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

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Neobacillus cucumis Ap-6 is a facultative anaerobe, spore-forming, Gram-positive prokaryote 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

Name and taxonomic classification

SI-ID 396494

LMG 29192,CCM 8651,CIP 110974,DSM 101566

@ref 20215

Last LPSN update 2025-12-16 10:01:30

Domain Bacillati

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	Growth
43773	Nutrient agar (NA)
24171	NUTRIENT AGAR (DSMZ Medium 1)
118809	CIP Medium 72

Culture temp

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
43773	facultative anaerobe
125439	obligate aerobe

Spore formation

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

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	Metabolite	Utilization activity	Kind of utilization tested
43773	2-deoxythymidine-5'-4-nitrophenyl phosphate	-	hydrolysis
43773	2-oxogluconate	-	builds acid from
43773	2-oxoglutarate	-	carbon source
43773	3-hydroxybenzoate	-	carbon source
43773	3-hydroxybutyrate	-	carbon source
43773	4-hydroxybenzoate	-	carbon source
43773	4-nitrophenyl alpha-D-glucopyranoside	+	hydrolysis
43773	4-nitrophenyl beta-D-galactopyranoside hydrolysate	-	hydrolysis
43773	4-nitrophenyl beta-D-glucopyranoside	-	hydrolysis
43773	4-nitrophenyl beta-D-glucuronide	-	hydrolysis
43773	4-nitrophenyl beta-D-xylopyranoside	-	hydrolysis
43773	acetate	-	carbon source
43773	adipate	-	carbon source
43773	amygdalin	-	builds acid from
43773	azelaate	-	carbon source
43773	beta-alanine	-	carbon source
43773	bis-4-nitrophenyl phosphate	-	hydrolysis
43773	bis-4-nitrophenyl-phenyl phosphonate	-	hydrolysis
43773	bis-4-nitrophenyl-phosphorylcholine	-	hydrolysis
43773	casein	-	hydrolysis
43773	cellobiose	-	builds acid from
43773	cellobiose	+/-	carbon source
43773	cis-aconitate	-	carbon source
43773	citrate	-	carbon source
43773	D-arabinose	-	builds acid from
43773	D-arabitol	-	builds acid from
43773	D-fructose	+	builds acid from
43773	D-fructose	+/-	carbon source
43773	D-galactose	-	carbon source
43773	D-glucose	+	builds acid from
43773	D-glucose	+/-	builds acid from
43773	D-glucose	+/-	carbon source
43773	D-mannitol	-	builds acid from
43773	D-mannitol	-	carbon source
43773	D-mannose	+/-	carbon source
43773	D-ribose	-	carbon source
43773	D-sorbitol	-	builds acid from
43773	D-sorbitol	-	carbon source
43773	D-tagatose	-	builds acid from
43773	D-xylose	-	builds acid from
43773	D-xylose	-	carbon source
43773	dna	-	hydrolysis
43773	erythritol	-	builds acid from
43773	esculin	+	hydrolysis
43773	fumarate	-	carbon source
43773	galactitol	-	builds acid from
43773	gamma-aminobutyric acid	-	carbon source
43773	gamma-L-glutamate-4-nitroanilide	-	hydrolysis
43773	gelatin	-	hydrolysis
43773	gentiobiose	-	builds acid from
43773	gluconate	-	carbon source
43773	glutaric acid	-	carbon source
43773	glycerol	-	builds acid from
43773	glycerol	-	carbon source
43773	glycogen	-	builds acid from
43773	itaconate	-	carbon source
43773	L-alanine	-	carbon source
43773	L-alanine 4-nitroanilide	-	hydrolysis
43773	L-arabinose	-	builds acid from
43773	L-arabinose	-	carbon source
43773	L-arabitol	-	builds acid from
43773	L-aspartate	-	carbon source
43773	L-fucose	-	builds acid from
43773	L-histidine	-	carbon source
43773	L-leucine	-	carbon source
43773	L-ornithine	-	carbon source
43773	L-phenylalanine	-	carbon source
43773	L-proline	-	carbon source
43773	L-proline-4-nitroanilide	-	hydrolysis
43773	L-rhamnose	-	builds acid from
43773	L-rhamnose	-	carbon source
43773	L-serine	-	carbon source
43773	L-sorbose	-	builds acid from
43773	L-tryptophan	-	carbon source
43773	L-xylose	-	builds acid from
43773	lactose	-	builds acid from
43773	maltitol	-	carbon source
43773	maltose	-	builds acid from
43773	maltose	+	builds acid from
43773	maltose	+/-	carbon source
43773	melezitose	-	builds acid from
43773	melibiose	-	builds acid from
43773	melibiose	+/-	carbon source
43773	mesaconate	-	carbon source
43773	methyl alpha-D-xylopyranoside	-	builds acid from
43773	methyl D-glucoside	-	builds acid from
43773	myo-inositol	-	builds acid from
43773	myo-inositol	-	carbon source
43773	N-acetylgalactosamine	-	carbon source
43773	N-acetylglucosamine	+	builds acid from
43773	N-acetylglucosamine	+/-	carbon source
43773	phenylacetate	-	carbon source
43773	propionate	-	carbon source
43773	putrescine	-	carbon source
43773	pyruvate	-	carbon source
43773	raffinose	-	builds acid from
43773	ribitol	-	builds acid from
43773	ribitol	-	carbon source
43773	ribose	-	builds acid from
43773	salicin	-	builds acid from
43773	salicin	+/-	carbon source
43773	starch	-	builds acid from
43773	starch	-	hydrolysis
43773	suberic acid	-	carbon source
43773	sucrose	-	builds acid from
43773	sucrose	+/-	carbon source
43773	trans-aconitate	-	carbon source
43773	trehalose	-	builds acid from
43773	turanose	-	builds acid from
43773	tyrosine	-	hydrolysis
43773	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
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

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

Genome browser: GCA_016908975

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: Neobacillus cucumis DSM 101566
NCBI: GCA_016908975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	87.70	no
125439	motility	BacteriaNetⓘ	yes	75.80	no
125439	gram_stain	BacteriaNetⓘ	variable	83.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	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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