Bacillus capparidis (DSM 103394, CGMCC 1.12820, KCTC 33514)

Name: Bacillus capparidis (DSM 103394, CGMCC 1.12820, KCTC 33514)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133067

Type strain

Culture col. no. DSM 103394 CGMCC 1.12820 KCTC 33514 EGI 6500252

NCBI tax ID(s) 1840411

Special Collections DSMZ KCTC Literature strains

History <- W.-J. Li, Sun Yat-sen Univ., Guangzhou, People's Republic of China; EGI 6500252 <- H.-F. Wang, Xinjiang Inst. of Ecol. and Geography (XIEG), Chin. Acad. of Scs., Urumchi, China

Links

Bacillus capparidis DSM 103394 is an aerobe, Gram-positive, rod-shaped prokaryote that forms circular colonies and was isolated from surface-sterilized roots of the medicinal plant Capparis spinosa L..

Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 405400

KCTC 33514,DSM 103394

@ref 20215

Last LPSN update 2025-12-16 10:01:40

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Bacillus

Species Bacillus capparidis

Full scientific name Bacillus capparidis Wang et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
25175	positive	1.98-2.30 µm	0.68 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
25175	white	circular	2 days	ISP2 agar medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
25175	ISP2 agar medium
24855	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24855	positive	growth	30	mesophilic
25175	positive	growth	10.0-40.0
25175	positive	optimum	25.0-30.0	mesophilic

Culture pH

@ref	Ability	Type	PH
25175	positive	optimum	7
25175	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25175	aerobe
125439	obligate aerobe	97.2

Spore formation

25175

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25175	NaCl		optimum	0.0-3.0 %
25175	NaCl	positive	growth	0.0-10.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25175	17521 ChEBI	(-)-quinic acid	+	respiration
25175	16004 ChEBI	(R)-lactate	+	respiration
25175	16651 ChEBI	(S)-lactate	+	respiration
25175	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
25175	64552 ChEBI	2-hydroxybutyrate	-	respiration
25175	16763 ChEBI	2-oxobutanoate	-	respiration
25175	30916 ChEBI	2-oxoglutarate	+	respiration
25175	37054 ChEBI	3-hydroxybutyrate	-	respiration
25175	73918 ChEBI	3-O-methyl-D-glucose	+	respiration
25175	18101 ChEBI	4-hydroxyphenylacetic acid	-	respiration
25175	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
25175	30089 ChEBI	acetate	+	respiration
25175	13705 ChEBI	acetoacetate	+	respiration
25175	17128 ChEBI	adipate	-	assimilation
25175	27613 ChEBI	amygdalin	+	builds acid from
25175	22599 ChEBI	arabinose	-	assimilation
25175	18305 ChEBI	arbutin	+	builds acid from
25175	73706 ChEBI	bromosuccinate	+	respiration
25175		casein	-	hydrolysis
25175	17057 ChEBI	cellobiose	+	respiration
25175	17057 ChEBI	cellobiose	+	builds acid from
25175	62968 ChEBI	cellulose	-	hydrolysis
25175	16947 ChEBI	citrate	-	assimilation
25175	16947 ChEBI	citrate	+	respiration
25175	17108 ChEBI	D-arabinose	-	builds acid from
25175	18333 ChEBI	D-arabitol	-	builds acid from
25175	18333 ChEBI	D-arabitol	+	respiration
25175	29990 ChEBI	D-aspartate	+	respiration
25175	15824 ChEBI	D-fructose	+	respiration
25175	78697 ChEBI	D-fructose 6-phosphate	+	respiration
25175	28847 ChEBI	D-fucose	-	builds acid from
25175	28847 ChEBI	D-fucose	+	respiration
25175	15895 ChEBI	D-galactonic acid lactone	+	respiration
25175	12936 ChEBI	D-galactose	-	builds acid from
25175	12936 ChEBI	D-galactose	+	respiration
25175	18024 ChEBI	D-galacturonic acid	+	respiration
25175	30612 ChEBI	D-glucarate	-	respiration
25175	8391 ChEBI	D-gluconate	+	respiration
25175	17634 ChEBI	D-glucose	+	respiration
25175	17634 ChEBI	D-glucose	+	builds acid from
25175	14314 ChEBI	D-glucose 6-phosphate	+	respiration
25175	15748 ChEBI	D-glucuronate	-	respiration
25175	62318 ChEBI	D-lyxose	-	builds acid from
25175	15588 ChEBI	D-malate	-	respiration
25175	16899 ChEBI	D-mannitol	+	respiration
25175	16899 ChEBI	D-mannitol	+	builds acid from
25175	16024 ChEBI	D-mannose	+	respiration
25175	16024 ChEBI	D-mannose	+	builds acid from
25175	16988 ChEBI	D-ribose	-	builds acid from
25175	16523 ChEBI	D-serine	-	respiration
25175	17924 ChEBI	D-sorbitol	+	respiration
25175	17924 ChEBI	D-sorbitol	+	builds acid from
25175	16443 ChEBI	D-tagatose	-	builds acid from
25175	65327 ChEBI	D-xylose	-	builds acid from
25175	27689 ChEBI	decanoate	-	assimilation
25175	23652 ChEBI	dextrin	+	respiration
25175	17113 ChEBI	erythritol	-	builds acid from
25175	4853 ChEBI	esculin	+	hydrolysis
25175	4853 ChEBI	esculin	+	builds acid from
25175	15740 ChEBI	formate	+	respiration
25175	28757 ChEBI	fructose	+	builds acid from
25175	16537 ChEBI	galactarate	-	respiration
25175	16813 ChEBI	galactitol	-	builds acid from
25175	16865 ChEBI	gamma-aminobutyric acid	+	respiration
25175	5291 ChEBI	gelatin	+	respiration
25175	28066 ChEBI	gentiobiose	+	respiration
25175	28066 ChEBI	gentiobiose	+	builds acid from
25175	24265 ChEBI	gluconate	+	builds acid from
25175	17234 ChEBI	glucose	-	fermentation
25175	17234 ChEBI	glucose	+	assimilation
25175	32323 ChEBI	glucuronamide	-	respiration
25175	17754 ChEBI	glycerol	-	builds acid from
25175	17754 ChEBI	glycerol	+	respiration
25175	70744 ChEBI	glycine-proline	+	respiration
25175	28087 ChEBI	glycogen	-	builds acid from
25175	73804 ChEBI	glycyl L-aspartic acid	+	respiration
25175	17596 ChEBI	inosine	+	respiration
25175	15443 ChEBI	inulin	+	builds acid from
25175	16977 ChEBI	L-alanine	+	respiration
25175	30849 ChEBI	L-arabinose	-	builds acid from
25175	18403 ChEBI	L-arabitol	-	builds acid from
25175	16467 ChEBI	L-arginine	+	respiration
25175	18287 ChEBI	L-fucose	-	builds acid from
25175	18287 ChEBI	L-fucose	+	respiration
25175	29985 ChEBI	L-glutamate	+	respiration
25175	15971 ChEBI	L-histidine	+	respiration
25175	15589 ChEBI	L-malate	+	respiration
25175	18183 ChEBI	L-pyroglutamic acid	-	respiration
25175	62345 ChEBI	L-rhamnose	-	builds acid from
25175	62345 ChEBI	L-rhamnose	+	respiration
25175	17115 ChEBI	L-serine	+	respiration
25175	17266 ChEBI	L-sorbose	-	builds acid from
25175	65328 ChEBI	L-xylose	-	builds acid from
25175	17716 ChEBI	lactose	-	builds acid from
25175	17716 ChEBI	lactose	+	respiration
25175	25115 ChEBI	malate	+	assimilation
25175	17306 ChEBI	maltose	+	assimilation
25175	17306 ChEBI	maltose	+	respiration
25175	17306 ChEBI	maltose	+	builds acid from
25175	29864 ChEBI	mannitol	+	assimilation
25175	37684 ChEBI	mannose	+	assimilation
25175	6731 ChEBI	melezitose	+	builds acid from
25175	28053 ChEBI	melibiose	+	respiration
25175	28053 ChEBI	melibiose	+	builds acid from
25175	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
25175	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
25175	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
25175	37657 ChEBI	methyl D-glucoside	+	respiration
25175	51850 ChEBI	methyl pyruvate	-	respiration
25175	17268 ChEBI	myo-inositol	-	builds acid from
25175	17268 ChEBI	myo-inositol	+	respiration
25175	63154 ChEBI	N-acetyl-beta-D-mannosamine	+	respiration
25175	28037 ChEBI	N-acetylgalactosamine	+	respiration
25175	506227 ChEBI	N-acetylglucosamine	-	assimilation
25175	506227 ChEBI	N-acetylglucosamine	-	respiration
25175	506227 ChEBI	N-acetylglucosamine	-	builds acid from
25175	35418 ChEBI	n-acetylneuraminate	+	respiration
25175	17632 ChEBI	nitrate	-	reduction
25175	17309 ChEBI	pectin	+	respiration
25175	18401 ChEBI	phenylacetate	-	assimilation
25175	32032 ChEBI	potassium gluconate	+	assimilation
25175	17272 ChEBI	propionate	-	respiration
25175	16634 ChEBI	raffinose	+	respiration
25175	16634 ChEBI	raffinose	+	builds acid from
25175	15963 ChEBI	ribitol	-	builds acid from
25175	17814 ChEBI	salicin	+	respiration
25175	17814 ChEBI	salicin	+	builds acid from
25175	17164 ChEBI	stachyose	+	respiration
25175	28017 ChEBI	starch	-	hydrolysis
25175	28017 ChEBI	starch	-	builds acid from
25175	17992 ChEBI	sucrose	+	respiration
25175	17992 ChEBI	sucrose	+	builds acid from
25175	27082 ChEBI	trehalose	+	respiration
25175	27082 ChEBI	trehalose	+	builds acid from
25175	32528 ChEBI	turanose	+	builds acid from
25175	32528 ChEBI	turanose	+	respiration
25175	53424 ChEBI	tween 20	-	hydrolysis
25175	53423 ChEBI	tween 40	-	hydrolysis
25175	53425 ChEBI	tween 60	-	hydrolysis
25175	53426 ChEBI	tween 80	-	hydrolysis
25175	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25175	16136 ChEBI	hydrogen sulfide

Metabolite tests

@ref	Chebi-ID	Metabolite	Methylred-test
25175	17234 ChEBI	glucose	-

Enzymes

@ref	Value	Activity	Ec
25175	catalase	+	1.11.1.6
25175	cytochrome oxidase	+	1.9.3.1
25175	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

25175

Fatty acid	Percentage
C15:0 iso	30.4
C15:0 anteiso	24
C17:0 anteiso	11
C15:0 2OH	2
C15:0 iso 3OH	1.5
C13:0 anteiso	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
24855	surface-sterilized roots of the medicinal plant Capparis spinosa L.	Capparis spinosa	Xinjiang, Urumqi city	China	CHN	Asia
25175							July 2014	TWYE agar	yeast 0.25 g, K2HPO4 0.5 g, agar 15.0 g, distilled water 1000 ml, pH 7.0–7.2) [7] supplemented with 3 % (w/v) NaCl	14-42 days	30

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24855	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4243214v1 assembly for Bacillus capparidis CGMCC 1.12820	scaffold	GCA_042432145			1840411	73.6
66792	ASM1783209v1 assembly for Bacillus capparidis DSM 103394	contig	GCA_017832095	1840411.3	2901263064	1840411	71.67

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
24855	Bacillus capparidis strain EGI 6500252 16S ribosomal RNA gene, partial sequence	KX119423	1514	1840411
24855	Bacillus capparidis strain EGI 6500252 16S ribosomal RNA gene, partial sequence	KY003162	1546	1840411
124043	Bacillus capparidis strain CGMCC 1.12820 16S ribosomal RNA gene, partial sequence.	MT759869	1331	1840411

GC content

@ref	GC-content (mol%)	Method
24855	39.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacillus capparidis DSM 103394
NCBI: GCA_017832095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	79.70	no
125439	motility	BacteriaNetⓘ	yes	70.60	no
125439	gram_stain	BacteriaNetⓘ	variable	83.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacillus capparidis strain DSM 103394
PATRIC: 1840411.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.49	yes
125438	anaerobic	anaerobicⓘ	no	96.67	yes
125438	spore-forming	spore-formingⓘ	yes	75.45	yes
125438	thermophilic	thermophileⓘ	no	93.98	yes
125438	aerobic	aerobicⓘ	yes	79.72	yes
125438	flagellated	motile2+ⓘ	yes	85.56	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L.	Wang HF, Li QL, Zhang YG, Xiao M, Zhou XK, Guo JW, Duan YQ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001616	2017

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 )
#24855	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103394
#25175	H. F. L. Wang, Q. L.,Zhang, Y. G.,Xiao, M.,Zhou, X. K.,Guo, J. W.,Duan, Y. Q.,Li, W. J.: Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L. IJSEM 67: 282 - 287 2017 ( DOI 10.1099/ijsem.0.001616 , PubMed 27902223 )
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Bacillus capparidis (DSM 103394, CGMCC 1.12820, KCTC 33514)

Name and taxonomic classification