Name: Lysinibacillus xylanilyticus XDB9
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1540

Type strain:

Species: Lysinibacillus xylanilyticus

Strain Designation: XDB9

Culture col. no.: DSM 23493, CCUG 57438, KCTC 13423

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 582475 (species)

SI-ID 403611

DSM 23493, CCUG 57438

Section

Lysinibacillus xylanilyticus XDB9 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Forest humus.

Gram-positive
motile
rod-shaped
spore-forming
aerobe
mesophilic
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	*Caryophanaceae*
	Genus	*Lysinibacillus*
	Species	**Lysinibacillus xylanilyticus**
	Full Scientific Name (LPSN)	Lysinibacillus xylanilyticus Lee et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29452]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29452]	Cell length	4 µm

[Ref.: #29452]	Cell width	0.9 µm

[Ref.: #29452]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #29452]	Motility	yes
[Ref.: #67771]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.07

[Ref.: #61329]

Incubation period

1-2 days

[Ref.: #29452]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17180]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #17180]

Culture medium growth

[Ref.: #17180]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17180]

Culture medium composition

expand / minimize

[Ref.: #17180]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17180]

Culture medium growth

[Ref.: #17180]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17180]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17180]	growth	30 °C
[Ref.: #29452]	growth	10-40 °C
[Ref.: #29452]	optimum	30 °C
[Ref.: #61329]	growth	25-30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #17180]	Temperature range	mesophilic
[Ref.: #29452]	Temperature range	mesophilic
[Ref.: #61329]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29452]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29452]	Oxygen tolerance	aerobe
[Ref.: #61329]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #67771]	Type of spore	endospore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #29452]	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.: #29452]		NaCl		growth	0-5	%

[Ref.: #17180]	Murein short key	A11.31
[Ref.: #17180]	Murein types	A4alpha L-Lys-D-Asp

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29452]	arabinose ChEBI	+	carbon source
[Ref.: #29452]	citrate ChEBI	+	carbon source
[Ref.: #29452]	esculin ChEBI	+	hydrolysis
[Ref.: #29452]	maltose ChEBI	+	carbon source
[Ref.: #29452]	melibiose ChEBI	+	carbon source
[Ref.: #29452]	rhamnose ChEBI	+	carbon source
[Ref.: #29452]	sorbitol ChEBI	+	carbon source
[Ref.: #29452]	sucrose ChEBI	+	carbon source
[Ref.: #29452]	xylose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29452]	acid phosphatase	+	3.1.3.2
[Ref.: #29452]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29452]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29452]	gelatinase	+

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

[Ref.: #17180]	Sample type/isolated from	Forest humus
[Ref.: #17180]	Geographic location (country and/or sea, region)	Gyeryong Mountain, Taejon
[Ref.: #17180]	Country	Republic of Korea
[Ref.: #17180]	Country ISO 3 Code	KOR
[Ref.: #17180]	Continent	Asia

[Ref.: #61329]	Sample type/isolated from	Forest humus
[Ref.: #61329]	Sampling date	2008-01-01
[Ref.: #61329]	Geographic location (country and/or sea, region)	Taejon,Mt Gyeryong
[Ref.: #61329]	Country	Republic of Korea
[Ref.: #61329]	Country ISO 3 Code	KOR
[Ref.: #61329]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Mt. Gyeryong
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Forest

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ477040 (>99% sequence identity) for Lysinibacillus from Microbeatlas

Aquatic Samples	238
Soil Samples	1393
Animal Samples	561
Plant Samples	37
Total Samples	2229

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

[Ref.: #17180]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #17180]	Lysinibacillus xylanilyticus strain XDB9 16S ribosomal RNA gene, partial sequence	FJ477040	1349	ENA	582475 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lysinibacillus xylanilyticus DSM 23493	GCA_001183605	scaffold	GenBank	582475 tax ID	*
[Ref.: #66792]	Lysinibacillus xylanilyticus KCTC 13423	GCA_004365535	scaffold	GenBank	582475 tax ID	*
[Ref.: #66792]	Lysinibacillus xylanilyticus strain DSM 23493	582475.4	wgs	PATRIC	582475 tax ID	*
[Ref.: #66792]	Lysinibacillus xylanilyticus strain KCTC 13423	582475.14	wgs	PATRIC	582475 tax ID	*
[Ref.: #66792]	Lysinibacillus xylanilyticus KCTC 13423	2740891852	draft	JGI IMG/M	582475 tax ID	*
[Ref.: #66792]	Lysinibacillus xylanilyticus DSM 23493	2639763065	draft	JGI IMG/M	582475 tax ID	*

[Ref.: #17180]

GC-content

37.2 mol%

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: Lysinibacillus xylanilyticus DSM 23493 NCBI: GCA_001183605.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lysinibacillus xylanilyticus DSM 23493 NCBI: GCA_001183605.1
[Ref.: #69480]	motile	yes	89.335	yes
[Ref.: #69480]	flagellated	yes	83.348	no
[Ref.: #69480]	gram-positive	yes	90.269	no
[Ref.: #69480]	anaerobic	no	97.738	yes
[Ref.: #69480]	aerobic	yes	91.298	yes
[Ref.: #69480]	halophile	no	94.12	no
[Ref.: #69480]	spore-forming	yes	97.188	no
[Ref.: #69480]	glucose-util	yes	86.23	no
[Ref.: #69480]	thermophile	no	99.894	yes
[Ref.: #69480]	glucose-ferment	no	88.523	no

Availability in culture collections External links

[Ref.: #17180]

Culture collection no.

DSM 23493, CCUG 57438, KCTC 13423

[Ref.: #71185]

SI-ID 403611

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant.	Burkett-Cadena M, Sastoque L, Cadena J, Dunlap CA	Antonie Van Leeuwenhoek	10.1007/s10482-019-01248-w	2019	*
Genetics	Draft Genome Sequence of Type Strain Lysinibacillus xylanilyticus DSM 23493T.	Liu GH, Liu B, Wang JP, Che JM, Zheng XF, Chen QQ, Ge CB	Genome Announc	10.1128/genomeA.01037-15	2015	*
Phylogeny	Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo.	Ouoba LII, Vouidibio Mbozo AB, Thorsen L, Anyogu A, Nielsen DS, Kobawila SC, Sutherland JP	Int J Syst Evol Microbiol	10.1099/ijsem.0.000570	2015	*
Phylogeny	Lysinibacillus contaminans sp. nov., isolated from surface water.	Kampfer P, Martin K, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.049593-0	2013	*
Phylogeny	Lysinibacillus xylanilyticus sp. nov., a xylan-degrading bacterium isolated from forest humus.	Lee CS, Jung YT, Park S, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.013367-0	2009	*

References

#17180

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23493

#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 )

#29452

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25857 (see below)

#61329 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57438

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#71185

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-ID403611.1 )

#25857

IJSEM 281 2010 ( DOI 10.1099/ijs.0.013367-0 , PubMed 19651743 )

* These data were automatically processed and therefore are not curated

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Lysinibacillus xylanilyticus DSM 23493

Lysinibacillus xylanilyticus DSM 23493

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