Phycicoccus ginsengisoli (DCY 87, KCTC 39635, JCM 31016)

Name: Phycicoccus ginsengisoli (DCY 87, KCTC 39635, JCM 31016)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133241

Type strain

Culture col. no. DCY 87 KCTC 39635 JCM 31016

NCBI tax ID(s) 1462998

Special Collections JCM KCTC Literature strains

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Phycicoccus ginsengisoli DCY 87 is an aerobe, Gram-positive, rod-shaped prokaryote that forms circular colonies and was isolated from Bulky and rhizosphere soil samples were obtained from a ginseng field.

Gram-positive rod-shaped colony-forming aerobe 16S sequence

Name and taxonomic classification

SI-ID 288116

KCTC 39635,JCM 31016

@ref 20215

Last LPSN update 2025-12-16 10:01:43

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Phycicoccus

Species Phycicoccus ginsengisoli

Full scientific name Phycicoccus ginsengisoli Kang et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
25082	positive	1.0-2.1 µm	0.5-0.6 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25082	0.7-0.8 mm	white	circular	2 days	R2A agar (Reasoner's 2A agar)

Culture and growth conditions

Culture medium

@ref	Name	Growth
25082	NA (Nutrient Agar)
25082	Reasoner's 2A agar (R2A)
25082	LB (lysogeny broth) agar
25082	TSA (Trypticase soy agar)

Culture temp

@ref	Growth	Type	Temperature (°C)
25082	positive	growth	10.0-37.0
25082	positive	optimum	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
25082	positive	optimum	7
25082	positive	growth	6.0-9.0

Physiology and metabolism

Oxygen tolerance

25082

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25082	NaCl	positive	growth	0.0-3.0 %(w/v)
25082	NaCl		optimum	2 %(w/v)

Murein

@ref	Murein short key	Type
25082	A31	A1gamma m-Dpm-direct

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25082	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
25082	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
25082	27613 ChEBI	amygdalin	-	builds acid from
25082	22599 ChEBI	arabinose	-	builds acid from
25082	22599 ChEBI	arabinose	-	assimilation
25082	18305 ChEBI	arbutin	-	builds acid from
25082	18305 ChEBI	arbutin	-	assimilation
25082		casein	+	hydrolysis
25082	17057 ChEBI	cellobiose	+	builds acid from
25082	17057 ChEBI	cellobiose	+	assimilation
25082	16947 ChEBI	citrate	-	carbon source
25082	18333 ChEBI	D-arabitol	+	builds acid from
25082	18333 ChEBI	D-arabitol	+	assimilation
25082	15824 ChEBI	D-fructose	+	builds acid from
25082	12936 ChEBI	D-galactose	+	builds acid from
25082	17634 ChEBI	D-glucose	+	builds acid from
25082	16899 ChEBI	D-mannitol	+	builds acid from
25082	16899 ChEBI	D-mannitol	+	assimilation
25082	16024 ChEBI	D-mannose	+	builds acid from
25082	16988 ChEBI	D-ribose	+	builds acid from
25082	17924 ChEBI	D-sorbitol	+	builds acid from
25082	17924 ChEBI	D-sorbitol	+	assimilation
25082	16991 ChEBI	dna	+	hydrolysis
25082	17113 ChEBI	erythritol	-	builds acid from
25082	4853 ChEBI	esculin	+	hydrolysis
25082	4853 ChEBI	esculin	+	builds acid from
25082	33984 ChEBI	fucose	-	builds acid from
25082	16813 ChEBI	galactitol	-	builds acid from
25082	5291 ChEBI	gelatin	+	hydrolysis
25082	28066 ChEBI	gentiobiose	+	builds acid from
25082	28066 ChEBI	gentiobiose	+	assimilation
25082	17234 ChEBI	glucose	-	fermentation
25082	17754 ChEBI	glycerol	+	assimilation
25082	14336 ChEBI	glycerol 1-phosphate	+	builds acid from
25082	15443 ChEBI	inulin	-	builds acid from
25082	15443 ChEBI	inulin	-	assimilation
25082	30849 ChEBI	L-arabinose	-	builds acid from
25082	30849 ChEBI	L-arabinose	+	assimilation
25082	18403 ChEBI	L-arabitol	-	builds acid from
25082	18287 ChEBI	L-fucose	-	builds acid from
25082	18287 ChEBI	L-fucose	-	assimilation
25082	15729 ChEBI	L-ornithine	-	assimilation
25082	62345 ChEBI	L-rhamnose	-	builds acid from
25082	62345 ChEBI	L-rhamnose	-	assimilation
25082	17266 ChEBI	L-sorbose	-	builds acid from
25082	17266 ChEBI	L-sorbose	-	assimilation
25082	17895 ChEBI	L-tyrosine	+	hydrolysis
25082	65328 ChEBI	L-xylose	-	builds acid from
25082	17716 ChEBI	lactose	+	builds acid from
25082	25097 ChEBI	lyxose	-	builds acid from
25082	25097 ChEBI	lyxose	-	assimilation
25082	17306 ChEBI	maltose	+	builds acid from
25082	6731 ChEBI	melezitose	+	assimilation
25082	28053 ChEBI	melibiose	+	builds acid from
25082	28053 ChEBI	melibiose	+	assimilation
25082	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
25082	320061 ChEBI	methyl alpha-D-glucopyranoside	+	assimilation
25082	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
25082	43943 ChEBI	methyl alpha-D-mannoside	-	assimilation
25082	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
25082	17268 ChEBI	myo-inositol	-	builds acid from
25082	17268 ChEBI	myo-inositol	-	assimilation
25082	506227 ChEBI	N-acetylglucosamine	+	builds acid from
25082	506227 ChEBI	N-acetylglucosamine	+	assimilation
25082	32032 ChEBI	potassium gluconate	-	builds acid from
25082	16634 ChEBI	raffinose	-	builds acid from
25082	16634 ChEBI	raffinose	-	assimilation
25082	15963 ChEBI	ribitol	-	builds acid from
25082	33942 ChEBI	ribose	+	assimilation
25082	17814 ChEBI	salicin	+	builds acid from
25082	53258 ChEBI	sodium citrate	-	assimilation
25082	28017 ChEBI	starch	+	hydrolysis
25082	28017 ChEBI	starch	+	assimilation
25082	17992 ChEBI	sucrose	+	assimilation
25082	33954 ChEBI	tagatose	-	builds acid from
25082	33954 ChEBI	tagatose	-	assimilation
25082	32528 ChEBI	turanose	+	builds acid from
25082	32528 ChEBI	turanose	+	assimilation
25082	53424 ChEBI	tween 20	-	hydrolysis
25082	53423 ChEBI	tween 40	+	hydrolysis
25082	53426 ChEBI	tween 80	+	hydrolysis
25082	16199 ChEBI	urea	-	hydrolysis
25082	17151 ChEBI	xylitol	+	assimilation
25082	18222 ChEBI	xylose	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
25082	15688 ChEBI	acetoin
25082	16136 ChEBI	hydrogen sulfide
25082	26672 ChEBI	siderophore

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
25082	15688 ChEBI	acetoin	-
25082	16947 ChEBI	citrate
25082	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
25082	6-phospho-beta-galactosidase	+	3.2.1.85
25082	acid phosphatase	+	3.1.3.2
25082	alkaline phosphatase	+	3.1.3.1
25082	alpha-chymotrypsin	-	3.4.21.1
25082	alpha-fucosidase	-	3.2.1.51
25082	alpha-galactosidase	+	3.2.1.22
25082	alpha-glucosidase	+	3.2.1.20
25082	alpha-mannosidase	+	3.2.1.24
25082	arginine dihydrolase	+	3.5.3.6
25082	beta-glucosidase	+	3.2.1.21
25082	beta-glucuronidase	-	3.2.1.31
25082	catalase	+	1.11.1.6
25082	cystine arylamidase	+	3.4.11.3
25082	cytochrome oxidase	-	1.9.3.1
25082	esterase (C 4)	+
25082	esterase Lipase (C 8)	+
25082	gelatinase	+
25082	leucine arylamidase	+	3.4.11.1
25082	lipase	-
25082	lysine decarboxylase	-	4.1.1.18
25082	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25082	naphthol-AS-BI-phosphohydrolase	+
25082	ornithine decarboxylase	-	4.1.1.17
25082	phenylalanine deaminase	-	4.3.1.5
25082	trypsin	+	3.4.21.4
25082	tryptophan deaminase	+	4.1.99.1
25082	urease	-	3.5.1.5
25082	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
25082	Bulky and rhizosphere soil samples were obtained from a ginseng field	Gochang County	Republic of Korea	KOR	Asia	35	126 35/126	R2A agar (Reasoner's 2A agar)	5 days	30
67770	Ginseng-cultivated soil	Gochang County	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KF915798 (>99% sequence identity) for Intrasporangiaceae from Microbeatlas

Aquatic Samples	17
Soil Samples	148
Animal Samples	133
Plant Samples	46
Total Samples	344

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25082	Phycicoccus ginsengisoli strain DCY87 16S ribosomal RNA gene, partial sequence	KF915798	1466		1462998

GC content

@ref	GC-content (mol%)	Method
67770	72.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.	Kang JP, Kim YJ, Nguyen NL, Hoang VA, Farh ME, Joo SC, Quan LH, Yang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001515	2016

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 )
#25082	J. P. K. Kang, Y. J.,Nguyen, N. L.,Hoang, V. A.,Farh, M. E.,Joo, S. C.,Quan, L. H.,Yang, D. C.: Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil. IJSEM 66: 5320 - 5327 2016 ( DOI 10.1099/ijsem.0.001515 , PubMed 27666743 )
#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 .
#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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Phycicoccus ginsengisoli (DCY 87, KCTC 39635, JCM 31016)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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