Planococcus donghaensis (DSM 22276, KCTC 13050, LMG 23779)

Name: Planococcus donghaensis (DSM 22276, KCTC 13050, LMG 23779)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11965

Type strain

Strain Designation JH1

Culture col. no. DSM 22276 KCTC 13050 LMG 23779 JH1

NCBI tax ID(s) 414778

Special Collections DSMZ KCTC

History <- LMG; LMG 23779 <- D.-H. Roh <- J. H. Choi, Chungbuk Natl. Univ., Republic of Korea; JH1 <- DH Roh, Chungbuk Natl. Univ.

Links

Planococcus donghaensis JH1 is an aerobe, motile, coccus-shaped bacterium that was isolated from deep sea sediment.

motile coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 292312

LMG 23779,KCTC 13050,DSM 22276

@ref 20215

Last LPSN update 2026-02-09 11:20:42

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Planococcus

Species Planococcus donghaensis

Full scientific name Planococcus donghaensis Choi et al. 2007

Morphology

Cell morphology

@ref	Cell shape	Motility	Gram stain
67771	coccus-shaped
67771			positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16172	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16172	positive	growth	28
67771	positive	growth	25-30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	95.7

Spore formation

@ref	Spore formation	Confidence
67771
125439		90.5

Murein

@ref	Murein short key	Type
16172	A11.33	A4alpha L-Lys-D-Glu

Observation

67771

Observationquinones: MK-7, MK-8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16172	deep sea sediment	East Sea	Republic of Korea	KOR	Asia
67771	From deep-sea sediment of the East Sea		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF079063 (>99% sequence identity) for Planococcus from Microbeatlas

Aquatic Samples	353
Soil Samples	566
Animal Samples	550
Plant Samples	97
Total Samples	1566

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16172	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Planococcus donghaensis LMG 23779	complete			2700988611	414778	98.95
66792	Planococcus donghaensis strain DSM 22276	complete		414778.4		414778	97.4
66792	ASM168766v2 assembly for Planococcus donghaensis DSM 22276	complete	GCA_001687665	414778.16	2773857989	414778	90.67

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16172	Planococcus donghaensis strain JH1 16S ribosomal RNA gene, partial sequence	EF079063	1452		414778
124043	Planococcus donghaensis strain DSM 22276 16S ribosomal RNA gene, partial sequence.	PP758375	1401		414778

GC content

@ref	GC-content (mol%)
16172	47
67771	47.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Planococcus donghaensis strain DSM 22276
PATRIC: 414778.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	90.50	no
125439	motility	BacteriaNetⓘ	yes	83.90	no
125439	gram_stain	BacteriaNetⓘ	variable	80.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Planococcus donghaensis DSM 22276
NCBI: GCA_001687665.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.31	yes
125438	anaerobic	anaerobicⓘ	no	97.36	yes
125438	aerobic	aerobicⓘ	yes	84.00	yes
125438	spore-forming	spore-formingⓘ	yes	54.33	yes
125438	thermophilic	thermophileⓘ	no	92.82	yes
125438	flagellated	motile2+ⓘ	yes	52.08	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Planococcus soli sp. nov., isolated from antarctic soil.	Zhang S, Ping W, Xin Y, Xin D, Zhang J	Antonie Van Leeuwenhoek	10.1007/s10482-021-01581-z	2021
Phylogeny	Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins.	Kim JH, Kang HJ, Yu BJ, Kim SC, Lee PC	Int J Syst Evol Microbiol	10.1099/ijsem.0.000423	2015
Phylogeny	Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea.	Choi JH, Im WT, Liu QM, Yoo JS, Shin JH, Rhee SK, Roh DH	Int J Syst Evol Microbiol	10.1099/ijs.0.65036-0	2007

References

#16172	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22276
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the 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.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Planococcus donghaensis (DSM 22276, KCTC 13050, LMG 23779)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001687665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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