • length: 1504
  • database: ena
  • NCBI tax ID: 1547447

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus oricebi CCUG 70868GCA_017883985scaffoldncbi1547447
66792Streptococcus oricebi strain CCUG 708681547447.3wgspatric1547447

GC content

  • @ref: 42745
  • GC-content: 42.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.543no
flagellatedno96.777yes
gram-positiveyes93.634yes
anaerobicno96.878yes
aerobicno95.799yes
halophileyes77.765no
spore-formingno94.031no
thermophileno99.2no
glucose-utilyes85.33no
glucose-fermentyes85.483no

External links

@ref: 42745

culture collection no.: CCUG 70868, DSM 100101, JCM 30719

straininfo link

  • @ref: 96531
  • straininfo: 407373

literature

  • topic: Phylogeny
  • Pubmed-ID: 26651833
  • title: Streptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin.
  • authors: Saito M, Shinozaki-Kuwahara N, Hirasawa M, Takada K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000834
  • year: 2015
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cebus/*microbiology, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Genes, Bacterial, Mouth/*microbiology, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptococcus/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
42745Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100101Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100101)
43819M. Saito, N. Shinozaki-Kuwahara, M. Hirasawa, K. TakadaStreptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin10.1099/ijsem.0.000834IJSEM 66: 1063-1067 201626651833
63760Curators of the CCUGhttps://www.ccug.se/strain?id=70868Culture Collection University of Gothenburg (CCUG) (CCUG 70868)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
96531Reimer, 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-ID407373.1