Name: Halalkalibacter wakoensis N-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1240

Type strain:

Species: Halalkalibacter wakoensis

Strain Designation: N-1

Culture col. no.: DSM 2521, ATCC 21832, FERM P-1138, JCM 9140, CIP 109022, FERM 1138

Strain history: K. Horikoshi N-1.

NCBI tax ID(s): 1236970 (strain), 127891 (species)

Section

Halalkalibacter wakoensis N-1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

Gram-positive
motile
rod-shaped
spore-forming
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Halalkalibacter*
	Species	**Halalkalibacter wakoensis**
	Full Scientific Name (LPSN)	Halalkalibacter wakoensis (Nogi et al. 2005) Joshi et al. 2022

	Synonym	Alkalihalobacillus wakoensis
	Synonym	Bacillus wakoensis

Information on morphological and physiological properties Morphology

[Ref.: #31483]	Gram stain	positive
[Ref.: #31483]	Cell length	1.75 µm
[Ref.: #31483]	Cell width	0.65 µm
[Ref.: #31483]	Cell shape	rod-shaped
[Ref.: #31483]	Motility	yes

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

[Ref.: #69480]	Motility	yes Confidence in %97.208

[Ref.: #31483]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1109]

Culture medium

ALKALINE NUTRIENT AGAR (DSMZ Medium 31)

[Ref.: #1109]

Culture medium growth

[Ref.: #1109]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1109]

Culture medium composition

expand / minimize

[Ref.: #40094]

Culture medium

MEDIUM 291 - for Bacillus horti

[Ref.: #40094]

Culture medium growth

[Ref.: #40094]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #1109]	growth	30 °C
[Ref.: #31483]	growth	10-40 °C
[Ref.: #31483]	optimum	37 °C
[Ref.: #40094]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #1109]	Temperature range	mesophilic
[Ref.: #31483]	Temperature range	mesophilic
[Ref.: #40094]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31483]			optimum	9.5
[Ref.: #31483]			growth	08-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31483]

Oxygen tolerance

aerobe

[Ref.: #31483]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #1109]

Name of produced compound

cellulase, alkaline

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31483]		NaCl		growth	0-10	%
[Ref.: #31483]		NaCl		optimum	5	%

[Ref.: #31483]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-6, MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31483]	cellobiose ChEBI	+	carbon source
[Ref.: #31483]	fructose ChEBI	+	carbon source
[Ref.: #31483]	glucose ChEBI	+	carbon source
[Ref.: #31483]	maltose ChEBI	+	carbon source
[Ref.: #31483]	mannitol ChEBI	+	carbon source
[Ref.: #31483]	mannose ChEBI	+	carbon source
[Ref.: #31483]	nitrate ChEBI	+	reduction
[Ref.: #31483]	salicin ChEBI	+	carbon source
[Ref.: #31483]	sorbitol ChEBI	+	carbon source
[Ref.: #31483]	sucrose ChEBI	+	carbon source
[Ref.: #31483]	trehalose ChEBI	+	carbon source
[Ref.: #31483]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31483]		catalase	+	1.11.1.6
[Ref.: #67770]		cellulase		3.2.1.4

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	polyamine pathway	73.91	17 of 23
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	vitamin B12 metabolism	47.06	16 of 34
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	daunorubicin biosynthesis	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.: #1109]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #1109]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #31483]	Bacillus wakoensis gene for 16S rRNA	AB043851	1524	GenBank	127891 tax ID
[Ref.: #20218]	Bacillus sp. N1 partial 16S rRNA gene	AJ786654	649	ENA	288813 tax ID	*
[Ref.: #20218]	Bacillus sp. N1 16S ribosomal RNA gene, partial sequence	DQ376939	1322	ENA	288813 tax ID	*
[Ref.: #20218]	Bacillus wakoensis 16S ribosomal RNA gene, partial sequence	FJ876429	600	ENA	127891 tax ID	*
[Ref.: #20218]	Bacillus sp. N1(2009) 16S ribosomal RNA gene, partial sequence	GU086413	1514	ENA	690148 tax ID	*
[Ref.: #20218]	Bacillus sp. N1(2011) 16S ribosomal RNA gene, partial sequence	HQ451884	1420	ENA	995018 tax ID	*
[Ref.: #20218]	Bacillus sp. N1(2012) 16S ribosomal RNA gene, partial sequence	JX272922	1155	ENA	1229622 tax ID	*
[Ref.: #20218]	Bacillus sp. N1(2013) 16S ribosomal RNA gene, partial sequence	KF051777	1449	ENA	1348145 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Alkalihalobacillus wakoensis JCM 9140 JCM 9140	GCA_000513095	contig	GenBank	1236970 tax ID
[Ref.: #67770]	Alkalihalobacillus wakoensis JCM 9140 JCM 9140	GCA_001315045	contig	GenBank	1236970 tax ID
[Ref.: #66792]	Bacillus wakoensis JCM 9140	1236970.3	wgs	PATRIC	1236970 tax ID	*
[Ref.: #66792]	Bacillus wakoensis JCM 9140	1236970.4	wgs	PATRIC	1236970 tax ID	*
[Ref.: #66792]	Bacillus wakoensis JCM 9140	2609459807	draft	JGI IMG/M	1236970 tax ID	*

[Ref.: #1109]	GC-content	37.2 mol%
[Ref.: #31483]	GC-content	38.1 mol%
[Ref.: #67770]	GC-content	38.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	38.3 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bacillus wakoensis JCM 9140 PATRIC: 1236970.4
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	spore-forming	yes	100	yes
[Ref.: #69480]	anaerobic	no	98.117	yes
[Ref.: #69480]	thermophile	no	99.562	yes
[Ref.: #69480]	motile	yes	97.208	yes

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bacillus wakoensis JCM 9140 PATRIC: 1236970.4
[Ref.: #69481]	spore-forming	yes	100	no

Availability in culture collections External links

[Ref.: #1109]

Culture collection no.

DSM 2521, ATCC 21832, FERM P-1138, JCM 9140, CIP 109022, FERM 1138

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang.	Liu B, Liu GH, Wang XY, Wang JP, Chen Z, Chen MC, Zhang HF, Singonca C	Int J Syst Evol Microbiol	10.1099/ijsem.0.003363	2019	*
Genetics	Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM 9152T.	Yuki M, Oshima K, Suda W, Oshida Y, Kitamura K, Iida T, Hattori M, Ohkuma M	Genome Announc	10.1128/genomeA.01258-13	2014	*
Phylogeny	Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species.	Nogi Y, Takami H, Horikoshi K	Int J Syst Evol Microbiol	10.1099/ijs.0.63649-0	2005	*

References

#1109

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2521

#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 )

#31483

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 #27781 (see below)

#40094 ; Curators of the CIP;

#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;

#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 )

#27781

IJSEM 2309 2005 ( DOI 10.1099/ijs.0.63649-0 , PubMed 16280488 )

* These data were automatically processed and therefore are not curated

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Bacillus wakoensis JCM 9140

Bacillus wakoensis JCM 9140

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