Neobacillus cucumis (DSM 101566, CCM 8651, CIP 110974)

Name: Neobacillus cucumis (DSM 101566, CCM 8651, CIP 110974)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132382

Type strain

Strain Designation Ap-6

Culture col. no. DSM 101566 CCM 8651 CIP 110974 Ap-6

NCBI tax ID(s) 1740721

Special Collections DSMZ CIP Literature strains

History DSMZ <- P. Kämpfer, Univ. Giessen, Germany; Ap-6 <-W.F. Mahaffee CIP <- 2015, P. Kampfer, Giessen Univ., Giessen, Germany: strain AP-6

Links

Neobacillus cucumis Ap-6 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from rhizosphere soil closely adhering to the roots of field-grown cucumber Cucumis sativus cultivar Straight 8.

spore-forming Gram-positive rod-shaped colony-forming facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396494

LMG 29192,CCM 8651,CIP 110974,DSM 101566

@ref 20215

Last LPSN update 2026-05-29 08:37:50

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Cytobacillaceae

Genus Neobacillus

Species Neobacillus cucumis

Full scientific name Neobacillus cucumis (Kämpfer et al. 2016) Patel and Gupta 2020

Synonyms (1)

Bacillus cucumis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43773	positive	3 µm	1 µm	rod-shaped
118809				rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43773	2 mm	Beige	circular	2 days	Nutrient agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43773	Nutrient agar (NA)
24171	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
118809	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
24171	positive	growth	30
43773	positive	growth	16-45
43773	positive	optimum	28-30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43773	facultative anaerobe
125439	obligate aerobe	97.264

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
43773	circular, subterminal	endospore
125438				92.881

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43773	NaCl	positive	growth	0.5-4 %(w/v)
43773	NaCl	positive	optimum	1-2 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43773		2-deoxythymidine-5'-4-nitrophenyl phosphate	-	hydrolysis
43773		2-oxogluconate	-	builds acid from
43773	30916 ChEBI	2-oxoglutarate	-	carbon source
43773	16193 ChEBI	3-hydroxybenzoate	-	carbon source
43773	37054 ChEBI	3-hydroxybutyrate	-	carbon source
43773	17879 ChEBI	4-hydroxybenzoate	-	carbon source
43773	91122 ChEBI	4-nitrophenyl alpha-D-glucopyranoside	+	hydrolysis
43773		4-nitrophenyl beta-D-galactopyranoside hydrolysate	-	hydrolysis
43773	90259 ChEBI	4-nitrophenyl beta-D-glucopyranoside	-	hydrolysis
43773	90146 ChEBI	4-nitrophenyl beta-D-glucuronide	-	hydrolysis
43773	90148 ChEBI	4-nitrophenyl beta-D-xylopyranoside	-	hydrolysis
43773	30089 ChEBI	acetate	-	carbon source
43773	17128 ChEBI	adipate	-	carbon source
43773	27613 ChEBI	amygdalin	-	builds acid from
43773	78208 ChEBI	azelaate	-	carbon source
43773	16958 ChEBI	beta-alanine	-	carbon source
43773	3122 ChEBI	bis-4-nitrophenyl phosphate	-	hydrolysis
43773	91050 ChEBI	bis-4-nitrophenyl-phenyl phosphonate	-	hydrolysis
43773	55394 ChEBI	bis-4-nitrophenyl-phosphorylcholine	-	hydrolysis
43773		casein	-	hydrolysis
43773	17057 ChEBI	cellobiose	-	builds acid from
43773	17057 ChEBI	cellobiose	+/-	carbon source
43773	16383 ChEBI	cis-aconitate	-	carbon source
43773	16947 ChEBI	citrate	-	carbon source
43773	17108 ChEBI	D-arabinose	-	builds acid from
43773	18333 ChEBI	D-arabitol	-	builds acid from
43773	15824 ChEBI	D-fructose	+	builds acid from
43773	15824 ChEBI	D-fructose	+/-	carbon source
43773	12936 ChEBI	D-galactose	-	carbon source
43773	17634 ChEBI	D-glucose	+	builds acid from
43773	17634 ChEBI	D-glucose	+/-	builds acid from
43773	17634 ChEBI	D-glucose	+/-	carbon source
43773	16899 ChEBI	D-mannitol	-	builds acid from
43773	16899 ChEBI	D-mannitol	-	carbon source
43773	16024 ChEBI	D-mannose	+/-	carbon source
43773	16988 ChEBI	D-ribose	-	carbon source
43773	17924 ChEBI	D-sorbitol	-	builds acid from
43773	17924 ChEBI	D-sorbitol	-	carbon source
43773	16443 ChEBI	D-tagatose	-	builds acid from
43773	65327 ChEBI	D-xylose	-	builds acid from
43773	65327 ChEBI	D-xylose	-	carbon source
43773	16991 ChEBI	dna	-	hydrolysis
43773	17113 ChEBI	erythritol	-	builds acid from
43773	4853 ChEBI	esculin	+	hydrolysis
43773	29806 ChEBI	fumarate	-	carbon source
43773	16813 ChEBI	galactitol	-	builds acid from
43773	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
43773		gamma-L-glutamate-4-nitroanilide	-	hydrolysis
43773	5291 ChEBI	gelatin	-	hydrolysis
43773	28066 ChEBI	gentiobiose	-	builds acid from
43773	24265 ChEBI	gluconate	-	carbon source
43773	17859 ChEBI	glutaric acid	-	carbon source
43773	17754 ChEBI	glycerol	-	builds acid from
43773	17754 ChEBI	glycerol	-	carbon source
43773	28087 ChEBI	glycogen	-	builds acid from
43773	17240 ChEBI	itaconate	-	carbon source
43773	16977 ChEBI	L-alanine	-	carbon source
43773		L-alanine 4-nitroanilide	-	hydrolysis
43773	30849 ChEBI	L-arabinose	-	builds acid from
43773	30849 ChEBI	L-arabinose	-	carbon source
43773	18403 ChEBI	L-arabitol	-	builds acid from
43773	29991 ChEBI	L-aspartate	-	carbon source
43773	18287 ChEBI	L-fucose	-	builds acid from
43773	15971 ChEBI	L-histidine	-	carbon source
43773	15603 ChEBI	L-leucine	-	carbon source
43773	15729 ChEBI	L-ornithine	-	carbon source
43773	17295 ChEBI	L-phenylalanine	-	carbon source
43773	17203 ChEBI	L-proline	-	carbon source
43773		L-proline-4-nitroanilide	-	hydrolysis
43773	62345 ChEBI	L-rhamnose	-	builds acid from
43773	62345 ChEBI	L-rhamnose	-	carbon source
43773	17115 ChEBI	L-serine	-	carbon source
43773	17266 ChEBI	L-sorbose	-	builds acid from
43773	16828 ChEBI	L-tryptophan	-	carbon source
43773	65328 ChEBI	L-xylose	-	builds acid from
43773	17716 ChEBI	lactose	-	builds acid from
43773	68428 ChEBI	maltitol	-	carbon source
43773	17306 ChEBI	maltose	-	builds acid from
43773	17306 ChEBI	maltose	+	builds acid from
43773	17306 ChEBI	maltose	+/-	carbon source
43773	6731 ChEBI	melezitose	-	builds acid from
43773	28053 ChEBI	melibiose	-	builds acid from
43773	28053 ChEBI	melibiose	+/-	carbon source
43773	36986 ChEBI	mesaconate	-	carbon source
43773		methyl alpha-D-xylopyranoside	-	builds acid from
43773	37657 ChEBI	methyl D-glucoside	-	builds acid from
43773	17268 ChEBI	myo-inositol	-	builds acid from
43773	17268 ChEBI	myo-inositol	-	carbon source
43773	28037 ChEBI	N-acetylgalactosamine	-	carbon source
43773	506227 ChEBI	N-acetylglucosamine	+	builds acid from
43773	506227 ChEBI	N-acetylglucosamine	+/-	carbon source
43773	18401 ChEBI	phenylacetate	-	carbon source
43773	17272 ChEBI	propionate	-	carbon source
43773	17148 ChEBI	putrescine	-	carbon source
43773	15361 ChEBI	pyruvate	-	carbon source
43773	16634 ChEBI	raffinose	-	builds acid from
43773	15963 ChEBI	ribitol	-	builds acid from
43773	15963 ChEBI	ribitol	-	carbon source
43773	33942 ChEBI	ribose	-	builds acid from
43773	17814 ChEBI	salicin	-	builds acid from
43773	17814 ChEBI	salicin	+/-	carbon source
43773	28017 ChEBI	starch	-	builds acid from
43773	28017 ChEBI	starch	-	hydrolysis
43773	9300 ChEBI	suberic acid	-	carbon source
43773	17992 ChEBI	sucrose	-	builds acid from
43773	17992 ChEBI	sucrose	+/-	carbon source
43773	15708 ChEBI	trans-aconitate	-	carbon source
43773	27082 ChEBI	trehalose	-	builds acid from
43773	32528 ChEBI	turanose	-	builds acid from
43773	18186 ChEBI	tyrosine	-	hydrolysis
43773	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43773	16136 ChEBI	hydrogen sulfide
43773	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43773	arginine dihydrolase	-	3.5.3.6
43773	beta-galactosidase	-	3.2.1.23
43773	catalase	+	1.11.1.6
43773	cytochrome oxidase	+	1.9.3.1
43773	lysine decarboxylase	-	4.1.1.18
43773	ornithine decarboxylase	-	4.1.1.17
43773	tryptophan deaminase	-	4.1.99.1
43773	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
24171	rhizosphere soil closely adhering to the roots of field-grown cucumber Cucumis sativus cultivar Straight 8	Cucumis sativus	Alabama, Tallassee (Elmore county), E.V. Smith Research Center	USA	USA	North America
43773	The rhizosphere soil of field-grown cucumber (Cucumis sativus) roots at the E.V. Smith Research Center		Elmore County, Alabama	USA	USA	North America
118809	Plant, Field-grown Cucumber plant		Tallassee , Alabama	United States of America	USA	North America	1996-07-01

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24171	1	Risk group (German classification)
118809	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1690897v1 assembly for Neobacillus cucumis DSM 101566	contig	GCA_016908975	1740721.8	2901240655	1740721	59.99
124043	ASM4243228v1 assembly for Neobacillus cucumis CCM 8651	contig	GCA_042432285			1740721	59.68
124043	ASM4265074v1 assembly for Neobacillus cucumis CCM 8651	scaffold	GCA_042650745			1740721	26.16

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24171	Neobacillus cucumis strain AP-6 16S ribosomal RNA gene, partial sequence	KT895286	1474		1740721
124043	Bacillus cucumis strain CCM 8651 16S ribosomal RNA gene, partial sequence.	MT760229	1385		1740721

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1690897v1 assembly for Neobacillus cucumis DSM 101566
BV-BRC: 1740721.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.26	no
125439	gram_stain	BacteriaNetⓘ	variable	67.32	no
125439	spore_formation	BacteriaNetⓘ	yes	84.19	no
125439	motility	BacteriaNetⓘ	yes	68.42	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Neobacillus cucumis strain DSM 101566
PATRIC: 1740721.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	75.81	no
125438	anaerobic	anaerobicⓘ	no	96.87	no
125438	spore-forming	spore-formingⓘ	yes	92.88	yes
125438	aerobic	aerobicⓘ	no	51.58	yes
125438	thermophilic	thermophileⓘ	no	89.98	no
125438	flagellated	motile2+ⓘ	no	72.77	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Neobacillus massiliamazoniensis sp. nov., a new bacterial species isolated from stool sample of an inhabitant of the Amazon region.	Mbaye B, Tidjani Alou M, Fadlane A, Fregiere L, Alibar S, Million M, Fenollar F, Lo CI.	New Microbes New Infect	10.1016/j.nmni.2021.100900	2021
Phylogeny	Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.	Hameed A, McDonagh F, Sengupta P, Miliotis G, Sivabalan SKM, Szydlowski L, Simpson A, Singh NK, Rekha PD, Raman K, Venkateswaran K.	Microbiol Spectr	10.1128/spectrum.01376-24	2025
Phylogeny	Bacillus salipaludis sp. nov., isolated from saline-alkaline soil.	Xue L, Tang L, Zhao J, Fang Z, Liu H, Qiao J, Zhang G	Arch Microbiol	10.1007/s00203-021-02239-0	2021
Phylogeny	Bacillus cucumis sp. nov. isolated from the rhizosphere of cucumber (Cucumis sativus).	Kampfer P, Busse HJ, Glaeser SP, Kloepper JW, Hu CH, McInroy JA	Int J Syst Evol Microbiol	10.1099/ijsem.0.000831	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 )
#24171	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101566
#43773	Peter Kämpfer, Hans-Jürgen Busse, Stefanie P. Glaeser, Joseph W. Kloepper, Chia-Hui Hu, John A. McInroy: Bacillus cucumis sp. nov. isolated from the rhizosphere of cucumber (Cucumis sativus). IJSEM 66: 1039 - 1044 2016 ( DOI 10.1099/ijsem.0.000831 , PubMed 26654465 )
#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) .
#118809	Collection of Institut Pasteur ; Curators of the CIP; CIP 110974
#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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Neobacillus cucumis (DSM 101566, CCM 8651, CIP 110974)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016908975

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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