Garicola koreensis (DSM 28238, JCm 18572, KACC 16909)

Name: Garicola koreensis (DSM 28238, JCm 18572, KACC 16909)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130439

Type strain

Strain Designation SJ5-4

Culture col. no. DSM 28238 JCm 18572 KACC 16909 SJ5-4

NCBI tax ID(s) 1262554

Special Collections DSMZ JCM

History <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; SJ5-4 <- S. H. Lee and C. O. Jeon C. O. Jeon SJ5-4.

Links

Garicola koreensis SJ5-4 is a bacterium that was isolated from saeu-jeot .

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397249

JCM 18572,DSM 28238

@ref 20215

Last LPSN update 2026-02-09 11:31:13

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Garicola

Species Garicola koreensis

Full scientific name Garicola koreensis Lo et al. 2015

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22146	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	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 (°C)
22146	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	90.5

Spore formation

@ref	Spore formation	Confidence
125439		92.2

Observation

67770

Observationquinones: MK-7, MK-8, MK-9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Vegetable (incl. Grains)
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
22146	saeu-jeot (Korean salted fermented shrimp)	Republic of Korea	KOR	Asia
67770	Seau-jeot, a traditional fermented seafood	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX152781 (>99% sequence identity) for Garicola koreensis subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	2
Animal Samples	143
Plant Samples	8
Total Samples	160

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22146	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3954392v1 assembly for Garicola koreensis JCM 18572	scaffold	GCA_039543925			1262554	73.94
66792	ASM1419544v1 assembly for Garicola koreensis DSM 28238	contig	GCA_014195445	1262554.3	2827611747	1262554	55.64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22146	Garicola koreensis strain SJ5-4 16S ribosomal RNA gene, partial sequence	JX152781	1459		1262554

GC content

@ref	GC-content (mol%)	Method
22146	61.8	fluorimetric
67770	61.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Garicola koreensis DSM 28238
NCBI: GCA_014195445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.20	no
125439	motility	BacteriaNetⓘ	no	52.80	no
125439	gram_stain	BacteriaNetⓘ	positive	69.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Garicola koreensis strain DSM 28238
PATRIC: 1262554.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	85.69	no
125438	anaerobic	anaerobicⓘ	no	92.32	no
125438	spore-forming	spore-formingⓘ	no	79.78	no
125438	aerobic	aerobicⓘ	yes	76.95	no
125438	thermophilic	thermophileⓘ	no	86.82	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Garicola koreensis gen. nov., sp. nov., isolated from saeu-jeot, traditional Korean fermented shrimp.	Lo N, Lee SH, Jin HM, Jung JY, Schumann P, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.000056	2015

References

#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 )
#22146	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28238
#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;
#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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Garicola koreensis (DSM 28238, JCm 18572, KACC 16909)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039543925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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