Name: Phycicoccus endophyticus JP6SC6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132430

Type strain:

Species: Phycicoccus endophyticus

Strain Designation: JP6SC6

Culture col. no.: DSM 100020, CGMCC 4.7300, JCM 31784

Strain history: CGMCC 4.7300 <-- S.-W. Liu; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; IP6SC6.

NCBI tax ID(s): 1690220 (species)

Section

Phycicoccus endophyticus JP6SC6 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized bark of Bruguiera gymnorhiza.

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

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Intrasporangiaceae*
	Genus	*Phycicoccus*
	Species	**Phycicoccus endophyticus**
	Full Scientific Name (PNU)	Phycicoccus endophyticus Liu et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43741]	Gram stain	positive
[Ref.: #43741]	Cell length	1.2-2 µm
[Ref.: #43741]	Cell width	0.5-0.8 µm
[Ref.: #43741]	Cell shape	rod-shaped
[Ref.: #43741]	Motility	no

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	no Confidence in %92.093

[Ref.: #43741]	Colony color	greyish-yellow
[Ref.: #43741]	Colony shape	circular
[Ref.: #43741]	Cultivation medium used	TSA plates

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Bennett's agar

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Culture medium growth

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Culture medium

ISP 2 agar

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Culture medium growth

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Culture medium

ISP 3 agar

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium

TSA plates

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Culture medium growth

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Culture medium

Yeast starch agar

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Culture medium growth

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Culture medium

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

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium composition

expand / minimize

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Culture medium

ISP 4 agar

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

		Temperature
[Ref.: #24219]	growth	28 °C
[Ref.: #43741]	growth	20-42 °C
[Ref.: #43741]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #24219]	Temperature range	mesophilic
[Ref.: #43741]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43741]			optimum	7
[Ref.: #43741]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43741]

Oxygen tolerance

aerobe

[Ref.: #43741]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.937

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43741]		NaCl		growth	0-8	%(w/v)
[Ref.: #43741]		NaCl		optimum	0-2	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43741]	adipate ChEBI	-	assimilation
[Ref.: #43741]	amygdalin ChEBI	+/-	builds acid from
[Ref.: #43741]	arbutin ChEBI	+	builds acid from
[Ref.: #43741]	casein	+	hydrolysis
[Ref.: #43741]	cellobiose ChEBI	+	builds acid from
[Ref.: #43741]	citrate ChEBI	-	assimilation
[Ref.: #43741]	D-arabinose ChEBI	-	assimilation
[Ref.: #43741]	D-arabinose ChEBI	+/-	builds acid from
[Ref.: #43741]	D-arabitol ChEBI	+	builds acid from
[Ref.: #43741]	D-fructose ChEBI	+	builds acid from
[Ref.: #43741]	D-galactose ChEBI	+	builds acid from
[Ref.: #43741]	D-glucose ChEBI	+	assimilation
[Ref.: #43741]	D-glucose ChEBI	+	builds acid from
[Ref.: #43741]	D-lyxose ChEBI	+	builds acid from
[Ref.: #43741]	D-mannitol ChEBI	+	assimilation
[Ref.: #43741]	D-mannose ChEBI	+	assimilation
[Ref.: #43741]	D-mannose ChEBI	+	builds acid from
[Ref.: #43741]	D-tagatose ChEBI	+	builds acid from
[Ref.: #43741]	D-xylose ChEBI	+	builds acid from
[Ref.: #43741]	decanoate ChEBI	-	assimilation
[Ref.: #43741]	esculin ChEBI	+	builds acid from
[Ref.: #43741]	esculin ChEBI	+	degradation
[Ref.: #43741]	gelatin ChEBI	+	hydrolysis
[Ref.: #43741]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43741]	gluconate ChEBI	+	assimilation
[Ref.: #43741]	glucose ChEBI	-	fermentation
[Ref.: #43741]	indole ChEBI	-	reduction
[Ref.: #43741]	lactose ChEBI	+	builds acid from
[Ref.: #43741]	malate ChEBI	+	assimilation
[Ref.: #43741]	maltose ChEBI	+	assimilation
[Ref.: #43741]	maltose ChEBI	+	builds acid from
[Ref.: #43741]	mannitol ChEBI	+	builds acid from
[Ref.: #43741]	methyl D-glucoside ChEBI	+	builds acid from
[Ref.: #43741]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43741]	N-acetylglucosamine ChEBI	+/-	builds acid from
[Ref.: #43741]	nitrate ChEBI	-	reduction
[Ref.: #43741]	phenylacetate ChEBI	-	assimilation
[Ref.: #43741]	salicin ChEBI	+	builds acid from
[Ref.: #43741]	starch ChEBI	-	hydrolysis
[Ref.: #43741]	sucrose ChEBI	+	builds acid from
[Ref.: #43741]	trehalose ChEBI	+	builds acid from
[Ref.: #43741]	turanose ChEBI	+	builds acid from
[Ref.: #43741]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43741]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43741]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43741]	xylitol ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #43741]		hydrogen sulfide ChEBI

	Enzyme	Enzyme activity	EC number
[Ref.: #43741]	acid phosphatase	+	3.1.3.2
[Ref.: #43741]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43741]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43741]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43741]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43741]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43741]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43741]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43741]	beta-galactosidase	-	3.2.1.23
[Ref.: #43741]	beta-glucosidase	+	3.2.1.21
[Ref.: #43741]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43741]	catalase	+	1.11.1.6
[Ref.: #43741]	cystine arylamidase	+	3.4.11.3
[Ref.: #43741]	cytochrome oxidase	+/-	1.9.3.1
[Ref.: #43741]	esterase (C 4)	+
[Ref.: #43741]	esterase Lipase (C 8)	+
[Ref.: #43741]	leucine arylamidase	+	3.4.11.1
[Ref.: #43741]	lipase (C 14)	-
[Ref.: #43741]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43741]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43741]	trypsin	-	3.4.21.4
[Ref.: #43741]	urease	-	3.5.1.5
[Ref.: #43741]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24219]	Sample type/isolated from	surface-sterilized bark of Bruguiera gymnorhiza
[Ref.: #24219]	Host species	Bruguiera gymnorhiza
[Ref.: #24219]	Geographic location (country and/or sea, region)	Guangdong, Zhanjiang Mangrove Forest National Nature Reserve (21° 34' 14'' N 109° 45' 21'' E)
[Ref.: #24219]	Country	China
[Ref.: #24219]	Country ISO 3 Code	CHN
[Ref.: #24219]	Continent	Asia
[Ref.: #24219]	Geographic location	21.1120°/110.3090°

[Ref.: #43741]	Sample type/isolated from	Surface-sterilized bark of Bruguiera gymnorhiza collected from Zhanjiang Mangrove Forest National Nature Reserve
[Ref.: #43741]	Geographic location (country and/or sea, region)	Guangdong
[Ref.: #43741]	Country	China
[Ref.: #43741]	Country ISO 3 Code	CHN
[Ref.: #43741]	Continent	Asia
[Ref.: #43741]	Geographic location	21.5700°/109.7550°

[Ref.: #67770]	Sample type/isolated from	Surface-sterilized bark of Bruguiera gymnorhiza from Zhanjiang Mangrove Forest National Nature Reserve
[Ref.: #67770]	Host species	Bruguiera gymnorhiza
[Ref.: #67770]	Geographic location (country and/or sea, region)	Guangdong
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Environmental	#Terrestrial	#Forest
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Bark
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT327645 (>99% sequence identity) for Phycicoccus endophyticus subclade from Microbeatlas

Aquatic Samples	669
Soil Samples	874
Animal Samples	412
Plant Samples	20
Total Samples	1975

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

[Ref.: #24219]

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.: #24219]	Phycicoccus endophyticus strain IP6SC6 16S ribosomal RNA gene, partial sequence	KT327645	1487	ENA	1690220 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phycicoccus endophyticus strain JCM 31784 chromosome, complete genome	CP060712		ENA	1690220 tax ID
[Ref.: #66792]	Phycicoccus endophyticus JCM 31784	GCA_014395645	complete	GenBank	1690220 tax ID	*
[Ref.: #66792]	Phycicoccus endophyticus CGMCC 4.7300	GCA_014646175	contig	GenBank	1690220 tax ID	*
[Ref.: #66792]	Phycicoccus endophyticus strain CGMCC 4.7300	1690220.5	wgs	PATRIC	1690220 tax ID	*
[Ref.: #66792]	Phycicoccus endophyticus strain JCM 31784	1690220.4	complete	PATRIC	1690220 tax ID	*
[Ref.: #66792]	Phycicoccus endophyticus JCM 31784	2894037358	complete	JGI IMG/M	1690220 tax ID	*

[Ref.: #24219]

GC-content

72.5 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phycicoccus endophyticus strain JCM 31784 PATRIC: 1690220.4
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	anaerobic	no	94.323	yes
[Ref.: #69480]	spore-forming	no	99.937	yes
[Ref.: #69480]	thermophile	no	99.685	no
[Ref.: #69480]	motile	no	92.093	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Phycicoccus endophyticus strain JCM 31784 PATRIC: 1690220.4
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #24219]

Culture collection no.

DSM 100020, CGMCC 4.7300, JCM 31784

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phycicoccus endophyticus sp. nov., an endophytic actinobacterium isolated from Bruguiera gymnorhiza.	Liu SW, Xu M, Tuo L, Li XJ, Hu L, Chen L, Li RF, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000842	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 )

#24219

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100020

#43741

Shao-Wei Liu, Min Xu, Li Tuo, Xiao-Jun Li, Lin Hu, Li Chen, Rong-Feng Li, Cheng-Hang Sun: Phycicoccus endophyticus sp. nov., an endophytic actinobacterium isolated from Bruguiera gymnorhiza. IJSEM 66: 1105 - 1111 2016 ( DOI 10.1099/ijsem.0.000842 , PubMed 26653143 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Phycicoccus endophyticus strain JCM 31784

Phycicoccus endophyticus strain JCM 31784

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