Microbulbifer agarilyticus (DSM 19200, JCM 14708, JAMB A3)

Name: Microbulbifer agarilyticus (DSM 19200, JCM 14708, JAMB A3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 467

Type strain

Culture col. no. DSM 19200 JCM 14708 JAMB A3

NCBI tax ID(s) 260552

Special Collections DSMZ JCM Literature strains

Links

Microbulbifer agarilyticus DSM 19200 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from deep-sea bacterial mat.

Gram-negative rod-shaped facultative anaerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 402863

JCM 14708,DSM 19200

@ref 20215

Last LPSN update 2025-12-16 09:46:52

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Microbulbiferaceae

Genus Microbulbifer

Species Microbulbifer agarilyticus

Full scientific name Microbulbifer agarilyticus Miyazaki et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
32443	negative	5 µm	0.55 µm	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7963	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
7963	positive	growth	30	mesophilic
32443	positive	growth	31-40
32443	positive	optimum	33	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
32443	positive	optimum	7.75
32443	positive	growth	6.5-9.5

Physiology and metabolism

Oxygen tolerance

32443

Oxygen tolerancefacultative anaerobe

Compound production

67770

CompoundThermostable beta-agarase

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32443	NaCl	positive	growth	<7 %
32443	NaCl	positive	optimum	2.5 %

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32443	17057 ChEBI	cellobiose	+	carbon source
32443	17234 ChEBI	glucose	+	carbon source
32443	17306 ChEBI	maltose	+	carbon source
32443	17632 ChEBI	nitrate	+	reduction
32443	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32443	catalase	+	1.11.1.6
32443	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	octane oxidation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	aerobactin biosynthesis	100	1 of 1
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	propionate fermentation	80	8 of 10
66794	starch degradation	80	8 of 10
66794	factor 420 biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	polyamine pathway	73.91	17 of 23
66794	d-xylose degradation	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	lipid metabolism	70.97	22 of 31
66794	urea cycle	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	histidine metabolism	68.97	20 of 29
66794	alanine metabolism	68.97	20 of 29
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	nitrate assimilation	66.67	6 of 9
66794	cysteine metabolism	66.67	12 of 18
66794	arginine metabolism	66.67	16 of 24
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	methane metabolism	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	tyrosine metabolism	64.29	9 of 14
66794	non-pathway related	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	tryptophan metabolism	60.53	23 of 38
66794	pyrimidine metabolism	60	27 of 45
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	degradation of pentoses	57.14	16 of 28
66794	d-mannose degradation	55.56	5 of 9
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	degradation of sugar acids	52	13 of 25
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	ketogluconate metabolism	50	4 of 8
66794	alginate biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	oxidative phosphorylation	43.96	40 of 91
66794	propanol degradation	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	ascorbate metabolism	36.36	8 of 22
66794	metabolism of disaccharids	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	toluene degradation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7963	deep-sea bacterial mat	Sagami Bay	Japan	JPN	Asia
67770	Sediment in Sagami Bay, at a depth of 1,174 m		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB158515 (>99% sequence identity) for Microbulbifer agarilyticus from Microbeatlas

Aquatic Samples	771
Soil Samples	67
Animal Samples	42
Plant Samples	28
Total Samples	908

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7963	1	Risk group (German classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7963	Microbulbifer agarilyticus gene for 16S rRNA, partial sequence, strain: JAMB A3	AB158515	1490		260552
124043	Microbulbifer agarilyticus strain JAMB A3 16S ribosomal RNA gene, partial sequence.	KY034407	1343		260552

GC content

@ref	GC-content (mol%)
7963	55.2
67770	55.2

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic insights into biosynthetic gene cluster diversity and structural variability in marine bacteria.	Al-Siyabi N, Al-Ansari A, Abri MAA, Sivakumar N.	Sci Rep	10.1038/s41598-025-21523-3	2025
	Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty.	Zhong W, Agarwal V.	Beilstein J Org Chem	10.3762/bjoc.20.146	2024
Phylogeny	Microbiological Characterization of the Biofilms Colonizing Bioplastics in Natural Marine Conditions: A Comparison between PHBV and PLA.	Marin A, Feijoo P, de Llanos R, Carbonetto B, Gonzalez-Torres P, Tena-Medialdea J, Garcia-March JR, Gamez-Perez J, Cabedo L.	Microorganisms	10.3390/microorganisms11061461	2023
Enzymology	Isolation and Characterization of a Glycosyl Hydrolase Family 16 beta-Agarase from a Mangrove Soil Metagenomic Library.	Mai Z, Su H, Zhang S.	Int J Mol Sci	10.3390/ijms17081360	2016
Enzymology	Molecular cloning, overexpression, and enzymatic characterization of glycosyl hydrolase family 16 beta-Agarase from marine bacterium Saccharophagus sp. AG21 in Escherichia coli.	Lee Y, Oh C, De Zoysa M, Kim H, Wickramaarachchi WD, Whang I, Kang DH, Lee J.	J Microbiol Biotechnol	10.4014/jmb.1209.09009	2013
	Shewanella algae and Microbulbifer elongatus from marine macro-algae - isolation and characterization of agar-hydrolysing bacteria.	Kandasamy KP, Subramanian RK, Srinivasan R, Ragunath S, Balaji G, Gracy M, Latha K.	Access Microbiol	10.1099/acmi.0.000170	2020
	Extracellular expression of a novel beta-agarase from Microbulbifer sp. Q7, isolated from the gut of sea cucumber.	Su Q, Jin T, Yu Y, Yang M, Mou H, Li L.	AMB Express	10.1186/s13568-017-0525-8	2017
Genetics	Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation.	Harada M, Ito K, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S.	G3 (Bethesda)	10.1534/g3.118.200978	2019
	Isolation and Characterization of a Novel Cold-Adapted Esterase, MtEst45, from Microbulbifer thermotolerans DAU221.	Lee YS.	Front Microbiol	10.3389/fmicb.2016.00218	2016
Enzymology	Characterization of AlgMsp, an alginate lyase from Microbulbifer sp. 6532A.	Swift SM, Hudgens JW, Heselpoth RD, Bales PM, Nelson DC.	PLoS One	10.1371/journal.pone.0112939	2014
Enzymology	Crystal structure of a cold-active protease (Pro21717) from the psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, at 1.4 Å resolution: Structural adaptations to cold and functional analysis of a laundry detergent enzyme.	Park HJ, Lee CW, Kim D, Do H, Han SJ, Kim JE, Koo BH, Lee JH, Yim JH.	PLoS One	10.1371/journal.pone.0191740	2018
Phylogeny	Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove.	Vashist P, Nogi Y, Ghadi SC, Verma P, Shouche YS	Int J Syst Evol Microbiol	10.1099/ijs.0.042978-0	2012
Phylogeny	Microbulbifer agarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov., agar-degrading bacteria isolated from deep-sea sediment.	Miyazaki M, Nogi Y, Ohta Y, Hatada Y, Fujiwara Y, Ito S, Horikoshi K	Int J Syst Evol Microbiol	10.1099/ijs.0.65507-0	2008

References

#7963	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19200
#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 )
#32443	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 #28665 (see below)
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Microbulbifer agarilyticus (DSM 19200, JCM 14708, JAMB A3)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Compound production

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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