Name: Arenibacter echinorum DSM 23522
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5485

Type strain:

Species: Arenibacter echinorum

Culture col. no.: DSM 23522, KCTC 22013, LMG 22574, KMM 6032

Strain history: <- KCTC; KCTC 22013 <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia

NCBI tax ID(s): 440515 (species)

SI-ID 132526

LMG 22574, KCTC 22013, DSM 23522

Section

Arenibacter echinorum DSM 23522 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin Strongylocentrotus intermedius.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Arenibacter*
	Species	**Arenibacter echinorum**
	Full Scientific Name (LPSN)	Arenibacter echinorum Nedashkovskaya et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32280]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #32280]	Cell length	2.1 µm

[Ref.: #32280]	Cell width	0.45 µm

[Ref.: #32280]	Cell shape	rod-shaped

[Ref.: #32280]	Motility	yes

[Ref.: #32280]	Flagellum arrangement	gliding

[Ref.: #32280]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17258]

Culture medium

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

[Ref.: #17258]

Culture medium growth

[Ref.: #17258]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17258]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17258]	growth	28 °C
[Ref.: #32280]	growth	04-35 °C
[Ref.: #32280]	optimum	25 °C

[Ref.: #17258]	Temperature range	mesophilic
[Ref.: #32280]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32280]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32280]		NaCl		growth	0-8	%
[Ref.: #32280]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32280]	arabinose ChEBI	+	carbon source
[Ref.: #32280]	cellobiose ChEBI	+	carbon source
[Ref.: #32280]	citrate ChEBI	+	carbon source
[Ref.: #32280]	dextrin ChEBI	+	carbon source
[Ref.: #32280]	glucose ChEBI	+	carbon source
[Ref.: #32280]	lactate ChEBI	+	carbon source
[Ref.: #32280]	lactose ChEBI	+	carbon source
[Ref.: #32280]	malate ChEBI	+	carbon source
[Ref.: #32280]	maltose ChEBI	+	carbon source
[Ref.: #32280]	mannitol ChEBI	+	carbon source
[Ref.: #32280]	mannose ChEBI	+	carbon source
[Ref.: #32280]	melibiose ChEBI	+	carbon source
[Ref.: #32280]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #32280]	raffinose ChEBI	+	carbon source
[Ref.: #32280]	rhamnose ChEBI	+	carbon source
[Ref.: #32280]	sucrose ChEBI	+	carbon source
[Ref.: #32280]	trehalose ChEBI	+	carbon source
[Ref.: #32280]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32280]	acid phosphatase	+	3.1.3.2
[Ref.: #32280]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32280]	alpha-galactosidase	+	3.2.1.22
[Ref.: #32280]	catalase	+	1.11.1.6
[Ref.: #32280]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #17258]	Sample type/isolated from	sea urchin Strongylocentrotus intermedius
[Ref.: #17258]	Host species	Strongylocentrotus intermedius
[Ref.: #17258]	Geographic location (country and/or sea, region)	Troitsa Bay, Gulf of Peter the Great, Sea of Japan
[Ref.: #17258]	Country	Japan
[Ref.: #17258]	Country ISO 3 Code	JPN
[Ref.: #17258]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Echinodermata
#Environmental	#Aquatic	#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF536748 (>99% sequence identity) for Arenibacter from Microbeatlas

Aquatic Samples	7063
Soil Samples	1235
Animal Samples	925
Plant Samples	168
Total Samples	9391

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

[Ref.: #17258]

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.: #17258]	Arenibacter echinorum strain KMM 6032 16S ribosomal RNA gene, partial sequence	EF536748	1431	ENA	440515 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arenibacter echinorum DSM 23522	GCA_003259375	scaffold	GenBank	440515 tax ID	*
[Ref.: #66792]	Arenibacter echinorum strain DSM 23522	440515.3	wgs	PATRIC	440515 tax ID	*
[Ref.: #66792]	Arenibacter echinorum DSM 23522	2593339296	draft	JGI IMG/M	440515 tax ID	*

[Ref.: #17258]	GC-content	39-40 mol%
[Ref.: #32280]	GC-content	39.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Arenibacter echinorum DSM 23522 NCBI: GCA_003259375.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arenibacter echinorum DSM 23522 NCBI: GCA_003259375.1
[Ref.: #69480]	motile	no	88.736	no
[Ref.: #69480]	flagellated	no	94.537	no
[Ref.: #69480]	gram-positive	no	97.826	yes
[Ref.: #69480]	anaerobic	no	99.649	no
[Ref.: #69480]	aerobic	yes	91.581	yes
[Ref.: #69480]	halophile	no	86.078	yes
[Ref.: #69480]	spore-forming	no	96.092	no
[Ref.: #69480]	glucose-util	yes	90.79	yes
[Ref.: #69480]	thermophile	no	99.252	yes
[Ref.: #69480]	glucose-ferment	no	88.31	no

Availability in culture collections External links

[Ref.: #17258]

Culture collection no.

DSM 23522, KCTC 22013, LMG 22574, KMM 6032

[Ref.: #74972]

SI-ID 132526

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat.	Jeong SH, Jin HM, Kim JM, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.040683-0	2012	*
Phylogeny	Arenibacter echinorum sp. nov., isolated from the sea urchin Strongylocentrotus intermedius.	Nedashkovskaya OI, Kim SB, Lysenko AM, Lee KH, Bae KS, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.65251-0	2007	*

References

#17258

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23522

#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 )

#32280

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28520 (see below)

#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) .

#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 )

#74972

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID132526.1 )

#28520

IJSEM 2655 2007 ( DOI 10.1099/ijs.0.65251-0 , PubMed 17978235 )

* These data were automatically processed and therefore are not curated

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