Name: Echinicola strongylocentroti MEBiC 08714
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133368

Type strain:

Species: Echinicola strongylocentroti

Culture col. no.: MEBiC 08714, KCTC 52052, JCM 31307

Strain history: S. S. Bae; Natl. Mar. Biodivers. Inst. of Korea, South Korea; MEBiC08714.

NCBI tax ID(s): 1795355 (species)

Special Collections

Section

Echinicola strongylocentroti MEBiC 08714 is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and has a yellowish-orange pigmentation.

colony-forming
Gram-negative
motile
pigmented
rod-shaped
aerobe
heterotroph
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Cyclobacteriaceae*
	Genus	*Echinicola*
	Species	**Echinicola strongylocentroti**
	Full Scientific Name (LPSN)	Echinicola strongylocentroti Jung et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25221]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.5

[Ref.: #25221]	Cell length	1.4-2.0 µm

[Ref.: #25221]	Cell width	0.5-0.6 µm

[Ref.: #25221]	Cell shape	rod-shaped

[Ref.: #25221]	Motility	yes

[Ref.: #25221]	Colony color	yellowish-orange
[Ref.: #25221]	Colony shape	circular
[Ref.: #25221]	Incubation period	2-3 days
[Ref.: #25221]	Cultivation medium used	marine agar (MA)

[Ref.: #25221]	Pigment production	yes
[Ref.: #25221]	Pigmentation color	yellowish-orange
[Ref.: #25221]	Pigment production	no
[Ref.: #25221]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25221]

Culture medium

marine agar (MA)

[Ref.: #25221]

Culture medium growth

		Temperature
[Ref.: #25221]	growth	20.0-35.0 °C
[Ref.: #25221]	optimum	25 °C
[Ref.: #67770]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #25221]			optimum	7
[Ref.: #25221]			growth	6.0-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25221]

Oxygen tolerance

aerobe

[Ref.: #25221]

Nutrition type

heterotroph

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25221]		NaCl		growth	0.0-13.0	%(w/v)
[Ref.: #25221]		NaCl		optimum	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25221]	(-)-quinic acid ChEBI	-	respiration
[Ref.: #25221]	2,3-butanediol ChEBI	-	respiration
[Ref.: #25221]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25221]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #25221]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #25221]	2-oxopentanoate ChEBI	-	respiration
[Ref.: #25221]	3-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25221]	4-hydroxy-L-proline ChEBI	-	respiration
[Ref.: #25221]	4-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25221]	4-hydroxyphenylacetic acid ChEBI	-	respiration
[Ref.: #25221]	acetate ChEBI	-	respiration
[Ref.: #25221]	agar ChEBI	+	hydrolysis
[Ref.: #25221]	alpha-cyclodextrin ChEBI	-	respiration
[Ref.: #25221]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #25221]	alpha-lactose ChEBI	+	respiration
[Ref.: #25221]	bromosuccinate ChEBI	-	respiration
[Ref.: #25221]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #25221]	carnitine ChEBI	-	respiration
[Ref.: #25221]	cellobiose ChEBI	+	respiration
[Ref.: #25221]	cis-aconitate ChEBI	-	respiration
[Ref.: #25221]	citrate ChEBI	-	respiration
[Ref.: #25221]	D-alanine ChEBI	-	respiration
[Ref.: #25221]	D-arabitol ChEBI	-	respiration
[Ref.: #25221]	D-fructose ChEBI	+	respiration
[Ref.: #25221]	D-galactonic acid lactone ChEBI	-	respiration
[Ref.: #25221]	D-galactose ChEBI	+	respiration
[Ref.: #25221]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #25221]	D-glucarate ChEBI	-	respiration
[Ref.: #25221]	D-gluconate ChEBI	+	respiration
[Ref.: #25221]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #25221]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #25221]	D-glucuronate ChEBI	-	respiration
[Ref.: #25221]	D-mannitol ChEBI	-	respiration
[Ref.: #25221]	D-mannose ChEBI	+	respiration
[Ref.: #25221]	D-psicose ChEBI	-	respiration
[Ref.: #25221]	D-serine ChEBI	-	respiration
[Ref.: #25221]	D-sorbitol ChEBI	-	respiration
[Ref.: #25221]	dextrin ChEBI	-	respiration
[Ref.: #25221]	erythritol ChEBI	-	respiration
[Ref.: #25221]	esculin ChEBI	+	hydrolysis
[Ref.: #25221]	ethanolamine ChEBI	-	respiration
[Ref.: #25221]	formate ChEBI	-	respiration
[Ref.: #25221]	gamma-aminobutyric acid ChEBI	-	respiration
[Ref.: #25221]	gentiobiose ChEBI	+	respiration
[Ref.: #25221]	glucose ChEBI	-	fermentation
[Ref.: #25221]	glucose 1-phosphate ChEBI	-	respiration
[Ref.: #25221]	glucuronamide ChEBI	-	respiration
[Ref.: #25221]	glycerol ChEBI	-	respiration
[Ref.: #25221]	glycerol 1-phosphate ChEBI	-	respiration
[Ref.: #25221]	glycogen ChEBI	-	respiration
[Ref.: #25221]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #25221]	glycyl-l-glutamate ChEBI	-	respiration
[Ref.: #25221]	inosine ChEBI	-	respiration
[Ref.: #25221]	itaconate ChEBI	-	respiration
[Ref.: #25221]	L-alaninamide ChEBI	+	respiration
[Ref.: #25221]	L-alanine ChEBI	+	respiration
[Ref.: #25221]	L-alanylglycine ChEBI	-	respiration
[Ref.: #25221]	L-arabinose ChEBI	-	respiration
[Ref.: #25221]	L-asparagine ChEBI	-	respiration
[Ref.: #25221]	L-aspartate ChEBI	-	respiration
[Ref.: #25221]	L-fucose ChEBI	-	respiration
[Ref.: #25221]	L-glutamate ChEBI	-	respiration
[Ref.: #25221]	L-histidine ChEBI	-	respiration
[Ref.: #25221]	L-leucine ChEBI	-	respiration
[Ref.: #25221]	L-ornithine ChEBI	-	respiration
[Ref.: #25221]	L-phenylalanine ChEBI	-	respiration
[Ref.: #25221]	L-proline ChEBI	-	respiration
[Ref.: #25221]	L-pyroglutamic acid ChEBI	-	respiration
[Ref.: #25221]	L-rhamnose ChEBI	-	respiration
[Ref.: #25221]	L-serine ChEBI	-	respiration
[Ref.: #25221]	L-threonine ChEBI	-	respiration
[Ref.: #25221]	lactate ChEBI	-	respiration
[Ref.: #25221]	lactulose ChEBI	+	respiration
[Ref.: #25221]	malonate ChEBI	-	respiration
[Ref.: #25221]	maltose ChEBI	+	respiration
[Ref.: #25221]	melibiose ChEBI	+	respiration
[Ref.: #25221]	methyl beta-D-glucopyranoside ChEBI	+	respiration
[Ref.: #25221]	methyl pyruvate ChEBI	+	respiration
[Ref.: #25221]	monomethyl succinate ChEBI	-	respiration
[Ref.: #25221]	myo-inositol ChEBI	-	respiration
[Ref.: #25221]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #25221]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #25221]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #25221]	nitrate ChEBI	-	reduction
[Ref.: #25221]	phenylethylamine ChEBI	-	respiration
[Ref.: #25221]	propionate ChEBI	-	respiration
[Ref.: #25221]	putrescine ChEBI	-	respiration
[Ref.: #25221]	raffinose ChEBI	-	respiration
[Ref.: #25221]	ribitol ChEBI	-	respiration
[Ref.: #25221]	sebacic acid ChEBI	-	respiration
[Ref.: #25221]	skimmed milk	-	hydrolysis
[Ref.: #25221]	starch ChEBI	+	hydrolysis
[Ref.: #25221]	succinamate ChEBI	-	respiration
[Ref.: #25221]	succinate ChEBI	-	respiration
[Ref.: #25221]	sucrose ChEBI	+	respiration
[Ref.: #25221]	thymidine ChEBI	-	respiration
[Ref.: #25221]	trehalose ChEBI	+	respiration
[Ref.: #25221]	tryptophan ChEBI	-	energy source
[Ref.: #25221]	turanose ChEBI	+	respiration
[Ref.: #25221]	tween 40 ChEBI	-	respiration
[Ref.: #25221]	tween 80 ChEBI	-	respiration
[Ref.: #25221]	uridine ChEBI	-	respiration
[Ref.: #25221]	urocanic acid ChEBI	-	respiration
[Ref.: #25221]	xylitol ChEBI	-	respiration
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25221]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25221]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25221]	acid phosphatase	+	3.1.3.2
[Ref.: #25221]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25221]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25221]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25221]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25221]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25221]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25221]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25221]	beta-galactosidase	-	3.2.1.23
[Ref.: #25221]	beta-glucosidase	+	3.2.1.21
[Ref.: #25221]	beta-glucuronidase	+	3.2.1.31
[Ref.: #25221]	catalase	+	1.11.1.6
[Ref.: #25221]	cystine arylamidase	-	3.4.11.3
[Ref.: #25221]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25221]	esterase (C 4)	+
[Ref.: #25221]	esterase Lipase (C 8)	+
[Ref.: #25221]	leucine arylamidase	+	3.4.11.1
[Ref.: #25221]	lipase (C 14)	-
[Ref.: #25221]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25221]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #25221]	trypsin	-	3.4.21.4
[Ref.: #25221]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25221]	urease	-	3.5.1.5
[Ref.: #25221]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25221]

Fatty acid	Percentage
C15:0 iso	27.5
C16:1ω7c / C16:1ω6c	20.3
C17:0 iso 3OH	11.5
C17:1 iso ω9c / C16:0 10-methyl	6.3
C15:0 anteiso	5.2
C16:1ω5c	4.7
C17:1ω6c	4.7
anteiso-C17:1 B / iso-C17:1 I	4.7
C15:0 iso 3OH	3.5
C16:0 3OH	1.8
C16:0 iso	1.8
C16:0 iso 3OH	1.2
C16:1 iso H	1.2

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

[Ref.: #25221]	Sample type/isolated from	sea urchin
[Ref.: #25221]	Geographic location (country and/or sea, region)	west edge of the East Sea (also known as the Sea of Japan)
[Ref.: #25221]	Country	Republic of Korea
[Ref.: #25221]	Country ISO 3 Code	KOR
[Ref.: #25221]	Continent	Asia
[Ref.: #25221]	Geographic location	39.8120°/134.4280°
[Ref.: #25221]	Enrichment culture	marine agar 2216 (MA; BD) medium
[Ref.: #25221]	Enrichment culture duration	7 days
[Ref.: #25221]	Enrichment culture temperature	25 ̊C
[Ref.: #25221]	Isolation/enrichment procedure	small piece of the sea urchin was homogenized with 2 ml sterilized sea water

[Ref.: #67770]	Sample type/isolated from	Sea urchin Strongylocentrotus intermedius
[Ref.: #67770]	Host species	Strongylocentrotus intermedius
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Echinodermata

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU647633 (>99% sequence identity) for Echinicola strongylocentroti subclade from Microbeatlas

Aquatic Samples	7
Soil Samples	4
Animal Samples	3
Plant Samples
Total Samples	14

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.: #25221]	Echinicola strongylocentroti strain MEBiC08714 16S ribosomal RNA gene, partial sequence	KU647633	1423	GenBank ENA	1795355 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Echinicola strongylocentroti MEBiC08714	GCA_003260975	complete	GenBank ENA	1795355 tax ID
[Ref.: #66792]	Echinicola strongylocentroti strain MEBiC08714	1795355.3	complete	PATRIC	1795355 tax ID	*

[Ref.: #67770]

GC-content

44.2 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Echinicola strongylocentroti strain MEBiC08714 PATRIC: 1795355.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.834	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.815	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.7	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.481	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87	no

Availability in culture collections External links

[Ref.: #25221]

Culture collection no.

MEBiC 08714, KCTC 52052, JCM 31307

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Echinicola soli sp. nov., isolated from alkaline saline soil.	Xing YT, Xu L, Wang HT, Huang XX, Wang S, Sun JQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004262	2020	*
Phylogeny	Echinicola strongylocentroti sp. nov., isolated from a sea urchin Strongylocentrotus intermedius.	Jung YJ, Yang SH, Kwon KK, Bae SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001691	2017	*

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 )

#25221

Y. J. Y. Jung, S. H.,Kwon, K. K.,Bae, S. S.: Echinicola strongylocentroti sp. nov., isolated from a sea urchin Strongylocentrotus intermedius. IJSEM 67: 670 - 675 2017 ( DOI 10.1099/ijsem.0.001691 , PubMed 27902316 )

#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) .

* These data were automatically processed and therefore are not curated

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Echinicola strongylocentroti strain MEBiC08714

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