Strain identifier
BacDive ID: 13464
Type strain: 
Species: Saccharopolyspora endophytica
Strain history: <- S Qin, Yunnan Inst., China
NCBI tax ID(s): 33915 (species), 543886 (species)
version 9.1 (current version)
General
@ref: 16793
BacDive-ID: 13464
DSM-Number: 45425
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Saccharopolyspora endophytica DSM 45425 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from plant sample.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 33915 | species |
| 543886 | species |
strain history
| @ref | history |
|---|---|
| 16793 | <- S.-K. Tang, YIM; YIM 61095 <- S. Qin et al. |
| 67771 | <- S Qin, Yunnan Inst., China |
doi: 10.13145/bacdive13464.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Saccharopolyspora
- species: Saccharopolyspora endophytica
- full scientific name: Saccharopolyspora endophytica Qin et al. 2021
@ref: 16793
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Saccharopolyspora
species: Saccharopolyspora sp.
full scientific name: Saccharopolyspora sp.
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | positive | |
| 69480 | positive | 90.723 |
Culture and growth conditions
culture medium
- @ref: 16793
- name: GPHF-MEDIUM (DSMZ Medium 553)
- growth: yes
- link: https://mediadive.dsmz.de/medium/553
- composition: Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 16793 | positive | growth | 28 |
| 67771 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 100
observation
- @ref: 67771
- observation: quinones: MK-9(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16793 | plant sample | Xishuangbanna, Yunnan Province | China | CHN | Asia |
| 67771 | From the root of Maytenus austroyunnanensis collected from a tropical rainforest of Xishuangbanna | Yunnan | China | CHN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
taxonmaps
- @ref: 69479
- File name: preview.99_11754.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1393;97_7142;98_8820;99_11754&stattab=map
- Last taxonomy: Saccharopolyspora
- 16S sequence: EU814512
- Sequence Identity:
- Total samples: 1272
- soil counts: 398
- aquatic counts: 39
- animal counts: 719
- plant counts: 116
Sequence information
16S sequences
- @ref: 16793
- description: Saccharopolyspora endophytica strain YIM 61095 16S ribosomal RNA gene, partial sequence
- accession: EU814512
- length: 1470
- database: nuccore
- NCBI tax ID: 543886
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Saccharopolyspora endophytica KCTC 19397 | GCA_018070075 | contig | ncbi | 543886 |
| 66792 | Saccharopolyspora endophytica strain KCTC 19397 | 543886.5 | wgs | patric | 543886 |
GC content
- @ref: 16793
- GC-content: 66.2
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.723 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.168 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 85.161 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.343 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.978 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 88 | no |
External links
@ref: 16793
culture collection no.: DSM 45425, CCTCC AA 208003, KCTC 19397, YIM 61095
straininfo link
- @ref: 82656
- straininfo: 399153
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18929936 | Saccharopolyspora endophytica sp. nov., an endophytic actinomycete isolated from the root of Maytenus austroyunnanensis. | Qin S, Li J, Zhao GZ, Chen HH, Xu LH, Li WJ | Syst Appl Microbiol | 10.1016/j.syapm.2008.08.001 | 2008 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Maytenus/*microbiology, Medicine, Chinese Traditional, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/*isolation & purification/physiology, Species Specificity | Enzymology |
| Metabolism | 26260388 | Characterization of the chromosomal integration of Saccharopolyspora plasmid pCM32 and its application to improve production of spinosyn in Saccharopolyspora spinosa. | Chen J, Xia H, Dang F, Xu Q, Li W, Qin Z | Appl Microbiol Biotechnol | 10.1007/s00253-015-6871-z | 2015 | Attachment Sites, Microbiological, DNA, Bacterial/chemistry/genetics, Escherichia coli/genetics, Gene Expression, Genetic Vectors, Macrolides/*metabolism, Metabolic Engineering/*methods, Open Reading Frames, Pesticides/*metabolism, *Plasmids, Recombinant Proteins/genetics/metabolism, *Recombination, Genetic, Saccharopolyspora/*genetics/*metabolism, Sequence Analysis, DNA, Transformation, Bacterial | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 16793 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45425) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45425 | |
| 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 | |
| 82656 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399153.1 | StrainInfo: A central database for resolving microbial strain identifiers |