Jeotgalibacillus malaysiensis (DSM 28777, KCTC 33550, D5)

Name: Jeotgalibacillus malaysiensis (DSM 28777, KCTC 33550, D5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131358

Type strain

Strain Designation D5

Culture col. no. DSM 28777 KCTC 33550 D5

NCBI tax ID(s) 1508404

Special Collections DSMZ KCTC

History DSMZ <- K. M. Goh, UTM, Fac, of Bioscs. and Med. Eng., Skudai, Johor, Malaysia; D5 KCTC <- Kian Mau Goh, Universiti Teknologi Malaysia

Links

Jeotgalibacillus malaysiensis D5 is an aerobe bacterium that was isolated from seawater from a sandy beach.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405296

KCTC 33550,DSM 28777

@ref 20215

Last LPSN update 2026-05-29 08:37:36

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Jeotgalibacillus

Species Jeotgalibacillus malaysiensis

Full scientific name Jeotgalibacillus malaysiensis Yaakop et al. 2015

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22585	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)
22585	positive	growth	30
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	94.12

Spore formation

@ref	Spore formation	Confidence
125439		95.372

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cellulose degradation	100	5 of 5
66794	ceramide biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	valine 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	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	glutathione metabolism	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	degradation of sugar alcohols	81.25	13 of 16
66794	methionine metabolism	80.77	21 of 26
66794	starch degradation	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	non-pathway related	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	citric acid cycle	71.43	10 of 14
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	67.03	61 of 91
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	tryptophan metabolism	65.79	25 of 38
66794	alanine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	lipid metabolism	58.06	18 of 31
66794	propanol degradation	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	sulfate reduction	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	tyrosine metabolism	50	7 of 14
66794	degradation of pentoses	46.43	13 of 28
66794	vitamin B6 metabolism	45.45	5 of 11
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	vitamin B12 metabolism	41.18	14 of 34
66794	degradation of sugar acids	40	10 of 25
66794	glycine metabolism	40	4 of 10
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	metabolism of disaccharids	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	octane oxidation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	lipid A biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sandy

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
22585	seawater from a sandy beach	Johor state, Desaru Beach	Malaysia	MYS	Asia	1.5456	104.264 1.5456/104.264
67771	From sea water collected from a sandy beach in a southern state of Malaysia		Malaysia	MYS	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22585	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	ASM81809v1 assembly for Jeotgalibacillus malaysiensis D5	complete	GCA_000818095	1508404.3	2636415895	1508404	67.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22585	Jeotgalibacillus malaysiensis strain D5 16S ribosomal RNA gene, partial sequence	KJ460028	1546		1508404

GC content

@ref	GC-content (mol%)	Method
22585	43.0	high performance liquid chromatography (HPLC)
22585	42.71	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM81809v1 assembly for Jeotgalibacillus malaysiensis D5
NCBI: GCA_000818095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.12	no
125439	gram_stain	BacteriaNetⓘ	variable	68.48	no
125439	spore_formation	BacteriaNetⓘ	yes	95.37	no
125439	motility	BacteriaNetⓘ	yes	83.35	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Jeotgalibacillus malaysiensis D5
NCBI: GCA_000818095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.89	no
125438	anaerobic	anaerobicⓘ	no	97.03	yes
125438	aerobic	aerobicⓘ	yes	78.05	no
125438	spore-forming	spore-formingⓘ	yes	87.89	no
125438	thermophilic	thermophileⓘ	no	87.81	no
125438	flagellated	motile2+ⓘ	yes	83.14	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Efficient Biotransformation of Icariin to Baohuoside I Using Two Novel GH1 beta-Glucosidases.	Zhang X, Wang Y, Zhang T, Yuan Z, Wei Y.	Molecules	10.3390/molecules29225280	2024
	In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes.	Teber R, Asakawa S.	Int J Mol Sci	10.3390/ijms25052566	2024
	Characterization of a New Glucose-Tolerant GH1 beta-Glycosidase from Aspergillus fumigatus with Transglycosylation Activity.	Pereira LMS, Bernardi AV, Gerolamo LE, Pedersoli WR, Carraro CB, Silva RDN, Uyemura SA, Dinamarco TM.	Int J Mol Sci	10.3390/ijms24054489	2023
	Characterization of a Novel Hyperthermophilic GH1 beta-Glucosidase from Acidilobus sp. and Its Application in the Hydrolysis of Soybean Isoflavone Glycosides.	He J, Li Y, Sun X, Zuo D, Wang M, Zheng X, Yu P, Shi P.	Microorganisms	10.3390/microorganisms12030533	2024
	The adolescent and young adult microbiome and its association with substance use: a scoping review.	Browning BD, Kirkland AE, Green R, Engevik M, Alekseyenko AV, Leggio L, Tomko RL, Squeglia LM.	Alcohol Alcohol	10.1093/alcalc/agad055	2024
Genetics	Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses.	Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, Goh KM.	Sci Rep	10.1038/srep33660	2016
Metabolism	Distribution and preservation of the components of the engulfment. What is beyond representative genomes?	Soto-Avila L, Merce RC, Santos W, Castaneda N, Gutierrez-Rios RM.	PLoS One	10.1371/journal.pone.0246651	2021
Genetics	Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes.	Galperin MY, Yutin N, Wolf YI, Vera Alvarez R, Koonin EV.	J Bacteriol	10.1128/jb.00079-22	2022
Transcriptome	Osmotic stress induces long-term biofilm survival in Liberibacter crescens.	Padgett-Pagliai KA, Pagliai FA, da Silva DR, Gardner CL, Lorca GL, Gonzalez CF.	BMC Microbiol	10.1186/s12866-022-02453-w	2022
Enzymology	High Diversity of beta-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals.	Su H, Xiao Z, Yu K, Zhang Q, Lu C, Wang G, Wang Y, Liang J, Huang W, Huang X, Wei F.	Int J Mol Sci	10.3390/ijms22073523	2021
Transcriptome	Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration.	Wang Y, Yang Z, Shi L, Yang R, Guo H, Zhang S, Geng G.	BMC Genomics	10.1186/s12864-021-08284-9	2022
	Characterization of a glucose-tolerant beta-glucosidase from Anoxybacillus sp. DT3-1.	Chan CS, Sin LL, Chan KG, Shamsir MS, Manan FA, Sani RK, Goh KM.	Biotechnol Biofuels	10.1186/s13068-016-0587-x	2016
	Revealing the Saline Adaptation Strategies of the Halophilic Bacterium Halomonas beimenensis through High-throughput Omics and Transposon Mutagenesis Approaches.	Chen YH, Lu CW, Shyu YT, Lin SS.	Sci Rep	10.1038/s41598-017-13450-9	2017
	Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens.	Salvador M, Argandona M, Naranjo E, Piubeli F, Nieto JJ, Csonka LN, Vargas C.	Front Microbiol	10.3389/fmicb.2018.01845	2018
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
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
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

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 .
#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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Jeotgalibacillus malaysiensis (DSM 28777, KCTC 33550, D5)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000818095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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