Arthrobacter echini (DSM 29493, KACC 18260, AM23)

Name: Arthrobacter echini (DSM 29493, KACC 18260, AM23)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132484

Type strain

Strain Designation AM23

Culture col. no. DSM 29493 KACC 18260 AM23

NCBI tax ID(s) 1529066

Special Collections DSMZ Literature strains

History <- J.-W. Bae, Kyung Hee Univ., Seoul, Republic of Korea; AM23 <- J. Y. Lee

Links

Arthrobacter echini AM23 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from gut of a purple sea urchin, Heliocidaris crassispina.

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

Name and taxonomic classification

SI-ID 400295

DSM 29493

@ref 20215

Last LPSN update 2026-02-09 11:31:43

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter echini

Full scientific name Arthrobacter echini Lee et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43993	positive	1.2-2.2 µm	1.2-2.2 µm	coccus-shaped
125439	positive					97

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43993	0.1-0.15 mm	dark pink	circular	3 days	Marine agar 2216

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43993	Marine agar (MA)
24273	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)
24273	positive	growth	20
43993	positive	growth	10-25
43993	positive	optimum	20

Culture pH

@ref	Ability	Type	PH	PH range
43993	positive	optimum	7
43993	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

43993

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43993	NaCl	positive	growth	0-8 %(w/v)
43993	NaCl	positive	optimum	1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43993	30916 ChEBI	2-oxoglutarate	+	energy source
43993	16724 ChEBI	4-hydroxybutyrate	+	energy source
43993	30089 ChEBI	acetate	+	energy source
43993	16335 ChEBI	adenosine	+	energy source
43993	17925 ChEBI	alpha-D-glucose	+	energy source
43993	16027 ChEBI	amp	+	energy source
43993	17057 ChEBI	cellobiose	+	energy source
43993	15824 ChEBI	D-fructose	+	energy source
43993	8391 ChEBI	D-gluconate	+	energy source
43993	17634 ChEBI	D-glucose	+	fermentation
43993	16024 ChEBI	D-mannose	+	energy source
43993	17754 ChEBI	glycerol	+	energy source
43993	17596 ChEBI	inosine	+	energy source
43993	75144 ChEBI	lactamide	+	energy source
43993		maltose hydrate	+	energy source
43993	61993 ChEBI	maltotriose	+	energy source
43993	75146 ChEBI	monomethyl succinate	+	energy source
43993	44337 ChEBI	N-acetyl-L-glutamate	+	energy source
43993	18394 ChEBI	palatinose	+	energy source
43993	17272 ChEBI	propionate	+	energy source
43993	15361 ChEBI	pyruvate	+	energy source
43993	143136 ChEBI	succinamate	+	energy source
43993	17992 ChEBI	sucrose	+	energy source
43993	32528 ChEBI	turanose	+	energy source
43993	53426 ChEBI	tween 80	+	energy source
43993	16199 ChEBI	urea	+	fermentation
43993	16704 ChEBI	uridine	+	energy source

Enzymes

@ref	Value	Activity	Ec
43993	acid phosphatase	+	3.1.3.2
43993	alpha-glucosidase	+	3.2.1.20
43993	catalase	+	1.11.1.6
43993	cytochrome oxidase	+	1.9.3.1
43993	esterase (C 4)	+
43993	esterase Lipase (C 8)	+
43993	leucine arylamidase	+	3.4.11.1
43993	naphthol-AS-BI-phosphohydrolase	+
43993	trypsin	+	3.4.21.4
43993	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	starch degradation	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	threonine metabolism	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	cyclohexanol degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	purine metabolism	70.21	66 of 94
66794	propionate fermentation	70	7 of 10
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	lipid metabolism	64.52	20 of 31
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	flavin biosynthesis	60	9 of 15
66794	glycine betaine biosynthesis	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	creatinine degradation	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	glutathione metabolism	57.14	8 of 14
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	oxidative phosphorylation	56.04	51 of 91
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	lysine metabolism	52.38	22 of 42
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	heme metabolism	50	7 of 14
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	ethanol fermentation	50	1 of 2
66794	methionine metabolism	50	13 of 26
66794	lactate fermentation	50	2 of 4
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	vitamin B1 metabolism	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	allantoin degradation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of sugar acids	36	9 of 25
66794	tyrosine metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lipid A biosynthesis	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

43993

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	575
C17:1 iso ω9c / C16:0 10-methyl	225
C15:0 anteiso	46.9
C15:0 iso	25.9
C17:0 anteiso	13.6
C17:0 iso	5.8
C16:0 iso	2.9
C16:0	0.9
C17:1 anteiso ω9c	0.7
C14:0 iso	0.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Host Body-Site	#Gastrointestinal tract	#Stomach
#Host	#Invertebrates (Other)	#Echinodermata
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Host species
24273	gut of a purple sea urchin, Heliocidaris crassispina	Dokdo island, coastal waters	Republic of Korea	KOR	Asia				Heliocidaris crassispina
43993	gut of a purple sea urchin Heliocidaris crassispina collected from the coastal waters of the Korean island Dokdo	Dokdo	Republic of Korea	KOR	Asia	Marine agar 2216	7 days	25

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24273	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM480350v1 assembly for Arthrobacter echini AM23	contig	GCA_004803505	1529066.3	2903061041	1529066	69.75

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24273	Arthrobacter echini strain AM23 16S ribosomal RNA gene, partial sequence	KJ789956	1468		1529066

GC content

@ref	GC-content (mol%)	Method
43993	67.3	real time PCR (RTD-PCR)
24273	67.3	fluorimetric

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arthrobacter echini AM23
NCBI: GCA_004803505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	50.30	no
125439	motility	BacteriaNetⓘ	no	88.00	no
125439	gram_stain	BacteriaNetⓘ	positive	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	85.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina.	Lee JY, Hyun DW, Soo Kim P, Sik Kim H, Shin NR, Yun JH, Jung MJ, Kim MS, Woong Whon T, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.000965	2016

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 )
#24273	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29493
#43993	June-Young Lee, Dong-Wook Hyun, Pil Soo Kim, Hyun Sik Kim, Na-Ri Shin, Ji-Hyun Yun, Mi-Ja Jung, Min-Soo Kim, Tae Woong Whon, Jin-Woo Bae: Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina. IJSEM 66: 1887 - 1893 2016 ( DOI 10.1099/ijsem.0.000965 , PubMed 26868361 )
#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) .
#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 )
#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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Arthrobacter echini (DSM 29493, KACC 18260, AM23)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004803505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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