Strain identifier
BacDive ID: 11973
Type strain: 
Species: Planococcus chinensis
Strain Designation: DX3-12
Strain history: Y. Zhou DX312.
NCBI tax ID(s): 272917 (species)
version 9.3 (current version)
General
@ref: 6868
BacDive-ID: 11973
DSM-Number: 17276
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Planococcus chinensis DX3-12 is a mesophilic bacterium that was isolated from coastal sediment.
NCBI tax id
- NCBI tax id: 272917
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6868 | <- JCM <- Y.-G.Zhou, DX3-12 |
| 67770 | Y. Zhou DX312. |
doi: 10.13145/bacdive11973.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Caryophanaceae
- genus: Planococcus
- species: Planococcus chinensis
- full scientific name: Planococcus chinensis (Dai et al. 2005) Gupta and Patel 2020
synonyms
- @ref: 20215
- synonym: Planomicrobium chinense
@ref: 6868
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Planococcus
species: Planococcus chinensis
full scientific name: Planococcus chinensis (Dai et al. 2005) Gupta and Patel 2020
strain designation: DX3-12
type strain: yes
Culture and growth conditions
culture medium
- @ref: 6868
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 6868 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6868 | coastal sediment | Eastern China Sea | China | CHN | Asia |
| 67770 | Coastal sediment of the East China Sea |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Coast |
Safety information
risk assessment
- @ref: 6868
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6868
- description: Planomicrobium chinense partial 16S rRNA gene, type strain DX3-12T
- accession: AJ697862
- length: 1510
- database: nuccore
- NCBI tax ID: 272917
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Planomicrobium chinense strain DSM 17276 | 272917.3 | wgs | patric | 272917 |
| 66792 | Planomicrobium chinense DSM 17276 | 2901061160 | draft | img | 272917 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6868 | 34.8 | |
| 67770 | 34.8 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 78.108 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.067 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 55.944 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.438 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.631 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 55.426 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 86.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 79.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 84.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative anaerobe | 69.7 |
External links
@ref: 6868
culture collection no.: DSM 17276, AS 1.3454, JCM 12466, CGMCC 1.3454
straininfo link
- @ref: 81185
- straininfo: 138017
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15774646 | Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov. | Dai X, Wang YN, Wang BJ, Liu SJ, Zhou YG | Int J Syst Evol Microbiol | 10.1099/ijs.0.63340-0 | 2005 | Base Sequence, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Gram-Positive Bacteria/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Genetics |
| Phylogeny | 24854007 | Planomicrobium soli sp. nov., isolated from soil. | Luo X, Zhang J, Li D, Xin Y, Xin D, Fan L | Int J Syst Evol Microbiol | 10.1099/ijs.0.055426-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6868 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17276) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17276 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 81185 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID138017.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |