Name: Neobacillus cucumis Ap-6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132382

Type strain:

Species: Neobacillus cucumis

Strain Designation: Ap-6

Culture col. no.: DSM 101566, CCM 8651, CIP 110974

Strain history: CIP <- 2015, P. Kampfer, Giessen Univ., Giessen, Germany: strain AP-6

NCBI tax ID(s): 1740721 (species)

SI-ID 396494

LMG 29192, CCM 8651, CIP 110974, DSM 101566

Section

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.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Neobacillus*
	Species	**Neobacillus cucumis**
	Full Scientific Name (LPSN)	Neobacillus cucumis (Kämpfer et al. 2016) Patel and Gupta 2020

Synonym

Bacillus cucumis

Information on morphological and physiological properties Morphology

[Ref.: #43773]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43773]	Cell length	3 µm

[Ref.: #43773]	Cell width	1 µm

[Ref.: #43773]	Cell shape	rod-shaped
[Ref.: #118809]	Cell shape	rod-shaped

[Ref.: #43773]	Motility	no
[Ref.: #118809]	Motility	no

[Ref.: #43773]	Colony size	2 mm
[Ref.: #43773]	Colony color	Beige
[Ref.: #43773]	Colony shape	circular
[Ref.: #43773]	Incubation period	2 days
[Ref.: #43773]	Cultivation medium used	Nutrient agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43773]

Culture medium

Nutrient agar (NA)

[Ref.: #43773]

Culture medium growth

[Ref.: #24171]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #24171]

Culture medium growth

[Ref.: #24171]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24171]

Culture medium composition

expand / minimize

[Ref.: #118809]

Culture medium

CIP Medium 72

[Ref.: #118809]

Culture medium growth

[Ref.: #118809]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #24171]	growth	30 °C
[Ref.: #43773]	growth	16-45 °C
[Ref.: #43773]	optimum	28-30 °C

[Ref.: #24171]	Temperature range	mesophilic
[Ref.: #43773]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43773]

Oxygen tolerance

facultative anaerobe

[Ref.: #43773]	Spore description	circular, subterminal
[Ref.: #43773]	Type of spore	endospore
[Ref.: #43773]	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

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43773]		NaCl		growth	0.5-4	%(w/v)
[Ref.: #43773]		NaCl		optimum	1-2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43773]	2-deoxythymidine-5'-4-nitrophenyl phosphate	-	hydrolysis
[Ref.: #43773]	2-oxogluconate	-	builds acid from
[Ref.: #43773]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #43773]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #43773]	3-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #43773]	4-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #43773]	4-nitrophenyl alpha-D-glucopyranoside ChEBI	+	hydrolysis
[Ref.: #43773]	4-nitrophenyl beta-D-galactopyranoside hydrolysate	-	hydrolysis
[Ref.: #43773]	4-nitrophenyl beta-D-glucopyranoside ChEBI	-	hydrolysis
[Ref.: #43773]	4-nitrophenyl beta-D-glucuronide ChEBI	-	hydrolysis
[Ref.: #43773]	4-nitrophenyl beta-D-xylopyranoside ChEBI	-	hydrolysis
[Ref.: #43773]	acetate ChEBI	-	carbon source
[Ref.: #43773]	adipate ChEBI	-	carbon source
[Ref.: #43773]	amygdalin ChEBI	-	builds acid from
[Ref.: #43773]	azelaate ChEBI	-	carbon source
[Ref.: #43773]	beta-alanine ChEBI	-	carbon source
[Ref.: #43773]	bis-4-nitrophenyl phosphate ChEBI	-	hydrolysis
[Ref.: #43773]	bis-4-nitrophenyl-phenyl phosphonate ChEBI	-	hydrolysis
[Ref.: #43773]	bis-4-nitrophenyl-phosphorylcholine ChEBI	-	hydrolysis
[Ref.: #43773]	casein	-	hydrolysis
[Ref.: #43773]	cellobiose ChEBI	-	builds acid from
[Ref.: #43773]	cellobiose ChEBI	+/-	carbon source
[Ref.: #43773]	cis-aconitate ChEBI	-	carbon source
[Ref.: #43773]	citrate ChEBI	-	carbon source
[Ref.: #43773]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43773]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43773]	D-fructose ChEBI	+	builds acid from
[Ref.: #43773]	D-fructose ChEBI	+/-	carbon source
[Ref.: #43773]	D-galactose ChEBI	-	carbon source
[Ref.: #43773]	D-glucose ChEBI	+	builds acid from
[Ref.: #43773]	D-glucose ChEBI	+/-	builds acid from
[Ref.: #43773]	D-glucose ChEBI	+/-	carbon source
[Ref.: #43773]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43773]	D-mannitol ChEBI	-	carbon source
[Ref.: #43773]	D-mannose ChEBI	+/-	carbon source
[Ref.: #43773]	D-ribose ChEBI	-	carbon source
[Ref.: #43773]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43773]	D-sorbitol ChEBI	-	carbon source
[Ref.: #43773]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43773]	D-xylose ChEBI	-	builds acid from
[Ref.: #43773]	D-xylose ChEBI	-	carbon source
[Ref.: #43773]	dna ChEBI	-	hydrolysis
[Ref.: #43773]	erythritol ChEBI	-	builds acid from
[Ref.: #43773]	esculin ChEBI	+	hydrolysis
[Ref.: #43773]	fumarate ChEBI	-	carbon source
[Ref.: #43773]	galactitol ChEBI	-	builds acid from
[Ref.: #43773]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #43773]	gamma-L-glutamate-4-nitroanilide	-	hydrolysis
[Ref.: #43773]	gelatin ChEBI	-	hydrolysis
[Ref.: #43773]	gentiobiose ChEBI	-	builds acid from
[Ref.: #43773]	gluconate ChEBI	-	carbon source
[Ref.: #43773]	glutaric acid ChEBI	-	carbon source
[Ref.: #43773]	glycerol ChEBI	-	builds acid from
[Ref.: #43773]	glycerol ChEBI	-	carbon source
[Ref.: #43773]	glycogen ChEBI	-	builds acid from
[Ref.: #43773]	itaconate ChEBI	-	carbon source
[Ref.: #43773]	L-alanine ChEBI	-	carbon source
[Ref.: #43773]	L-alanine 4-nitroanilide	-	hydrolysis
[Ref.: #43773]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43773]	L-arabinose ChEBI	-	carbon source
[Ref.: #43773]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43773]	L-aspartate ChEBI	-	carbon source
[Ref.: #43773]	L-fucose ChEBI	-	builds acid from
[Ref.: #43773]	L-histidine ChEBI	-	carbon source
[Ref.: #43773]	L-leucine ChEBI	-	carbon source
[Ref.: #43773]	L-ornithine ChEBI	-	carbon source
[Ref.: #43773]	L-phenylalanine ChEBI	-	carbon source
[Ref.: #43773]	L-proline ChEBI	-	carbon source
[Ref.: #43773]	L-proline-4-nitroanilide	-	hydrolysis
[Ref.: #43773]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43773]	L-rhamnose ChEBI	-	carbon source
[Ref.: #43773]	L-serine ChEBI	-	carbon source
[Ref.: #43773]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43773]	L-tryptophan ChEBI	-	carbon source
[Ref.: #43773]	L-xylose ChEBI	-	builds acid from
[Ref.: #43773]	lactose ChEBI	-	builds acid from
[Ref.: #43773]	maltitol ChEBI	-	carbon source
[Ref.: #43773]	maltose ChEBI	-	builds acid from
[Ref.: #43773]	maltose ChEBI	+	builds acid from
[Ref.: #43773]	maltose ChEBI	+/-	carbon source
[Ref.: #43773]	melezitose ChEBI	-	builds acid from
[Ref.: #43773]	melibiose ChEBI	-	builds acid from
[Ref.: #43773]	melibiose ChEBI	+/-	carbon source
[Ref.: #43773]	mesaconate ChEBI	-	carbon source
[Ref.: #43773]	methyl alpha-D-xylopyranoside	-	builds acid from
[Ref.: #43773]	methyl D-glucoside ChEBI	-	builds acid from
[Ref.: #43773]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43773]	myo-inositol ChEBI	-	carbon source
[Ref.: #43773]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #43773]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #43773]	N-acetylglucosamine ChEBI	+/-	carbon source
[Ref.: #43773]	phenylacetate ChEBI	-	carbon source
[Ref.: #43773]	propionate ChEBI	-	carbon source
[Ref.: #43773]	putrescine ChEBI	-	carbon source
[Ref.: #43773]	pyruvate ChEBI	-	carbon source
[Ref.: #43773]	raffinose ChEBI	-	builds acid from
[Ref.: #43773]	ribitol ChEBI	-	builds acid from
[Ref.: #43773]	ribitol ChEBI	-	carbon source
[Ref.: #43773]	ribose ChEBI	-	builds acid from
[Ref.: #43773]	salicin ChEBI	-	builds acid from
[Ref.: #43773]	salicin ChEBI	+/-	carbon source
[Ref.: #43773]	starch ChEBI	-	builds acid from
[Ref.: #43773]	starch ChEBI	-	hydrolysis
[Ref.: #43773]	suberic acid ChEBI	-	carbon source
[Ref.: #43773]	sucrose ChEBI	-	builds acid from
[Ref.: #43773]	sucrose ChEBI	+/-	carbon source
[Ref.: #43773]	trans-aconitate ChEBI	-	carbon source
[Ref.: #43773]	trehalose ChEBI	-	builds acid from
[Ref.: #43773]	turanose ChEBI	-	builds acid from
[Ref.: #43773]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43773]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43773]		hydrogen sulfide ChEBI	no
[Ref.: #43773]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43773]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43773]	beta-galactosidase	-	3.2.1.23
[Ref.: #43773]	catalase	+	1.11.1.6
[Ref.: #43773]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43773]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43773]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43773]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43773]	urease	-	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24171]	Sample type/isolated from	rhizosphere soil closely adhering to the roots of field-grown cucumber Cucumis sativus cultivar Straight 8
[Ref.: #24171]	Host species	Cucumis sativus
[Ref.: #24171]	Geographic location (country and/or sea, region)	Alabama, Tallassee (Elmore county), E.V. Smith Research Center
[Ref.: #24171]	Country	USA
[Ref.: #24171]	Country ISO 3 Code	USA
[Ref.: #24171]	Continent	North America

[Ref.: #43773]	Sample type/isolated from	The rhizosphere soil of field-grown cucumber (Cucumis sativus) roots at the E.V. Smith Research Center
[Ref.: #43773]	Geographic location (country and/or sea, region)	Elmore County, Alabama
[Ref.: #43773]	Country	USA
[Ref.: #43773]	Country ISO 3 Code	USA
[Ref.: #43773]	Continent	North America

[Ref.: #118809]	Sample type/isolated from	Plant, Field-grown Cucumber plant
[Ref.: #118809]	Geographic location (country and/or sea, region)	Tallassee , Alabama
[Ref.: #118809]	Country	United States of America
[Ref.: #118809]	Country ISO 3 Code	USA
[Ref.: #118809]	Continent	North America
[Ref.: #118809]	Isolation date	1996-07-01
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #24171]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118809]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #24171]	Bacillus cucumis strain AP-6 16S ribosomal RNA gene, partial sequence	KT895286	1474	ENA	1740721 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Neobacillus cucumis DSM 101566	GCA_016908975	contig	GenBank	1740721 tax ID	*
[Ref.: #66792]	Neobacillus cucumis strain DSM 101566	1740721.8	wgs	PATRIC	1740721 tax ID	*
[Ref.: #66792]	Neobacillus cucumis DSM 101566	2901240655	draft	JGI IMG/M	1740721 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Neobacillus cucumis strain DSM 101566 PATRIC: 1740721.7
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Neobacillus cucumis strain DSM 101566 PATRIC: 1740721.8
[Ref.: #69480]	motile	no	85.692	yes
[Ref.: #69480]	gram-positive	yes	87.604	yes
[Ref.: #69480]	anaerobic	no	98.738	yes
[Ref.: #69480]	aerobic	yes	69.364	yes
[Ref.: #69480]	halophile	no	85.089	no
[Ref.: #69480]	spore-forming	yes	92.11	yes
[Ref.: #69480]	thermophile	no	98.299	no
[Ref.: #69480]	glucose-util	yes	87.006	no
[Ref.: #69480]	flagellated	no	69.513	no
[Ref.: #69480]	glucose-ferment	no	84.679	no

Availability in culture collections External links

[Ref.: #24171]

Culture collection no.

DSM 101566, CCM 8651, CIP 110974

[Ref.: #90725]

SI-ID 396494

Literature:

Topic	Title	Authors	Journal	DOI	Year
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) .

#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 )

#90725

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID396494.1 )

#118809 Collection of Institut Pasteur ; Curators of the CIP; CIP 110974
* These data were automatically processed and therefore are not curated

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Neobacillus cucumis strain DSM 101566

Neobacillus cucumis strain DSM 101566

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