Amycolatopsis marina (DSM 45569, CGMCC 4.3568, NBRC 104263)

Name: Amycolatopsis marina (DSM 45569, CGMCC 4.3568, NBRC 104263)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13267

Type strain

Strain Designation Ms392A

Culture col. no. DSM 45569 CGMCC 4.3568 NBRC 104263 Ms392A JCM 16121

NCBI tax ID(s) 490629

Special Collections DSMZ JCM Literature strains

Links

Amycolatopsis marina Ms392A is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from ocean-sediment.

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404573

NBRC 104263,JCM 16121,DSM 45569

@ref 20215

Last LPSN update 2025-12-16 09:50:03

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis marina

Full scientific name Amycolatopsis marina Bian et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Confidence
28874	positive
125438		90.5
125439	positive	97.1

Pigmentation

28874

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17661	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17661	positive	growth	28	mesophilic
28874	positive	growth	10-55
28874	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
28874	positive	optimum	7.5
28874	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28874	aerobe
125438	aerobe	91.992
125439	obligate aerobe	95.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28874	NaCl	positive	growth	0.5-12 %
28874	NaCl	positive	optimum	5 %

Observation

67770

Observationquinones: MK-8(H₄), MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28874	17057 ChEBI	cellobiose	+	carbon source
28874	28757 ChEBI	fructose	+	carbon source
28874	28260 ChEBI	galactose	+	carbon source
28874	5291 ChEBI	gelatin	+	carbon source
28874	17306 ChEBI	maltose	+	carbon source
28874	29864 ChEBI	mannitol	+	carbon source
28874	26546 ChEBI	rhamnose	+	carbon source
28874	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28874	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	octane oxidation	100	3 of 3
66794	kanosamine biosynthesis II	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	100	2 of 2
66794	4-hydroxymandelate degradation	100	9 of 9
66794	acetate fermentation	100	4 of 4
66794	aspartate and asparagine metabolism	100	9 of 9
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	phenylmercury acetate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	glycine betaine biosynthesis	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	citric acid cycle	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	histidine metabolism	82.76	24 of 29
66794	proline metabolism	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	factor 420 biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	3-chlorocatechol degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	3-phenylpropionate degradation	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	purine metabolism	78.72	74 of 94
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	non-pathway related	76.32	29 of 38
66794	arginine metabolism	75	18 of 24
66794	phenol degradation	75	15 of 20
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	aclacinomycin biosynthesis	71.43	5 of 7
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	threonine metabolism	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	oxidative phosphorylation	69.23	63 of 91
66794	pyrimidine metabolism	68.89	31 of 45
66794	degradation of sugar alcohols	68.75	11 of 16
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	IAA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	polyamine pathway	60.87	14 of 23
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	D-cycloserine biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of hexoses	55.56	10 of 18
66794	lysine metabolism	54.76	23 of 42
66794	carotenoid biosynthesis	54.55	12 of 22
66794	vitamin B6 metabolism	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	cholesterol biosynthesis	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	chlorophyll metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	methanogenesis from CO2	33.33	4 of 12
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	methane metabolism	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	arachidonic acid metabolism	27.78	5 of 18
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17661	ocean-sediment	South China Sea	China	CHN	Asia
67770	Deep-ocean sediment	South China Sea

Taxonmaps

69479

Global distribution of 16S sequence EU329845 (>99% sequence identity) for Amycolatopsis marina from Microbeatlas

Aquatic Samples	28
Soil Samples	157
Animal Samples	183
Plant Samples	90
Total Samples	458

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17661	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	IMG-taxon 2667527405 annotated assembly for Amycolatopsis marina CGMCC 4.3568	scaffold	GCA_900111885	490629.6	2667527405	490629	65.05

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17661	Amycolatopsis marina strain MS392A 16S ribosomal RNA gene, partial sequence	EU329845	1485		490629

GC content

@ref	GC-content (mol%)	Method
17661	70.1
67770	68.2	genome sequence analysis
67770	70.1	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: Amycolatopsis marina CGMCC 4.3568
NCBI: GCA_900111885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	63.10	no
125439	motility	BacteriaNetⓘ	no	84.40	no
125439	gram_stain	BacteriaNetⓘ	positive	97.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis marina strain CGMCC 4.3568
PATRIC: 490629.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.66	no
125438	anaerobic	anaerobicⓘ	no	95.83	no
125438	spore-forming	spore-formingⓘ	yes	75.60	no
125438	aerobic	aerobicⓘ	yes	91.99	yes
125438	thermophilic	thermophileⓘ	no	93.23	no
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The Rare Actinobacterium Crossiella sp. Is a Potential Source of New Bioactive Compounds with Activity against Bacteria and Fungi.	Gonzalez-Pimentel JL, Dominguez-Monino I, Jurado V, Laiz L, Caldeira AT, Saiz-Jimenez C.	Microorganisms	10.3390/microorganisms10081575	2022
Genetics	Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina.	Gao H, Murugesan B, Hossbach J, Evans SK, Stark WM, Smith MCM	BMC Biotechnol	10.1186/s12896-019-0521-y	2019
Phylogeny	Amycolatopsis flava sp. nov., a halophilic actinomycete isolated from Dead Sea.	Wei X, Jiang Y, Chen X, Jiang Y, Lai H	Antonie Van Leeuwenhoek	10.1007/s10482-015-0542-z	2015
Phylogeny	Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake.	Tang SK, Wang Y, Guan TW, Lee JC, Kim CJ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.012427-0	2009
Phylogeny	Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment.	Bian J, Li Y, Wang J, Song FH, Liu M, Dai HQ, Ren B, Gao H, Hu X, Liu ZH, Li WJ, Zhang LX	Int J Syst Evol Microbiol	10.1099/ijs.0.000026-0	2009

References

#17661	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45569
#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 )
#25314	IJSEM 477 2009 ( DOI 10.1099/ijs.0.000026-0 , PubMed 19244425 )
#28874	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 #25314
#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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Amycolatopsis marina (DSM 45569, CGMCC 4.3568, NBRC 104263)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900111885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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