Name: Amycolatopsis marina Ms392A
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13267

Type strain:

Species: Amycolatopsis marina

Strain Designation: Ms392A

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

Strain history: CGMCC 4.3568 <-- J. Bian et al. Ms392A.

NCBI tax ID(s): 490629 (species)

SI-ID 404573

DSM 45569

Special Collections

Section

Amycolatopsis marina Ms392A is an aerobe, spore-forming, Gram-positive bacterium that was isolated from ocean-sediment.

Gram-positive
spore-forming
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Amycolatopsis*
	Species	**Amycolatopsis marina**
	Full Scientific Name (LPSN)	Amycolatopsis marina Bian et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28874]	Gram stain	positive

[Ref.: #28874]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.5

[Ref.: #28874]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17661]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #17661]

Culture medium growth

[Ref.: #17661]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17661]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17661]	growth	28 °C
[Ref.: #28874]	growth	10-55 °C
[Ref.: #28874]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #28874]			optimum	7.5
[Ref.: #28874]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28874]	Oxygen tolerance	aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %91.992

[Ref.: #69481]

Ability of spore formation

yes Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28874]		NaCl		growth	0.5-12	%
[Ref.: #28874]		NaCl		optimum	5	%

[Ref.: #67770]

Observation

quinones: MK-8(H₄), MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28874]	cellobiose ChEBI	+	carbon source
[Ref.: #28874]	fructose ChEBI	+	carbon source
[Ref.: #28874]	galactose ChEBI	+	carbon source
[Ref.: #28874]	gelatin ChEBI	+	carbon source
[Ref.: #28874]	maltose ChEBI	+	carbon source
[Ref.: #28874]	mannitol ChEBI	+	carbon source
[Ref.: #28874]	rhamnose ChEBI	+	carbon source
[Ref.: #28874]	trehalose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #28874]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	histidine metabolism	82.76	24 of 29
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	3-phenylpropionate degradation	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	non-pathway related	76.32	29 of 38
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	aclacinomycin biosynthesis	71.43	5 of 7
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	daunorubicin biosynthesis	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.: #17661]	Sample type/isolated from	ocean-sediment
[Ref.: #17661]	Geographic location (country and/or sea, region)	South China Sea
[Ref.: #17661]	Country	China
[Ref.: #17661]	Country ISO 3 Code	CHN
[Ref.: #17661]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep-ocean sediment
[Ref.: #67770]	Geographic location (country and/or sea, region)	South China Sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #17661]

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.: #17661]	Amycolatopsis marina strain MS392A 16S ribosomal RNA gene, partial sequence	EU329845	1485	GenBank ENA	490629 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amycolatopsis marina CGMCC 4.3568	GCA_900111885	scaffold	GenBank ENA	490629 tax ID
[Ref.: #66792]	Amycolatopsis marina strain CGMCC 4.3568	490629.6	wgs	PATRIC	490629 tax ID	*
[Ref.: #66792]	Amycolatopsis marina CGMCC 4.3568	2667527405	draft	JGI IMG/M	490629 tax ID	*

[Ref.: #17661]	GC-content	70.1 mol%
[Ref.: #67770]	GC-content	68.2 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	70.1 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Amycolatopsis marina CGMCC 4.3568 NCBI: GCA_900111885.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amycolatopsis marina strain CGMCC 4.3568 PATRIC: 490629.6
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.658	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.825	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	75.598	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	91.992	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.225	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90.5	no

Availability in culture collections External links

[Ref.: #17661]

Culture collection no.

DSM 45569, CGMCC 4.3568, NBRC 104263, JCM 16121

[Ref.: #82471]

SI-ID 404573

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (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) .

#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 .

#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 )

#82471

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-ID404573.1 )

#25314

IJSEM 477 2009 ( DOI 10.1099/ijs.0.000026-0 , PubMed 19244425 )

* These data were automatically processed and therefore are not curated

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Amycolatopsis marina CGMCC 4.3568

Amycolatopsis marina strain CGMCC 4.3568

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