Name: Halobacillus halophilus 3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1327

Type strain:

Species: Halobacillus halophilus

Strain Designation: 3

Culture col. no.: DSM 2266, ATCC 35676, NCIMB 2269, JCM 20832, CCM 3527, CECT 5013, IAM 12846, IAM 13060, KCTC 3685, LMG 17431, NBRC 102448

Strain history: IAM 13060 <-- M. V. Hao and K. Komagata HK 814 <-- CCM 3527 <-- DSM 2266 <-- H. J. Rolf 3.

NCBI tax ID(s): 866895 (strain), 1570 (species)

SI-ID 9982

LMG 17431, ATCC 35676, DSM 2266, NCIMB 2269, CCM 3527, CECT 5013, KCTC 3685, NCIB 2269, IAM 12846, IAM 13060, JCM 2486, JCM 20832, NBRC 102448

Other strains from Halobacillus halophilus

H. halophilus 6, DSM 2500, JCM 20836, IAM 13064
H. halophilus 11, DSM 2501, JCM 20837, IAM 13065
H. halophilus 14, DSM 2502
H. halophilus MA 21, DSM 6116
H. halophilus MA 28, DSM 6117
H. halophilus MA 30, DSM 6118
H. halophilus MA 15, DSM 6120
H. halophilus MA 16, DSM 6121
H. halophilus MA 22, DSM 6123
H. halophilus MA 5, DSM 5938
H. halophilus MA 7, DSM 5939
H. halophilus MA 8, DSM 5965
H. halophilus MA13, DSM 5980
H. halophilus 18, DSM 2503, JCM 20838, IAM 13066
H. halophilus 19, strain 19, DSM 2504
H. halophilus 20, DSM 2505
H. halophilus 23, DSM 2506, JCM 20839, IAM 13067
H. halophilus 24, DSM 2507, JCM 20840, IAM 13068
H. halophilus 26, DSM 2508
H. halophilus 27, DSM 2509
H. halophilus JCM 20833, IAM 13061
H. halophilus JCM 20834, IAM 13062
H. halophilus JCM 20835, IAM 13063
H. halophilus JCM 20841, IAM 13069
H. halophilus JCM 20842, IAM 13070
H. halophilus JCM 20843, IAM 13071

Section

Halobacillus halophilus 3 is an obligate aerobe, moderately halophilic, chemoorganotroph bacterium that has a orange pigmentation and was isolated from salt marsh soil.

Gram-positive
motile
pigmented
rod-shaped
spore-forming
chemoorganotroph
mesophilic
moderately halophilic
obligate aerobe
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	*Bacillaceae*
	Genus	*Halobacillus*
	Species	**Halobacillus halophilus**
	Full Scientific Name (LPSN)	Halobacillus halophilus (Claus et al. 1984) Spring et al. 1996

Synonym

Sporosarcina halophila

Information on morphological and physiological properties Morphology

[Ref.: #22983]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #22983]	Cell shape	rod-shaped

[Ref.: #22983]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %94.579

[Ref.: #22983]	Pigment production	yes
[Ref.: #22983]	Pigmentation color	orange

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1011]

Culture medium

MARINE AGAR (DSMZ Medium 123)

[Ref.: #1011]

Culture medium growth

[Ref.: #1011]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1011]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1011]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #1011]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #22983]

Oxygen tolerance

obligate aerobe

[Ref.: #22983]

Nutrition type

chemoorganotroph

[Ref.: #22983]	Type of spore	endospore
[Ref.: #22983]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

[Ref.: #22983]

Halophily / tolerance level

moderately halophilic

[Ref.: #1011]	Murein short key	A21.04
[Ref.: #1011]	Murein types	A4ß L-Orn-D-Asp

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #22983]		nitrate ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #22983]		acetoin ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #22983]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #22983]	catalase	+	1.11.1.6
[Ref.: #22983]	cytochrome oxidase	+	1.9.3.1
[Ref.: #22983]	DNase	+
[Ref.: #22983]	urease	-	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	alanine metabolism	89.66	26 of 29
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	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]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	chlorophyll 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.: #1011]	Sample type/isolated from	salt marsh soil
[Ref.: #1011]	Geographic location (country and/or sea, region)	Sylt
[Ref.: #1011]	Country	Germany
[Ref.: #1011]	Country ISO 3 Code	DEU
[Ref.: #1011]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Salt marsh soil
[Ref.: #67770]	Country	Germany
[Ref.: #67770]	Country ISO 3 Code	DEU
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Salt marsh
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681790 (>99% sequence identity) for Halobacillus from Microbeatlas

Aquatic Samples	246
Soil Samples	116
Animal Samples	13
Plant Samples	73
Total Samples	448

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

[Ref.: #1011]

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.: #67770]	Halobacillus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 102448	AB681790	1492	ENA	1570 tax ID
[Ref.: #20218]	Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: A492	AB367151	492	ENA	866895 tax ID	*
[Ref.: #20218]	Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: B492	AB367152	492	ENA	866895 tax ID	*
[Ref.: #20218]	Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 740	AB367153	740	ENA	866895 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halobacillus halophilus DSM 2266 type strain: DSM 2266	GCA_000284515	complete	GenBank	866895 tax ID	*
[Ref.: #66792]	Halobacillus halophilus DSM 2266	866895.3	complete	PATRIC	866895 tax ID	*
[Ref.: #66792]	Halobacillus halophilus DSM 2266 strain type strain: DSM 2266	866895.15	plasmid	PATRIC	866895 tax ID	*
[Ref.: #66792]	Halobacillus halophilus DSM 2266 strain type strain: DSM 2266	866895.14	plasmid	PATRIC	866895 tax ID	*
[Ref.: #66792]	Halobacillus halophilus DSM 2266	2513237186	complete	JGI IMG/M	866895 tax ID	*

[Ref.: #22983]	GC-content	40-43 mol%
[Ref.: #1011]	GC-content	40.8 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: Halobacillus halophilus DSM 2266 type strain: DSM 2266 NCBI: GCA_000284515.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halobacillus halophilus DSM 2266 type strain: DSM 2266 NCBI: GCA_000284515.1
[Ref.: #69480]	motile	yes	86.855	no
[Ref.: #69480]	flagellated	yes	80.834	no
[Ref.: #69480]	gram-positive	yes	88.278	yes
[Ref.: #69480]	anaerobic	no	98.806	no
[Ref.: #69480]	aerobic	yes	95.318	yes
[Ref.: #69480]	halophile	yes	94.114	no
[Ref.: #69480]	spore-forming	yes	91.973	no
[Ref.: #69480]	thermophile	no	99.193	yes
[Ref.: #69480]	glucose-util	yes	89.239	no
[Ref.: #69480]	glucose-ferment	no	86.087	no

Availability in culture collections External links

[Ref.: #1011]

Culture collection no.

DSM 2266, ATCC 35676, NCIMB 2269, JCM 20832, CCM 3527, CECT 5013, IAM 12846, IAM 13060, KCTC 3685, LMG 17431, NBRC 102448

[Ref.: #70977]

SI-ID 9982

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halobacillus andaensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soil.	Wang K, Zhang L, Yang Y, Pan Y, Meng L, Liu H, Hong S, Huang H, Jiang J	Int J Syst Evol Microbiol	10.1099/ijs.0.000198	2015	*
Phylogeny	Sporosarcina halophila sp. nov., an Obligate, Slightly Halophilic Bacterium from Salt Marsh Soils.	Claus D, Fahmy F, Rolf HJ, Tosunoglu N	Syst Appl Microbiol	10.1016/S0723-2020(83)80007-1	1983	*

References

#1011

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2266

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#22983

S. SPRING,W. LUDWIG,M. C. MARQUEZ,A. VENTOSA,K.-H. SCHLEIFER: Halobacillus gen. nov., with Descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and Transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov.. IJSEM 46: 492 - 496 1996 ( DOI 10.1099/00207713-46-2-492 )

#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 )

#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 .

#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 )

#70977

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-ID9982.1 )

* These data were automatically processed and therefore are not curated

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Halobacillus halophilus DSM 2266 type strain: DSM 2266

Halobacillus halophilus DSM 2266 type strain: DSM 2266

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