Name: Demequina mangrovi HI08-69
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17842

Type strain:

Species: Demequina mangrovi

Strain Designation: HI08-69

Culture col. no.: DSM 24868, NBRC 105856

Strain history: <- M. Hamada, NBRC, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; HI08-69

NCBI tax ID(s): 1043493 (species)

SI-ID 398995

DSM 24868

Section

Demequina mangrovi HI08-69 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere soil of mangrove .

Gram-positive
ovoid-shaped
facultative anaerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Demequinaceae*
	Genus	*Demequina*
	Species	**Demequina mangrovi**
	Full Scientific Name (LPSN)	Demequina mangrovi (Hamada et al. 2012) Nouioui et al. 2018

Synonym

Lysinimicrobium mangrovi

Information on morphological and physiological properties Morphology

[Ref.: #30414]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30414]	Cell length	0.75 µm

[Ref.: #30414]	Cell width	0.55 µm

[Ref.: #30414]	Cell shape	ovoid-shaped

[Ref.: #30414]	Motility	no

[Ref.: #17793]

Incubation period

2-3 days

[Ref.: #30414]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17793]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #17793]

Culture medium growth

[Ref.: #17793]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17793]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17793]	growth	28 °C
[Ref.: #30414]	growth	15-28 °C
[Ref.: #30414]	optimum	28 °C

[Ref.: #17793]	Temperature range	mesophilic
[Ref.: #30414]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30414]			optimum	7.5
[Ref.: #30414]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30414]

Oxygen tolerance

facultative anaerobe

[Ref.: #30414]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30414]		NaCl		growth	0-7	%

[Ref.: #17793]	Murein short key	A11.33
[Ref.: #17793]	Murein types	A4alpha L-Lys-D-Glu

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30414]	arabinose ChEBI	+	carbon source
[Ref.: #30414]	cellobiose ChEBI	+	carbon source
[Ref.: #30414]	esculin ChEBI	+	hydrolysis
[Ref.: #30414]	fructose ChEBI	+	carbon source
[Ref.: #30414]	galactose ChEBI	+	carbon source
[Ref.: #30414]	glucose ChEBI	+	carbon source
[Ref.: #30414]	glycogen ChEBI	+	carbon source
[Ref.: #30414]	lactose ChEBI	+	carbon source
[Ref.: #30414]	maltose ChEBI	+	carbon source
[Ref.: #30414]	mannose ChEBI	+	carbon source
[Ref.: #30414]	rhamnose ChEBI	+	carbon source
[Ref.: #30414]	ribose ChEBI	+	carbon source
[Ref.: #30414]	salicin ChEBI	+	carbon source
[Ref.: #30414]	sucrose ChEBI	+	carbon source
[Ref.: #30414]	trehalose ChEBI	+	carbon source
[Ref.: #30414]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30414]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	pyrimidine metabolism	93.33	42 of 45
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		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.: #17793]	Sample type/isolated from	rhizosphere soil of mangrove (Bruguiera gymnorhiza)
[Ref.: #17793]	Host species	Bruguiera gymnorhiza
[Ref.: #17793]	Geographic location (country and/or sea, region)	Okinawa, Iriomote Island
[Ref.: #17793]	Country	Japan
[Ref.: #17793]	Country ISO 3 Code	JPN
[Ref.: #17793]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB639012 (>99% sequence identity) for Demequina from Microbeatlas

Aquatic Samples	48
Soil Samples	61
Animal Samples	137
Plant Samples	6
Total Samples	252

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

[Ref.: #17793]

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.: #17793]	Lysinimicrobium mangrovi gene for 16S rRNA, partial sequence	AB639012	1478	ENA	1043493 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Demequina mangrovi DSM 24868	GCA_900109245	contig	GenBank	1043493 tax ID	*
[Ref.: #66792]	Demequina mangrovi NBRC 105856	GCA_000759715	scaffold	GenBank	1043493 tax ID	*
[Ref.: #66792]	Lysinimicrobium mangrovi NBRC 105856	1043493.3	wgs	PATRIC	1043493 tax ID	*
[Ref.: #66792]	Lysinimicrobium mangrovi strain DSM 24868	1043493.4	wgs	PATRIC	1043493 tax ID	*
[Ref.: #66792]	Lysinimicrobium mangrovi DSM 24868	2687453759	draft	JGI IMG/M	1043493 tax ID	*
[Ref.: #66792]	Lysinimicrobium mangrovi NBRC 105856	2700989458	draft	JGI IMG/M	1043493 tax ID	*

[Ref.: #17793]	GC-content	71.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30414]	GC-content	71.7 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: Demequina mangrovi NBRC 105856 NCBI: GCA_000759715.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Demequina mangrovi NBRC 105856 NCBI: GCA_000759715.1
[Ref.: #69480]	motile	yes	72.154	no
[Ref.: #69480]	flagellated	no	88.274	yes
[Ref.: #69480]	gram-positive	yes	90.339	yes
[Ref.: #69480]	anaerobic	no	97.723	yes
[Ref.: #69480]	aerobic	no	68.011	yes
[Ref.: #69480]	halophile	no	78.036	no
[Ref.: #69480]	spore-forming	no	91.726	no
[Ref.: #69480]	glucose-util	yes	87.183	yes
[Ref.: #69480]	thermophile	no	98.377	yes
[Ref.: #69480]	glucose-ferment	no	65.247	no

Availability in culture collections External links

[Ref.: #17793]

Culture collection no.

DSM 24868, NBRC 105856

[Ref.: #86833]

SI-ID 398995

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Proposal of nine novel species of the genus Lysinimicrobium and emended description of the genus Lysinimicrobium.	Hamada M, Shibata C, Saitou S, Tamura T, Komaki H, Ichikawa N, Oguchi A, Hosoyama A, Fujita N, Yamamura H, Hayakawa M, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijsem.0.000587	2015	*
Genetics	Draft Genome Sequence of Lysinimicrobium mangrovi NBRC 105856T, Isolated from the Rhizosphere of a Mangrove.	Hamada M, Ichikawa N, Oguchi A, Fujita N	Genome Announc	10.1128/genomeA.01131-14	2014	*
Phylogeny	Lysinimicrobium mangrovi gen. nov., sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.	Hamada M, Tamura T, Yamamura H, Suzuki KI, Hayakawa M	Int J Syst Evol Microbiol	10.1099/ijs.0.035493-0	2011	*

References

#17793

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24868

#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 )

#30414

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 #26750 (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 )

#86833

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-ID398995.1 )

#26750

IJSEM 1731 2012 ( DOI 10.1099/ijs.0.035493-0 , PubMed 21930679 )

* These data were automatically processed and therefore are not curated

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Demequina mangrovi NBRC 105856

Demequina mangrovi NBRC 105856

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