Endozoicomonas elysicola (DSM 22380, IAM 15107, JCM 21568)

Name: Endozoicomonas elysicola (DSM 22380, IAM 15107, JCM 21568)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5855

Type strain

Culture col. no. DSM 22380 IAM 15107 JCM 21568 KCTC 12372 MKT 110 2 more

NCBI tax ID(s) 1121862 305900

Special Collections DSMZ JCM KCTC

History <- KCTC <- M. Kurahashi, Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan IAM 15107 <-- M. Kurahashi MKT110.

Links

Endozoicomonas elysicola DSM 22380 is a mesophilic prokaryote that was isolated from gastrointestinal tract of the mollusk sea slug Elysia ornata.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 232853

KCTC 12372,IAM 15107,JCM 21568,DSM 22380

@ref 20215

Last LPSN update 2026-02-09 11:19:04

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Endozoicomonadaceae

Genus Endozoicomonas

Species Endozoicomonas elysicola

Full scientific name Endozoicomonas elysicola Kurahashi and Yokota 2007

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.494
125439	negative	99.7

Multimedia

@ref:	66793
multimedia content:	EM_DSM_22380_1.jpg
multimedia.multimedia content:	EM_DSM_22380_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_22380_2.jpg
multimedia.multimedia content:	EM_DSM_22380_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_22380_3.jpg
multimedia.multimedia content:	EM_DSM_22380_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_22380_4.jpg
multimedia.multimedia content:	EM_DSM_22380_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_22380_5.jpg
multimedia.multimedia content:	EM_DSM_22380_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16315	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16315	positive	growth	28	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		90.24
125439		99.6

Observation

67770

Observationquinones: Q-8

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16315	gastrointestinal tract of the mollusk sea slug Elysia ornata	Elysia ornata	Tokyo, seawater off the coast of Izu-Miyake Island (at a depth of 15 m)	Japan	JPN	Asia
67770	Sea slug Elysia ornata collected in seawater off the coast of Izu-Miyake Island	Elysia ornata		Japan	JPN	Asia

Taxonmaps

69479

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16315	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM71077v1 assembly for Endozoicomonas elysicola DSM 22380	scaffold	GCA_000710775	305900.3	2574179787	305900	74
67770	ASM37394v1 assembly for Endozoicomonas elysicola DSM 22380	scaffold	GCA_000373945	1121862.3	2515154160	1121862	71.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16315	Endozoicimonas elysicola gene for 16S ribosomal RNA, partial sequence	AB196667	1437		1091502

GC content

@ref	GC-content (mol%)	Method
16315	50.4
67770	50.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Endozoicomonas elysicola DSM 22380
NCBI: GCA_000373945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	86.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	motility	BacteriaNetⓘ	yes	82.80	no
125439	spore_formation	BacteriaNetⓘ	no	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Endozoicomonas elysicola DSM 22380
PATRIC: 1121862.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	94.21	no
125438	spore-forming	spore-formingⓘ	no	90.24	no
125438	aerobic	aerobicⓘ	yes	62.47	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	82.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity.	Qi W, Cascarano MC, Schlapbach R, Katharios P, Vaughan L, Seth-Smith HMB.	Genome Biol Evol	10.1093/gbe/evy092	2018
Pathogenicity	The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes.	Collins FWJ, Walsh CJ, Gomez-Sala B, Guijarro-Garcia E, Stokes D, Jakobsdottir KB, Kristjansson K, Burns F, Cotter PD, Rea MC, Hill C, Ross RP.	Gut Microbes	10.1080/19490976.2021.1921924	2021
	Whole-genome sequences of three symbiotic endozoicomonas strains.	Neave MJ, Michell CT, Apprill A, Voolstra CR.	Genome Announc	10.1128/genomea.00802-14	2014
	Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral.	Ide K, Nishikawa Y, Maruyama T, Tsukada Y, Kogawa M, Takeda H, Ito H, Wagatsuma R, Miyaoka R, Nakano Y, Kinjo K, Ito M, Hosokawa M, Yura K, Suda S, Takeyama H.	Microbiome	10.1186/s40168-022-01395-9	2022
	New glycoside hydrolase families of beta-1,2-glucanases.	Nakajima M, Tanaka N, Motouchi S, Kobayashi K, Shimizu H, Abe K, Hosoyamada N, Abara N, Morimoto N, Hiramoto N, Nakata R, Takashima A, Hosoki M, Suzuki S, Shikano K, Fujimaru T, Imagawa S, Kawadai Y, Wang Z, Kitano Y, Nihira T, Nakai H, Taguchi H.	Protein Sci	10.1002/pro.70147	2025
	Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts.	Schreiber L, Kjeldsen KU, Funch P, Jensen J, Obst M, Lopez-Legentil S, Schramm A.	Front Microbiol	10.3389/fmicb.2016.01042	2016
Genetics	Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host.	Ding JY, Shiu JH, Chen WM, Chiang YR, Tang SL.	Front Microbiol	10.3389/fmicb.2016.00251	2016
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 )
#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 .
#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 .
#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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Endozoicomonas elysicola (DSM 22380, IAM 15107, JCM 21568)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000710775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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