Name: Marininema mesophilum DSM 45610
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24643

Type strain:

Species: Marininema mesophilum

Culture col. no.: DSM 45610, CCTCC AA 2011006, SCSIO 10219

Strain history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 10219

NCBI tax ID(s): 1048340 (species)

SI-ID 406700

DSM 45610

Section

Marininema mesophilum DSM 45610 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediments from South China Sea.

Gram-positive
spore-forming
aerobe
mesophilic
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Thermoactinomycetaceae*
	Genus	*Marininema*
	Species	**Marininema mesophilum**
	Full Scientific Name (LPSN)	Marininema mesophilum Li et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30395]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21233]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #21233]

Culture medium growth

[Ref.: #21233]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21233]

Culture medium composition

expand / minimize

[Ref.: #21233]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #21233]

Culture medium growth

[Ref.: #21233]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21233]

Culture medium composition

expand / minimize

[Ref.: #21233]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #21233]

Culture medium growth

[Ref.: #21233]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21233]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21233]	growth	28 °C
[Ref.: #30395]	growth	25-35 °C
[Ref.: #30395]	optimum	30 °C

[Ref.: #21233]	Temperature range	mesophilic
[Ref.: #30395]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30395]			optimum	6.5
[Ref.: #30395]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30395]

Oxygen tolerance

aerobe

[Ref.: #30395]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.237

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30395]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[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.: #21233]	Sample type/isolated from	sediments from South China Sea
[Ref.: #21233]	Geographic location (country and/or sea, region)	South China Sea (113° 3.752' E 18° 1.722' N) at a depth of 2105 m
[Ref.: #21233]	Country	China
[Ref.: #21233]	Country ISO 3 Code	CHN
[Ref.: #21233]	Continent	Asia
[Ref.: #21233]	Geographic location	18.0287°/113.0630°
* 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 JN006758 (>99% sequence identity) for Marininema mesophilum from Microbeatlas

Aquatic Samples	55
Soil Samples	302
Animal Samples	133
Plant Samples	32
Total Samples	522

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

[Ref.: #21233]

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.: #21233]	Marininema mesophilum strain SCSIO 10219 16S ribosomal RNA gene, partial sequence	JN006758	1540	ENA	1048340 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marininema mesophilum DSM 45610	GCA_900106775	scaffold	GenBank	1048340 tax ID	*
[Ref.: #66792]	Marininema mesophilum strain DSM 45610	1048340.6	wgs	PATRIC	1048340 tax ID	*
[Ref.: #66792]	Marininema mesophilum DSM 45610	2693429881	draft	JGI IMG/M	1048340 tax ID	*

[Ref.: #21233]	GC-content	46.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30395]	GC-content	46.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Marininema mesophilum DSM 45610 NCBI: GCA_900106775.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Marininema mesophilum DSM 45610 NCBI: GCA_900106775.1
[Ref.: #69480]	motile	no	85.957	no
[Ref.: #69480]	glucose-ferment	no	93.927	no
[Ref.: #69480]	flagellated	no	94.298	no
[Ref.: #69480]	gram-positive	yes	91.312	no
[Ref.: #69480]	anaerobic	no	99.155	yes
[Ref.: #69480]	aerobic	yes	96.192	yes
[Ref.: #69480]	halophile	no	71.27	no
[Ref.: #69480]	spore-forming	yes	93.336	yes
[Ref.: #69480]	thermophile	yes	78.942	no
[Ref.: #69480]	glucose-util	yes	87.022	no

Availability in culture collections External links

[Ref.: #21233]

Culture collection no.

DSM 45610, CCTCC AA 2011006, SCSIO 10219

[Ref.: #88484]

SI-ID 406700

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae.	Zarparvar P, Amoozegar MA, Nikou MM, Schumann P, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.064766-0	2014	*
Phylogeny	Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012.	Zhang XM, He J, Zhang DF, Chen W, Jiang Z, Sahu MK, Sivakumar K, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.052142-0	2013	*
Phylogeny	Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae.	Li J, Zhang GT, Yang J, Tian XP, Wang FZ, Zhang CS, Zhang S, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.035071-0	2011	*

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 )

#21233

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45610

#30395

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 #26732 (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 )

#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 )

#88484

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-ID406700.1 )

#26732

IJSEM 1383 2012 ( DOI 10.1099/ijs.0.035071-0 , PubMed 21828010 )

* These data were automatically processed and therefore are not curated

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