Endozoicomonas elysicola | Type strain | DSM 22380, IAM 15107, JCM 21568, KCTC 12372, MKT 110, BCRC 17936, KCTC 23743 | BacDiveID:5855

Strain identifier

BacDive ID: 5855

Type strain:

Species: Endozoicomonas elysicola

Culture col. no.: DSM 22380, IAM 15107, JCM 21568, KCTC 12372, MKT 110, BCRC 17936, KCTC 23743

Strain history: IAM 15107 <-- M. Kurahashi MKT110.

NCBI tax ID(s): 1121862 (strain), 305900 (species)

SI-ID 232853

KCTC 12372, IAM 15107, JCM 21568, DSM 22380

Special Collections

Section

When using BacDive for research please cite our paper

Endozoicomonas elysicola DSM 22380 is a mesophilic, Gram-negative bacterium that was isolated from gastrointestinal tract of the mollusk sea slug Elysia ornata.

Gram-negative
mesophilic
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Endozoicomonadaceae*
	Genus	*Endozoicomonas*
	Species	**Endozoicomonas elysicola**
	Full Scientific Name (LPSN)	Endozoicomonas elysicola Kurahashi and Yokota 2007

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %98.494
[Ref.: #125439]	Gram stain	negative Confidence in %99.7

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

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

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16315]			growth	28 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125438]	Ability of spore formation	no Confidence in %90.24
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.6

Observation

quinones: Q-8

	Pathway	Enzyme coverage	Annotated reactions	External links
	Pathway annotation	Computationally determined by
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	alanine metabolism	93.1	27 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	92.86	26 of 28
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	myo-inositol biosynthesis	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	52.94	9 of 17
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #16315]	Sample type/isolated from	gastrointestinal tract of the mollusk sea slug Elysia ornata
[Ref.: #16315]	Host species	Elysia ornata
[Ref.: #16315]	Geographic location (country and/or sea, region)	Tokyo, seawater off the coast of Izu-Miyake Island (at a depth of 15 m)
[Ref.: #16315]	Country	Japan
[Ref.: #16315]	Country ISO 3 Code	JPN
[Ref.: #16315]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sea slug Elysia ornata collected in seawater off the coast of Izu-Miyake Island
[Ref.: #67770]	Host species	Elysia ornata
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

Global distribution of 16S sequence AB196667 (>99% sequence identity) for Endozoicomonas elysicola subclade from Microbeatlas

Aquatic Samples	279
Soil Samples	54
Animal Samples	42
Plant Samples
Total Samples	375

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

Biosafety level

1

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.: #16315]	Endozoicimonas elysicola gene for 16S ribosomal RNA, partial sequence	AB196667	1437	GenBank ENA	1091502 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Endozoicomonas elysicola DSM 22380	GCA_000373945	scaffold	GenBank ENA	1121862 tax ID
[Ref.: #67770]	Endozoicomonas elysicola DSM 22380	GCA_000710775	scaffold	GenBank ENA	305900 tax ID
[Ref.: #66792]	Endozoicomonas elysicola DSM 22380	1121862.3	wgs	PATRIC	1121862 tax ID	*
[Ref.: #66792]	Endozoicomonas elysicola strain DSM 22380	305900.3	wgs	PATRIC	305900 tax ID	*
[Ref.: #66792]	Endozoicomonas elysicola MKT110, DSM 22380	2515154160	draft	JGI IMG/M	1121862 tax ID	*

[Ref.: #16315]	GC-content	50.4 mol%
[Ref.: #67770]	GC-content	50.4 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Endozoicomonas elysicola DSM 22380 PATRIC: 1121862.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.494	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.205	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.24	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	62.47	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	82.71	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Endozoicomonas elysicola DSM 22380 NCBI: GCA_000373945
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	86.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	82.8
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.6

Availability in culture collections External links

Culture collection no.

DSM 22380, IAM 15107, JCM 21568, KCTC 12372, MKT 110, BCRC 17936, KCTC 23743

SI-ID 232853

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata.	Hyun DW, Shin NR, Kim MS, Oh SJ, Kim PS, Whon TW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.060780-0	2014	*
Phylogeny	Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007.	Nishijima M, Adachi K, Katsuta A, Shizuri Y, Yamasato K	Int J Syst Evol Microbiol	10.1099/ijs.0.042077-0	2012	*
Phylogeny	Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata.	Yang CS, Chen MH, Arun AB, Chen CA, Wang JT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.014357-0	2009	*
Phylogeny	Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata.	Kurahashi M, Yokota A	Syst Appl Microbiol	10.1016/j.syapm.2006.07.003	2006	*

References

#16315

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22380

#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 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#75336

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-ID232853.1 )

#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 .

* These data were automatically processed and therefore are not curated

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