Strain identifier
BacDive ID: 16129
Type strain: 
Species: Kitasatospora xanthocidica
Strain Designation: IPCR 51-4
Strain history: KCC S-0243 <-- S. Suzuki 51-4.
NCBI tax ID(s): 83382 (species)
version 8.1 (current version)
General
@ref: 9656
BacDive-ID: 16129
DSM-Number: 40575
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Kitasatospora xanthocidica IPCR 51-4 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from Soil.
NCBI tax id
- NCBI tax id: 83382
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9656 | <- E.B. Shirling, ISP <- Y. Okami, IPCR 51-4 |
| 67770 | KCC S-0243 <-- S. Suzuki 51-4. |
doi: 10.13145/bacdive16129.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Kitasatosporales
- family: Streptomycetaceae
- genus: Kitasatospora
- species: Kitasatospora xanthocidica
- full scientific name: Kitasatospora xanthocidica (Asahi et al. 1966) Nouioui et al. 2018
synonyms
- @ref: 20215
- synonym: Streptomyces xanthocidicus
@ref: 9656
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Kitasatospora
species: Kitasatospora xanthocidica
full scientific name: Kitasatospora xanthocidica (Asahi et al. 1966) Nouioui et al. 2018
strain designation: IPCR 51-4
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.196 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9656 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
| 9656 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 9656 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
compound production
| @ref | compound |
|---|---|
| 9656 | xanthocidin |
| 20216 | Xanthocidin |
metabolite production
- @ref: 67770
- metabolite: xanthocidin
- production: yes
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soil
- geographic location: Rikugo-machi, Yamanashi Pref.
- country: Japan
- origin.country: JPN
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_208.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_148;97_159;98_177;99_208&stattab=map
- Last taxonomy: Streptomycetaceae
- 16S sequence: AY999858
- Sequence Identity:
- Total samples: 2039
- soil counts: 1733
- aquatic counts: 54
- animal counts: 127
- plant counts: 125
Safety information
risk assessment
- @ref: 9656
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces xanthocidicus strain IFO 13469 16S ribosomal RNA gene, partial sequence | AY999858 | 1420 | ena | 83382 |
| 20218 | Streptomyces xanthocidicus gene for 16S rRNA, partial sequence | AB018208 | 120 | ena | 83382 |
| 20218 | Streptomyces xanthocidicus gene for 16S rRNA, partial sequence, strain: NBRC 13469 | AB184427 | 1457 | ena | 83382 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kitasatospora xanthocidica JCM 4862 | GCA_014656195 | scaffold | ncbi | 83382 |
| 66792 | Kitasatospora xanthocidica strain JCM 4862 | 83382.6 | wgs | patric | 83382 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 97.85 | no |
| gram-positive | yes | 90.707 | no |
| anaerobic | no | 99.204 | no |
| aerobic | yes | 90.661 | no |
| halophile | no | 94.49 | no |
| spore-forming | yes | 93.579 | no |
| glucose-util | yes | 91.836 | no |
| thermophile | no | 98.826 | no |
| motile | no | 93.98 | no |
| glucose-ferment | no | 89.335 | no |
External links
@ref: 9656
culture collection no.: DSM 40575, ATCC 27480, CBS 770.72, IFO 13469, ISP 5575, JCM 4243, JCM 4862, NBRC 13469, RIA 1430, BCRC 11874, CGMCC 4.1424, KCTC 19978, NRRL B-12504, VKM Ac-872
straininfo link
- @ref: 85194
- straininfo: 13367
literature
- topic: Phylogeny
- Pubmed-ID: 25491896
- title: Streptomyces lactacystinicus sp. nov. and Streptomyces cyslabdanicus sp. nov., producing lactacystin and cyslabdan, respectively.
- authors: Take A, Matsumoto A, Omura S, Takahashi Y
- journal: J Antibiot (Tokyo)
- DOI: 10.1038/ja.2014.162
- year: 2014
- mesh: Acetylcysteine/*analogs & derivatives/metabolism, Anti-Bacterial Agents/*metabolism, DNA, Bacterial/genetics, Diterpenes/*metabolism, Gene Expression Regulation, Bacterial/physiology, Phylogeny, Species Specificity, Streptomyces/*classification/*metabolism/ultrastructure
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9656 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40575) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40575 | |||
| 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 | |||
| 20216 | Curators of the HKI | http://www.leibniz-hki.de/de/ | Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 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. | 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 | |||
| 85194 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13367.1 | StrainInfo: A central database for resolving microbial strain identifiers |