Strain identifier
BacDive ID: 155979
Type strain: 
Species: Stenotrophomonas panacihumi
Strain history: M. K. Kim MK06.
NCBI tax ID(s): 676599 (species)
version 9.1 (current version)
General
@ref: 62146
BacDive-ID: 155979
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative
description: Stenotrophomonas panacihumi CCUG 59872 is an aerobe, Gram-negative bacterium that was isolated from Soil of a ginseng field.
NCBI tax id
- NCBI tax id: 676599
- Matching level: species
strain history
- @ref: 67770
- history: M. K. Kim MK06.
doi: 10.13145/bacdive155979.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Stenotrophomonas
- species: Stenotrophomonas panacihumi
- full scientific name: Stenotrophomonas panacihumi Yi et al. 2010
@ref: 62146
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Lysobacterales
family: Lysobacteraceae
genus: Stenotrophomonas
species: Stenotrophomonas panacihumi
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.75
Culture and growth conditions
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 62146 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 62146
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 91.422 |
| 69481 | no | 100 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 62146 | Soil of a ginseng field | Republic of Korea | KOR | Asia |
| 67770 | Soil of a ginseng field in Daejeon | 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_6021.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_27;98_4467;99_6021&stattab=map
- Last taxonomy: Stenotrophomonas
- 16S sequence: GQ856217
- Sequence Identity:
- Total samples: 1494
- soil counts: 588
- aquatic counts: 169
- animal counts: 387
- plant counts: 350
Sequence information
16S sequences
- @ref: 67770
- description: Stenotrophomonas panacihumi strain MK06 16S ribosomal RNA gene, partial sequence
- accession: GQ856217
- length: 1476
- database: nuccore
- NCBI tax ID: 676599
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Stenotrophomonas panacihumi strain JCM 16536 | 676599.3 | wgs | patric | 676599 |
| 66792 | Stenotrophomonas panacihumi JCM 16536 | 2744054482 | draft | img | 676599 |
| 67770 | Stenotrophomonas panacihumi JCM 16536 | GCA_001431645 | contig | ncbi | 676599 |
GC content
- @ref: 67770
- GC-content: 67.8
- 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 | no | 98.75 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.844 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 91.422 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 82.785 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.962 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 70.051 | no |
External links
@ref: 62146
culture collection no.: CCUG 59872, KCTC 22893, JCM 16536
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 62146 | Curators of the CCUG | https://www.ccug.se/strain?id=59872 | Culture Collection University of Gothenburg (CCUG) (CCUG 59872) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 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 |