Strain identifier

BacDive ID: 140137

Type strain: Yes

Species: Streptococcus panodentis

Strain history: M. Okamoto; Tsurumi Univ., Japan; TKU50.

NCBI tax ID(s): 1581472 (species)

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General

@ref: 42744

BacDive-ID: 140137

DSM-Number: 29921

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

description: Streptococcus panodentis DSM 29921 is a microaerophile, mesophilic bacterium that was isolated from oral cavity of a chimpanzee in good oral health ).

NCBI tax id

  • NCBI tax id: 1581472
  • Matching level: species

strain history

@refhistory
42744<- M. Okamoto, Tsurumi Univ., Yokohama, Japan; TKU50 <- M. Okamoto and S. Imai
67770M. Okamoto; Tsurumi Univ., Japan; TKU50.

doi: 10.13145/bacdive140137.20230509.8.1

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 panodentis
  • full scientific name: Streptococcus panodentis Okamoto et al. 2016

@ref: 42744

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus panodentis

full scientific name: Streptococcus panodentis Okamoto et al. 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no96.371
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
42744COLUMBIA 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
42744TRYPTICASE 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
63759positivegrowth37mesophilic
42744positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 63759
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.936

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

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

enzymes

@refvalueactivityec
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
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
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
42744+++-+--+-++-+---+++/-+++---+--+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
42744oral cavity of a chimpanzee in good oral health (Pan troglodytes))Pan troglodytesKyoto University, Primate Research InstituteJapanJPNAsia
63759Chimpanzee,oral cavity
67770Oral cavities of chimpanzee (Pan troglodytes)Pan troglodytes

isolation source categories

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

Sequence information

16S sequences

  • @ref: 42744
  • description: Streptococcus panodentis gene for 16S ribosomal RNA, partial sequence, strain: TKU50
  • accession: LC012889
  • length: 1471
  • database: ena
  • NCBI tax ID: 1581472

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus panodentis CCUG 70867GCA_017884005scaffoldncbi1581472
66792Streptococcus panodentis strain CCUG 708671581472.3wgspatric1581472

GC content

  • @ref: 42744
  • GC-content: 46.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.489no
flagellatedno94.274no
gram-positiveyes91.762no
anaerobicno91.374no
aerobicno94.662yes
halophileyes59.862no
spore-formingno87.456no
thermophileno99.37yes
glucose-utilyes88.723no
glucose-fermentyes77.596no

External links

@ref: 42744

culture collection no.: DSM 29921, JCM 30579, CCUG 70867, TKU 50

straininfo link

  • @ref: 96530
  • straininfo: 403797

literature

  • topic: Phylogeny
  • Pubmed-ID: 26242550
  • title: Streptococcus panodentis sp. nov. from the oral cavities of chimpanzees.
  • authors: Okamoto M, Imai S, Miyanohara M, Saito W, Momoi Y, Nomura Y, Ikawa T, Ogawa T, Miyabe-Nishiwaki T, Kaneko A, Watanabe A, Watanabe S, Hayashi M, Tomonaga M, Hanada N
  • journal: Microbiol Immunol
  • DOI: 10.1111/1348-0421.12290
  • year: 2015
  • mesh: Aerobiosis, Anaerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases, Fermentation, Molecular Sequence Data, Mouth/*microbiology, *Pan troglodytes, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptococcus/*classification/genetics/*isolation & purification
  • topic2: 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
42744Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29921Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29921)
63759Curators of the CCUGhttps://www.ccug.se/strain?id=70867Culture Collection University of Gothenburg (CCUG) (CCUG 70867)
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
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
96530Reimer, 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-ID403797.1