Name: Jeotgalibacillus malaysiensis D5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 131358

Type strain:

Species: Jeotgalibacillus malaysiensis

Strain Designation: D5

Culture col. no.: DSM 28777, KCTC 33550

Strain history: <- Kian Mau Goh, Universiti Teknologi Malaysia

NCBI tax ID(s): 1508404 (species)

SI-ID 405296

DSM 28777

Section

Jeotgalibacillus malaysiensis D5 is an aerobe, spore-forming, mesophilic bacterium that was isolated from seawater from a sandy beach.

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	*Caryophanaceae*
	Genus	*Jeotgalibacillus*
	Species	**Jeotgalibacillus malaysiensis**
	Full Scientific Name (LPSN)	Jeotgalibacillus malaysiensis Yaakop et al. 2015

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	yes Confidence in %95.575

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22585]

Culture medium

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

[Ref.: #22585]

Culture medium growth

[Ref.: #22585]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22585]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22585]			growth	30 °C
[Ref.: #67771]			growth	37 °C

[Ref.: #22585]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[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]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	nitrate assimilation	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.: #22585]	Sample type/isolated from	seawater from a sandy beach
[Ref.: #22585]	Geographic location (country and/or sea, region)	Johor state, Desaru Beach
[Ref.: #22585]	Country	Malaysia
[Ref.: #22585]	Country ISO 3 Code	MYS
[Ref.: #22585]	Continent	Asia
[Ref.: #22585]	Geographic location	1.5456°/104.2640°

[Ref.: #67771]	Sample type/isolated from	From sea water collected from a sandy beach in a southern state of Malaysia
[Ref.: #67771]	Country	Malaysia
[Ref.: #67771]	Country ISO 3 Code	MYS
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KJ460028 (>99% sequence identity) for Jeotgalibacillus from Microbeatlas

Aquatic Samples	234
Soil Samples	48
Animal Samples	1026
Plant Samples	18
Total Samples	1326

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

[Ref.: #22585]

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.: #22585]	Jeotgalibacillus malaysiensis strain D5 16S ribosomal RNA gene, partial sequence	KJ460028	1546	ENA	1508404 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Jeotgalibacillus malaysiensis	GCA_000818095	complete	GenBank	1508404 tax ID	*
[Ref.: #66792]	Jeotgalibacillus malaysiensis D5	2636415895	draft	JGI IMG/M	1508404 tax ID	*

[Ref.: #22585]	GC-content	43.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #22585]	GC-content	42.71 mol%	sequence analysis

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: Jeotgalibacillus malaysiensis D5 NCBI: GCA_000818095.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Jeotgalibacillus malaysiensis D5 NCBI: GCA_000818095.1
[Ref.: #69480]	motile	yes	91.098	no
[Ref.: #69480]	flagellated	yes	89.409	no
[Ref.: #69480]	gram-positive	yes	89.583	no
[Ref.: #69480]	anaerobic	no	98.352	yes
[Ref.: #69480]	aerobic	yes	95.787	yes
[Ref.: #69480]	halophile	yes	85.156	no
[Ref.: #69480]	spore-forming	yes	89.199	no
[Ref.: #69480]	glucose-util	yes	89.429	no
[Ref.: #69480]	thermophile	no	97.354	no
[Ref.: #69480]	glucose-ferment	no	89.226	no

Availability in culture collections External links

[Ref.: #22585]

Culture collection no.

DSM 28777, KCTC 33550

[Ref.: #89798]

SI-ID 405296

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Purification and characterization of a novel GH1 beta-glucosidase from Jeotgalibacillus malaysiensis.	Liew KJ, Lim L, Woo HY, Chan KG, Shamsir MS, Goh KM	Int J Biol Macromol	10.1016/j.ijbiomac.2018.04.156	2018	*
Phylogeny	Isolation of Jeotgalibacillus malaysiensis sp. nov. from a sandy beach, and emended description of the genus Jeotgalibacillus.	Yaakop AS, Chan KG, Ee R, Kahar UM, Kon WC, Goh KM	Int J Syst Evol Microbiol	10.1099/ijs.0.000242	2015	*
Genetics	Complete genome of Jeotgalibacillus malaysiensis D5(T) consisting of a chromosome and a circular megaplasmid.	Goh KM, Chan KG, Yaakop AS, Ee R	J Biotechnol	10.1016/j.jbiotec.2015.03.007	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 )

#22585

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28777

#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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#89798

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-ID405296.1 )

* These data were automatically processed and therefore are not curated

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