Name: Saccharibacillus endophyticus JM-1350
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133027

Type strain:

Species: Saccharibacillus endophyticus

Strain Designation: JM-1350

Culture col. no.: DSM 103533, CCM 8702, LMG 29710, CIP 111111

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1350

NCBI tax ID(s): 2060666 (species)

SI-ID 401753

DSM 103533

Section

Saccharibacillus endophyticus JM-1350 is a spore-forming, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from inner tissues of field grown cotton .

colony-forming
Gram-positive
rod-shaped
spore-forming
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	*Paenibacillaceae*
	Genus	*Saccharibacillus*
	Species	**Saccharibacillus endophyticus**
	Full Scientific Name (LPSN)	Saccharibacillus endophyticus Kämpfer et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25105]	Gram stain	positive
[Ref.: #119031]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25105]	Cell length	4.0-6.5 µm

[Ref.: #25105]	Cell width	0.8-1.3 µm

[Ref.: #25105]	Cell shape	rod-shaped
[Ref.: #119031]	Cell shape	rod-shaped

[Ref.: #25105]	Motility	no
[Ref.: #119031]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.97

[Ref.: #25105]	Colony size	2.0-3.0 mm
[Ref.: #25105]	Colony color	beige
[Ref.: #25105]	Colony shape	circular
[Ref.: #25105]	Incubation period	2 days
[Ref.: #25105]	Cultivation medium used	TSA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25105]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #25105]

Culture medium growth

[Ref.: #42167]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #42167]

Culture medium growth

[Ref.: #42167]

Culture medium composition

expand / minimize

[Ref.: #24815]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #24815]

Culture medium growth

[Ref.: #24815]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24815]

Culture medium composition

expand / minimize

[Ref.: #119031]

Culture medium

CIP Medium 72

[Ref.: #119031]

Culture medium growth

[Ref.: #119031]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #24815]		growth	30 °C
[Ref.: #25105]		growth	10-36 °C
[Ref.: #25105]		optimum	28-30 °C
[Ref.: #25105]	no	growth	4 °C
[Ref.: #25105]	no	growth	45 °C
[Ref.: #42167]		growth	25 °C

[Ref.: #24815]	Temperature range	mesophilic
[Ref.: #25105]	Temperature range	mesophilic
[Ref.: #25105]	Temperature range	psychrophilic
[Ref.: #25105]	Temperature range	thermophilic
[Ref.: #42167]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25105]			optimum	7.0-8.0
[Ref.: #25105]			growth	5.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25105]	Spore description	oval, formed in a terminal position in a swollen sporangium
[Ref.: #25105]	Type of spore	endospore
[Ref.: #25105]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25105]		NaCl		growth	1.0-7.0	%
[Ref.: #25105]		NaCl	no	growth	9	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25105]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #25105]	4-nitrophenyl beta-D-galactopyranoside hydrolysate	+	hydrolysis
[Ref.: #25105]	acetate ChEBI	-	carbon source
[Ref.: #25105]	adipate ChEBI	-	carbon source
[Ref.: #25105]	arbutin ChEBI	+	carbon source
[Ref.: #25105]	azelaate ChEBI	-	carbon source
[Ref.: #25105]	casein	-	hydrolysis
[Ref.: #25105]	cellobiose ChEBI	-	builds acid from
[Ref.: #25105]	cellobiose ChEBI	+	carbon source
[Ref.: #25105]	cis-aconitate ChEBI	-	carbon source
[Ref.: #25105]	citrate ChEBI	-	carbon source
[Ref.: #25105]	D-arabitol ChEBI	-	builds acid from
[Ref.: #25105]	D-fructose ChEBI	+	carbon source
[Ref.: #25105]	D-galactose ChEBI	+	carbon source
[Ref.: #25105]	D-glucose ChEBI	+	builds acid from
[Ref.: #25105]	D-glucose ChEBI	+	carbon source
[Ref.: #25105]	D-mannitol ChEBI	-	builds acid from
[Ref.: #25105]	D-mannitol ChEBI	+	carbon source
[Ref.: #25105]	D-mannose ChEBI	-	builds acid from
[Ref.: #25105]	D-mannose ChEBI	-	assimilation
[Ref.: #25105]	D-mannose ChEBI	+	carbon source
[Ref.: #25105]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #25105]	D-sorbitol ChEBI	+	carbon source
[Ref.: #25105]	D-xylose ChEBI	-	builds acid from
[Ref.: #25105]	D-xylose ChEBI	+	carbon source
[Ref.: #25105]	erythritol ChEBI	-	builds acid from
[Ref.: #25105]	esculin ChEBI	+	hydrolysis
[Ref.: #25105]	galactitol ChEBI	-	builds acid from
[Ref.: #25105]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #25105]	gelatin ChEBI	-	hydrolysis
[Ref.: #25105]	gluconate ChEBI	-	carbon source
[Ref.: #25105]	itaconate ChEBI	-	carbon source
[Ref.: #25105]	L-alanine 4-nitroanilide	+	hydrolysis
[Ref.: #25105]	L-arabinose ChEBI	-	assimilation
[Ref.: #25105]	L-arabinose ChEBI	+	builds acid from
[Ref.: #25105]	L-arabinose ChEBI	+	carbon source
[Ref.: #25105]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25105]	L-rhamnose ChEBI	-	carbon source
[Ref.: #25105]	lactose ChEBI	-	builds acid from
[Ref.: #25105]	malate ChEBI	-	carbon source
[Ref.: #25105]	malate ChEBI	-	assimilation
[Ref.: #25105]	maltitol ChEBI	+	carbon source
[Ref.: #25105]	maltose ChEBI	-	builds acid from
[Ref.: #25105]	maltose ChEBI	-	assimilation
[Ref.: #25105]	maltose ChEBI	+	carbon source
[Ref.: #25105]	melibiose ChEBI	-	builds acid from
[Ref.: #25105]	melibiose ChEBI	-	carbon source
[Ref.: #25105]	mesaconate ChEBI	-	carbon source
[Ref.: #25105]	myo-inositol ChEBI	+	carbon source
[Ref.: #25105]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25105]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25105]	nitrate ChEBI	+	reduction
[Ref.: #25105]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25105]	propionate ChEBI	-	carbon source
[Ref.: #25105]	putrescine ChEBI	-	carbon source
[Ref.: #25105]	pyruvate ChEBI	-	carbon source
[Ref.: #25105]	raffinose ChEBI	-	builds acid from
[Ref.: #25105]	ribitol ChEBI	-	builds acid from
[Ref.: #25105]	ribitol ChEBI	-	carbon source
[Ref.: #25105]	ribose ChEBI	-	carbon source
[Ref.: #25105]	salicin ChEBI	-	builds acid from
[Ref.: #25105]	salicin ChEBI	+	carbon source
[Ref.: #25105]	sodium citrate ChEBI	-	assimilation
[Ref.: #25105]	starch ChEBI	-	hydrolysis
[Ref.: #25105]	sucrose ChEBI	-	builds acid from
[Ref.: #25105]	sucrose ChEBI	+	carbon source
[Ref.: #25105]	trans-aconitate ChEBI	-	carbon source
[Ref.: #25105]	trehalose ChEBI	-	builds acid from
[Ref.: #25105]	trehalose ChEBI	+	carbon source
[Ref.: #25105]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25105]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test	Citrate test
[Ref.: #25105]		citrate ChEBI		-
[Ref.: #25105]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25105]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25105]	beta-galactosidase	+	3.2.1.23
[Ref.: #25105]	catalase	-	1.11.1.6
[Ref.: #25105]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25105]	gelatinase	-
[Ref.: #25105]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25105]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25105]	tryptophan deaminase	-	4.1.99.1

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

[Ref.: #24815]	Sample type/isolated from	inner tissues of field grown cotton (Gossypium hirsutum, cultivar 'DES-119')
[Ref.: #24815]	Host species	Gossypium hirsutum
[Ref.: #24815]	Geographic location (country and/or sea, region)	Alabama, Tallassee
[Ref.: #24815]	Country	USA
[Ref.: #24815]	Country ISO 3 Code	USA
[Ref.: #24815]	Continent	North America

[Ref.: #25105]	Sample type/isolated from	healthy inner stem tissue of a field-grown cotton plant (Gossypium hirsutum, cultivar ‘DES-119’)

[Ref.: #119031]	Sample type/isolated from	Tissues of field grown cotton, Gossypium hirsutum
[Ref.: #119031]	Geographic location (country and/or sea, region)	Tallassee, Alabama, USA
[Ref.: #119031]	Country	United States of America
[Ref.: #119031]	Country ISO 3 Code	USA
[Ref.: #119031]	Continent	North America
[Ref.: #119031]	Isolation date	1990-01-02
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX523193 (>99% sequence identity) for Saccharibacillus endophyticus subclade from Microbeatlas

Aquatic Samples	74
Soil Samples	74
Animal Samples	101
Plant Samples	270
Total Samples	519

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

[Ref.: #24815]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119031]	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.: #24815]	Saccharibacillus endophyticus strain JM-1350 16S ribosomal RNA gene, partial sequence	KX523193	1454	ENA	2060666 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Saccharibacillus endophyticus CCM 8702	GCA_013185185	contig	GenBank	2060666 tax ID	*
[Ref.: #66792]	Saccharibacillus endophyticus CCM 8702	GCA_014635605	scaffold	GenBank	2060666 tax ID	*
[Ref.: #66792]	Saccharibacillus endophyticus strain CCM 8702	2060666.4	wgs	PATRIC	2060666 tax ID	*
[Ref.: #66792]	Saccharibacillus endophyticus strain CCM 8702	2060666.5	wgs	PATRIC	2060666 tax ID	*
[Ref.: #66792]	Saccharibacillus endophyticus CCM 8702	2910409337	draft	JGI IMG/M	2060666 tax ID	*

[Ref.: #25105]	GC-content	55.2 mol%	Thermal denaturation, fluorometry
[Ref.: #24815]	GC-content	55.2 mol%	fluorimetric

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: Saccharibacillus endophyticus strain CCM 8702 PATRIC: 2060666.5
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Saccharibacillus endophyticus CCM 8702 NCBI: GCA_014635605.1
[Ref.: #69480]	flagellated	yes	75.802	no
[Ref.: #69480]	gram-positive	yes	90.12	yes
[Ref.: #69480]	anaerobic	no	97.609	no
[Ref.: #69480]	aerobic	yes	71.443	no
[Ref.: #69480]	halophile	no	86.939	no
[Ref.: #69480]	spore-forming	yes	93.341	yes
[Ref.: #69480]	thermophile	no	99.872	no
[Ref.: #69480]	glucose-util	yes	89.092	yes
[Ref.: #69480]	motile	yes	87.637	no
[Ref.: #69480]	glucose-ferment	no	66.236	no

Availability in culture collections External links

[Ref.: #24815]

Culture collection no.

DSM 103533, CCM 8702, LMG 29710, CIP 111111

[Ref.: #91297]

SI-ID 401753

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Saccharibacillus endophyticus sp. nov., an endophyte of cotton.	Kampfer P, Busse HJ, Kleinhagauer T, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.001484	2016	*

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 )

#24815

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103533

#25105

P. B. Kämpfer, H. J.,Kleinhagauer, T.,McInroy, J. A.,Glaeser, S. P.: Saccharibacillus endophyticus sp. nov., an endophyte of cotton. IJSEM 66: 5134 - 5139 2016 ( DOI 10.1099/ijsem.0.001484 , PubMed 27613514 )

#42167 ; 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) .

#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 .

#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 )

#91297

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-ID401753.1 )

#119031 Collection of Institut Pasteur ; Curators of the CIP; CIP 111111
* These data were automatically processed and therefore are not curated

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Saccharibacillus endophyticus strain CCM 8702

Saccharibacillus endophyticus CCM 8702

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