Name: Planococcus chinensis DX3-12
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11973

Type strain:

Species: Planococcus chinensis

Strain Designation: DX3-12

Culture col. no.: DSM 17276, AS 1.3454, JCM 12466, CGMCC 1.3454

Strain history: Y. Zhou DX312.

NCBI tax ID(s): 272917 (species)

SI-ID 138017

AS 1.3454, JCM 12466, DSM 17276, CGMCC 1.3454

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Planococcus chinensis DX3-12 is a mesophilic bacterium that was isolated from coastal sediment.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Caryophanaceae*
	Genus	*Planococcus*
	Species	**Planococcus chinensis**
	Full Scientific Name (LPSN)	Planococcus chinensis (Dai et al. 2005) Gupta and Patel 2020

Synonym

Planomicrobium chinense

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6868]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6868]

Culture medium growth

[Ref.: #6868]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6868]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6868]			growth	28 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: MK-8

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6868]	Sample type/isolated from	coastal sediment
[Ref.: #6868]	Geographic location (country and/or sea, region)	Eastern China Sea
[Ref.: #6868]	Country	China
[Ref.: #6868]	Country ISO 3 Code	CHN
[Ref.: #6868]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Coastal sediment of the East China Sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6868]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6868]	Planomicrobium chinense partial 16S rRNA gene, type strain DX3-12T	AJ697862	1510	GenBank ENA	272917 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Planomicrobium chinense strain DSM 17276	272917.3	wgs	PATRIC	272917 tax ID	*
[Ref.: #66792]	Planomicrobium chinense DSM 17276	2901061160	draft	JGI IMG/M	272917 tax ID	*

[Ref.: #6868]	GC-content	34.8 mol%
[Ref.: #67770]	GC-content	34.8 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planomicrobium chinense strain DSM 17276 PATRIC: 272917.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	78.108	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.067	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	55.944	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	81.438	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.631	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	55.426	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Planomicrobium chinense DSM 17276 IMG: 2901061160
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	86.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	79.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	84.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative anaerobe	69.7

Availability in culture collections External links

[Ref.: #6868]

Culture collection no.

DSM 17276, AS 1.3454, JCM 12466, CGMCC 1.3454

[Ref.: #81185]

SI-ID 138017

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*

References

#6868

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17276

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#81185

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID138017.1 )

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Planomicrobium chinense strain DSM 17276

Planomicrobium chinense DSM 17276

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