Strain identifier
BacDive ID: 23283
Type strain:
Species: Sphingopyxis panaciterrae
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 363841 (species)
General
@ref: 19123
BacDive-ID: 23283
DSM-Number: 27164
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Sphingopyxis panaciterrae DSM 27164 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.
NCBI tax id
- NCBI tax id: 363841
- Matching level: species
strain history
@ref | history |
---|---|
19123 | <- KCTC <- W.-T. Im, Korean Advanced Institute of Science and Technology, KAIST, Daejeon |
67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive23283.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingopyxis
- species: Sphingopyxis panaciterrae
- full scientific name: Sphingopyxis panaciterrae Lee et al. 2011
@ref: 19123
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingopyxis
species: Sphingopyxis panaciterrae
full scientific name: Sphingopyxis panaciterrae Lee et al. 2011
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
67771 | negative | |
69480 | negative | 99.872 |
multimedia
- @ref: 19123
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27164.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 19123
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19123 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.907 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19123 | soil of ginseng field | Pocheon Province | Republic of Korea | KOR | Asia |
67771 | From soil of ginseng field | Pocheon Province | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_4432.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1020;97_1190;98_3332;99_4432&stattab=map
- Last taxonomy: Sphingopyxis
- 16S sequence: AB245353
- Sequence Identity:
- Total samples: 1625
- soil counts: 407
- aquatic counts: 362
- animal counts: 572
- plant counts: 284
Safety information
risk assessment
- @ref: 19123
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19123
- description: Sphingopyxis panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 124
- accession: AB245353
- length: 1449
- database: ena
- NCBI tax ID: 363841
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingopyxis panaciterrae DSM 27164 | GCA_011762125 | contig | ncbi | 363841 |
66792 | Sphingopyxis panaciterrae strain DSM 27164 | 363841.3 | wgs | patric | 363841 |
66792 | Sphingopyxis panaciterrae DSM 27164 | 2828390859 | draft | img | 363841 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.308 | yes |
anaerobic | no | 99.488 | yes |
halophile | no | 95.05 | no |
spore-forming | no | 93.841 | no |
glucose-util | yes | 82.122 | no |
aerobic | yes | 94.351 | yes |
flagellated | no | 79.461 | no |
thermophile | no | 98.536 | no |
motile | yes | 69.277 | no |
glucose-ferment | no | 93.57 | no |
External links
@ref: 19123
culture collection no.: DSM 27164, KCTC 12580, LMG 24003, Gsoil 124
straininfo link
- @ref: 87504
- straininfo: 408026
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18600040 | Sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field. | Lee HW, Ten IL, Jung HM, Liu QM, Im WT, Lee ST | J Microbiol Biotechnol | 7422 | 2008 | Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Korea, Nucleic Acid Hybridization, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*genetics/*isolation & purification | Phenotype |
Phylogeny | 23264504 | Sphingopyxis italica sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.046573-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysis | Genetics |
Phylogeny | 26040579 | Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid. | Oelschlagel M, Ruckert C, Kalinowski J, Schmidt G, Schlomann M, Tischler D | Int J Syst Evol Microbiol | 10.1099/ijs.0.000371 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Phenylacetates/*metabolism, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Styrene/*metabolism, Ubiquinone/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
19123 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27164) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27164 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
69479 | João 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
87504 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408026.1 | StrainInfo: A central database for resolving microbial strain identifiers |