Mangrovibacterium marinum (DSM 28823, CICC 10903, KCTC 42253)

Name: Mangrovibacterium marinum (DSM 28823, CICC 10903, KCTC 42253)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132971

Type strain

Strain Designation FA423

Culture col. no. DSM 28823 CICC 10903 KCTC 42253 FA423

NCBI tax ID(s) 1639118

Special Collections DSMZ KCTC

History <- Z.-J. Du, Shandong University at Weihai, China; FA423 <- Q. Liu

Links

Mangrovibacterium marinum FA423 is a mesophilic prokaryote that was isolated from coastal marine sediment.

mesophilic genome sequence

Name and taxonomic classification

SI-ID 397491

KCTC 42253,DSM 28823

@ref 20215

Last LPSN update 2026-02-09 11:31:50

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Prolixibacteraceae

Genus Mangrovibacterium

Species Mangrovibacterium marinum

Full scientific name Mangrovibacterium marinum Wu et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24759	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)	Range
24759	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	enterobactin biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
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	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	100	14 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	histidine metabolism	86.21	25 of 29
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B12 metabolism	82.35	28 of 34
66794	pentose phosphate pathway	81.82	9 of 11
66794	vitamin B6 metabolism	81.82	9 of 11
66794	degradation of sugar alcohols	81.25	13 of 16
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	polyamine pathway	78.26	18 of 23
66794	d-mannose degradation	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	lysine metabolism	73.81	31 of 42
66794	degradation of hexoses	72.22	13 of 18
66794	citric acid cycle	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	methionine metabolism	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	degradation of pentoses	67.86	19 of 28
66794	cyanate degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	tyrosine metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	tryptophan metabolism	55.26	21 of 38
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	lipid metabolism	51.61	16 of 31
66794	cyclohexanol degradation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	ethanol fermentation	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	oxidative phosphorylation	49.45	45 of 91
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	factor 420 biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	urea cycle	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	phenol degradation	30	6 of 20
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	androgen and estrogen metabolism	25	4 of 16
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22

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	Latitude	Longitude
24759	coastal marine sediment	Weihai (122° 03' 44.01'' E 37° 32' 01.93'' N)	China	CHN	Asia	37.5339	122.062 37.5339/122.062

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24759	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	ASM304662v1 assembly for Mangrovibacterium marinum DSM 28823	scaffold	GCA_003046625	1639118.3	2734482189	1639118	65.61

GC content

@ref	GC-content (mol%)	Method
24759	47.4	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: Mangrovibacterium marinum DSM 28823
NCBI: GCA_003046625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.80	no
125439	motility	BacteriaNetⓘ	yes	57.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	63.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mangrovibacterium marinum DSM 28823
NCBI: GCA_003046625.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	83.53	no
125438	anaerobic	anaerobicⓘ	no	67.51	no
125438	aerobic	aerobicⓘ	no	65.89	no
125438	spore-forming	spore-formingⓘ	no	86.55	no
125438	thermophilic	thermophileⓘ	no	94.88	yes
125438	flagellated	motile2+ⓘ	no	84.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen.	Laanto E, Ravantti JJ, Sundberg LR.	Microorganisms	10.3390/microorganisms8121919	2020
Phylogeny	Mangrovibacterium lignilyticum sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment.	Sun C, Zeng X, Lai Q, Wang Z, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004305	2020
Phylogeny	Mangrovibacterium marinum sp. nov., isolated from a coastal sediment.	Wu WJ, Zhou YX, Liu Y, Chen GJ, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-015-0452-0	2015

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 )
#24759	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28823
#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 )
#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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Mangrovibacterium marinum (DSM 28823, CICC 10903, KCTC 42253)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003046625

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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