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)
General
@ref: 6868
BacDive-ID: 11973
DSM-Number: 17276
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Planococcus chinensis DX3-12 is a mesophilic, Gram-positive 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/bacdive11973.20230509.8.1
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
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
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 | range |
---|---|---|---|---|
6868 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 90.6
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: ena
- 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
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 78 | no |
motile | yes | 80.271 | no |
gram-positive | yes | 92.235 | no |
anaerobic | no | 98.441 | no |
halophile | yes | 67.59 | no |
spore-forming | no | 51.05 | no |
glucose-util | yes | 86.955 | no |
aerobic | yes | 94.916 | no |
flagellated | no | 54.709 | no |
thermophile | no | 99.222 | yes |
glucose-ferment | no | 90.29 | no |
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/ | ||
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) | |
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 |