Strain identifier
BacDive ID: 140137
Type strain: 
Species: Streptococcus panodentis
Strain history: M. Okamoto; Tsurumi Univ., Japan; TKU50.
NCBI tax ID(s): 1581472 (species)
version 9.1 (current version)
General
@ref: 42744
BacDive-ID: 140137
DSM-Number: 29921
keywords: genome sequence, 16S sequence, Bacteria, microaerophile
description: Streptococcus panodentis DSM 29921 is a microaerophile 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
| @ref | history |
|---|---|
| 42744 | <- M. Okamoto, Tsurumi Univ., Yokohama, Japan; TKU50 <- M. Okamoto and S. Imai |
| 67770 | M. Okamoto; Tsurumi Univ., Japan; TKU50. |
doi: 10.13145/bacdive140137.20240916.9.1
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
- @ref: 69480
- motility: no
- confidence: 90.646
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 42744 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
| 42744 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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
| @ref | growth | type | temperature |
|---|---|---|---|
| 63759 | positive | growth | 37 |
| 42744 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 63759
- oxygen tolerance: microaerophile
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68381 | 29016 | arginine | + | hydrolysis |
| 68381 | 16988 | D-ribose | - | builds acid from |
| 68381 | 16899 | D-mannitol | + | builds acid from |
| 68381 | 30911 | sorbitol | - | builds acid from |
| 68381 | 17716 | lactose | + | builds acid from |
| 68381 | 27082 | trehalose | + | builds acid from |
| 68381 | 16634 | raffinose | - | builds acid from |
| 68381 | 17992 | sucrose | + | builds acid from |
| 68381 | 30849 | L-arabinose | - | builds acid from |
| 68381 | 18333 | D-arabitol | - | builds acid from |
| 68381 | 40585 | alpha-cyclodextrin | - | builds acid from |
| 68381 | 606565 | hippurate | - | hydrolysis |
| 68381 | 28087 | glycogen | - | builds acid from |
| 68381 | 27941 | pullulan | - | builds acid from |
| 68381 | 17306 | maltose | + | builds acid from |
| 68381 | 28053 | melibiose | - | builds acid from |
| 68381 | 6731 | melezitose | - | builds acid from |
| 68381 | 320055 | methyl beta-D-glucopyranoside | + | builds acid from |
| 68381 | 16443 | D-tagatose | - | builds acid from |
| 68381 | 16199 | urea | - | 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
| @ref | value | activity | ec |
|---|---|---|---|
| 68381 | urease | - | 3.5.1.5 |
| 68381 | beta-mannosidase | - | 3.2.1.25 |
| 68381 | glycyl tryptophan arylamidase | + | |
| 68381 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
| 68381 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
| 68381 | Alanyl-Phenylalanyl-Proline arylamidase | + | |
| 68381 | alkaline phosphatase | - | 3.1.3.1 |
| 68381 | alpha-galactosidase | + | 3.2.1.22 |
| 68381 | beta-glucuronidase | - | 3.2.1.31 |
| 68381 | beta-glucosidase | + | 3.2.1.21 |
| 68381 | arginine dihydrolase | + | 3.5.3.6 |
API rID32STR
| @ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42744 | + | + | + | - | + | - | - | + | - | + | + | - | + | - | - | - | + | + | +/- | + | + | + | - | - | - | + | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 42744 | oral cavity of a chimpanzee in good oral health (Pan troglodytes)) | Pan troglodytes | Kyoto University, Primate Research Institute | Japan | JPN | Asia |
| 63759 | Chimpanzee,oral cavity | |||||
| 67770 | Oral cavities of chimpanzee (Pan troglodytes) | Pan troglodytes |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #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: nuccore
- NCBI tax ID: 1581472
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptococcus panodentis CCUG 70867 | GCA_017884005 | scaffold | ncbi | 1581472 |
| 66792 | Streptococcus panodentis strain CCUG 70867 | 1581472.3 | wgs | patric | 1581472 |
GC content
- @ref: 42744
- GC-content: 46.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 82.625 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 89.087 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 94.326 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 77.109 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.375 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 90.646 | no |
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
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 42744 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29921 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29921) | |
| 63759 | Curators of the CCUG | https://www.ccug.se/strain?id=70867 | Culture Collection University of Gothenburg (CCUG) (CCUG 70867) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 68381 | Automatically annotated from API rID32STR | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 96530 | Reimer, 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 identifiers | 10.60712/SI-ID403797.1 |