Heyndrickxia shackletonii (DSM 18868, CIP 107762, KCTC 13003)

Name: Heyndrickxia shackletonii (DSM 18868, CIP 107762, KCTC 13003)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1257

Type strain

Strain Designation B1724

Culture col. no. DSM 18868 CIP 107762 KCTC 13003 LMG 18435 B1724

NCBI tax ID(s) 157838

Special Collections DSMZ KCTC CIP Literature strains

Links

Heyndrickxia shackletonii B1724 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from volcanic soil.

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

Name and taxonomic classification

SI-ID 12024

LMG 18435,CIP 107762,DSM 18868,BCRC 17468,CCRC 17468,KCTC 13003

@ref 20215

Last LPSN update 2025-12-16 09:47:03

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Heyndrickxia

Species Heyndrickxia shackletonii

Full scientific name Heyndrickxia shackletonii (Logan et al. 2004) Narsing Rao et al. 2023

Synonyms (2)

Margalitia shackletonii
Bacillus shackletonii

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29918	variable	3.5 µm	0.8 µm	rod-shaped
122577	positive			rod-shaped

Colony morphology

Pigmentation

29918

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7755	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38229	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122577	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7755	positive	growth	30	mesophilic
29918	positive	growth	15-55
29918	positive	optimum	37	mesophilic
38229	positive	growth	30	mesophilic
122577	positive	growth	22-45
122577	negative	growth	10
122577	negative	growth	55

Culture pH

@ref	Ability	Type	PH	PH range
29918	positive	optimum	7
29918	positive	growth	4.5-9.0	alkaliphile
122577	positive	growth	6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29918	aerobe
122577	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
29918
122577
125438		91.836
125439		92.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122577	NaCl	positive	growth	0-4 %
122577	NaCl		growth	6 %
122577	NaCl		growth	8 %
122577	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122577	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
29918	4853 ChEBI	esculin	+	hydrolysis
122577	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
29918	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
122577	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
29918	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
29918	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
122577	17632 ChEBI	nitrate	-	reduction
122577	17632 ChEBI	nitrate	-	respiration
122577	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
29918	33942 ChEBI	ribose	+	carbon source
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
29918	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122577	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122577	15688 ChEBI	acetoin	-
122577	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122577	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
122577	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
122577	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122577	caseinase	+	3.4.21.50
29918	catalase	+	1.11.1.6
122577	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
122577	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122577	gamma-glutamyltransferase	-	2.3.2.2
122577	gelatinase	-
122577	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122577	lipase	-
68382	lipase (C 14)	-		from API zym
122577	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122577	ornithine decarboxylase	-	4.1.1.17
122577	oxidase	+
122577	protease	-
68382	trypsin	+	3.4.21.4	from API zym
122577	tween esterase	+
122577	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	vitamin K metabolism	100	5 of 5
66794	starch degradation	100	10 of 10
66794	methylglyoxal degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	lipoate biosynthesis	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	aspartate and asparagine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	teichoic acid biosynthesis	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	pyrimidine metabolism	88.89	40 of 45
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	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	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	alanine metabolism	82.76	24 of 29
66794	methionine metabolism	80.77	21 of 26
66794	glycine betaine biosynthesis	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	biotin biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	coenzyme A metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	lysine metabolism	64.29	27 of 42
66794	metabolism of disaccharids	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	non-pathway related	57.89	22 of 38
66794	heme metabolism	57.14	8 of 14
66794	urea cycle	53.85	7 of 13
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	polyamine pathway	52.17	12 of 23
66794	degradation of sugar acids	52	13 of 25
66794	lipid metabolism	51.61	16 of 31
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	butanoate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	phenol degradation	45	9 of 20
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	glutathione metabolism	42.86	6 of 14
66794	ascorbate metabolism	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	cellulose degradation	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	vitamin B12 metabolism	29.41	10 of 34
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	nitrate assimilation	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122577	-	+	+	+	-	+	-	-	+	+	+	+	+	-	-	-	-	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122577	not determinedn.d.	+/-	-	-	-	+/-	-	-	-	-	+/-	+	+	+/-	-	-	-	-	+/-	-	-	-	+/-	+/-	+/-	+	+/-	+/-	+/-	-	-	-	+	-	-	-	-	+	-	+	-	-	+/-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122577	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Volcanic
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
7755	volcanic soil
122577	Environment, Volcanic soil	Iceland	ISL	Europe	1997

Taxonmaps

69479

Global distribution of 16S sequence AJ250318 (>99% sequence identity) for Bacillus from Microbeatlas

Aquatic Samples	54
Soil Samples	166
Animal Samples	127
Plant Samples	31
Total Samples	378

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7755	1	Risk group (German classification) According to TRBA 466
122577	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM142071v1 assembly for Heyndrickxia shackletonii LMG 18435	scaffold	GCA_001420715	157838.3	2651869806	157838	65.45
66792	ASM1100880v1 assembly for Heyndrickxia shackletonii LMG 18435	contig	GCA_011008805	157838.12		157838	56.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7755	Bacterium LMG 18435 16S rRNA gene, strain LMG 18435	AJ250318	1503		157838

GC content

7755

GC-content (mol%)35.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Heyndrickxia shackletonii LMG 18435
NCBI: GCA_001420715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	92.50	no
125439	motility	BacteriaNetⓘ	yes	81.40	no
125439	gram_stain	BacteriaNetⓘ	variable	83.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	88.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Margalitia shackletonii LMG 18435
NCBI: GCA_001420715.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.94	yes
125438	anaerobic	anaerobicⓘ	no	94.63	yes
125438	aerobic	aerobicⓘ	yes	74.04	yes
125438	spore-forming	spore-formingⓘ	yes	91.84	yes
125438	thermophilic	thermophileⓘ	no	83.82	no
125438	flagellated	motile2+ⓘ	yes	80.47	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Bacillus shackletonii LMG 18435T, Isolated from Volcanic Mossy Soil.	Wang JP, Liu B, Liu GH, Ge CB, Xiao RF, Zheng XF, Shi H	Genome Announc	10.1128/genomeA.01689-15	2016
Phylogeny	Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu.	Xie J, Cheng K, Zhao D, Yang G, Qiao Z, Qiu S, Yu X, Liu H, Li T, Feng H, Yao S, Zhai L	Int J Syst Evol Microbiol	10.1099/ijsem.0.004185	2020
Metabolism	Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern.	Zhou YX, Liu GH, Liu B, Chen GJ, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0692-7	2016
Phylogeny	Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments.	Zhu D, Zhang P, Niu L, Xie C, Li P, Sun J, Hang F	Int J Syst Evol Microbiol	10.1099/ijsem.0.000763	2015
Phylogeny	Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil.	Cui X, Wang Y, Liu J, Chang M, Zhao Y, Zhou S, Zhuang L	Arch Microbiol	10.1007/s00203-015-1082-7	2015
Phylogeny	Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago.	Logan NA, Lebbe L, Verhelst A, Goris J, Forsyth G, Rodriguez-Diaz M, Heyndrickx M, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.02661-0	2004

References

#7755	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18868
#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 )
#29918	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 #26289 (see below)
#38229	; 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 )
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122577	Collection of Institut Pasteur ; Curators of the CIP; CIP 107762
#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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Heyndrickxia shackletonii (DSM 18868, CIP 107762, KCTC 13003)

Name and taxonomic classification

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Genome browser: GCA_001420715

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