Lysinibacillus composti (DSM 24785, JCM 18777, KCTC 13796)

Name: Lysinibacillus composti (DSM 24785, JCM 18777, KCTC 13796)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23758

Type strain

Culture col. no. DSM 24785 JCM 18777 KCTC 13796 NCCP 36

NCBI tax ID(s) 720633

Special Collections DSMZ JCM KCTC

History DSMZ <- I. Ahmed, National Agricultural Research Centre, Pakistan; NCCP-36 <- R. Hayat and I. Ahmed JCM <-- I. Ahmed NCCP-36. KCTC <- I Ahmed, NCCP, Pakistan

Links

Lysinibacillus composti DSM 24785 is an aerobe, spore-forming, motile bacterium that was isolated from aerobic compost of fruit and vegetable wastes.

spore-forming motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402542

JCM 18777,KCTC 13796,DSM 24785

@ref 20215

Last LPSN update 2026-05-29 08:30:29

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Lysinibacillus

Species Lysinibacillus composti

Full scientific name Lysinibacillus composti Hayat et al. 2014

Synonyms (1)

Ureibacillus composti

Morphology

Cell morphology

@ref	Cell shape	Motility	Gram stain
67771	rod-shaped
67771			negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21165	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21165	positive	growth	30
67770	positive	growth	30
67771	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	92.202

Spore formation

@ref	Type of spore	Spore formation
67771	endospore

Murein

@ref	Murein short key	Type
21165	A11.31	A4alpha L-Lys-D-Asp

Observation

@ref	Observation
67770	quinones: MK-7
67771	quinones: MK-7

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gallate degradation	100	5 of 5
66794	propanol degradation	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	aspartate and asparagine metabolism	100	9 of 9
66794	vitamin K metabolism	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	95.45	21 of 22
66794	citric acid cycle	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	glutamate and glutamine metabolism	92.86	26 of 28
66794	vitamin B1 metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	heme metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	leucine metabolism	84.62	11 of 13
66794	3-chlorocatechol degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	lysine metabolism	78.57	33 of 42
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	purine metabolism	77.66	73 of 94
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	arginine metabolism	70.83	17 of 24
66794	phenol degradation	70	14 of 20
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	non-pathway related	68.42	26 of 38
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	pentose phosphate pathway	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	oxidative phosphorylation	61.54	56 of 91
66794	cysteine metabolism	61.11	11 of 18
66794	factor 420 biosynthesis	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	degradation of sugar acids	56	14 of 25
66794	vitamin B6 metabolism	54.55	6 of 11
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycogen biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	starch degradation	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	cyclohexanol degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	lipid A biosynthesis	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	coenzyme M biosynthesis	40	4 of 10
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	IAA biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	myo-inositol biosynthesis	30	3 of 10
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Domestic waste
#Host	#Plants	#Decomposing plant

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21165	aerobic compost of fruit and vegetable wastes	Rawaldpindi, research farm of the Pir Mehr Ali Shah Arid Agriculture University	Pakistan	PAK	Asia
67770	Compost of fruit and vegetable wastes prepared aerobically	PMAS Arid Agriculture University, Rawalpindi	Pakistan	PAK	Asia
67771	From aerobic compost of fruit and vegetable wastes	Research farm of the Pir Mehr Ali Shah(PMAS) Arid Agriculture University, Rawalpindi	Pakistan	PAK	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB547124 (>99% sequence identity) for Lysinibacillus from Microbeatlas

Aquatic Samples	50
Soil Samples	441
Animal Samples	119
Plant Samples	37
Total Samples	647

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21165	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1690846v1 assembly for Lysinibacillus composti DSM 24785	contig	GCA_016908465	720633.8	2901136890	720633	55.51

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
21165	Lysinibacillus composti gene for 16S rRNA, partial sequence	AB547124	1475	720633
124043	Lysinibacillus composti strain NCCP-36 16S ribosomal RNA gene, partial sequence.	PV803117	1475	720633
124043	Lysinibacillus composti strain NCCP-36 16S ribosomal RNA gene, partial sequence.	OR660262	1166	720633

GC content

@ref	GC-content (mol%)	Method
21165	37.0	high performance liquid chromatography (HPLC)
67770	37	high performance liquid chromatography (HPLC)
67771	37.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1690846v1 assembly for Lysinibacillus composti DSM 24785
NCBI: GCA_016908465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.20	no
125439	motility	BacteriaNetⓘ	yes	49.93	no
125439	gram_stain	BacteriaNetⓘ	variable	48.54	no
125439	spore_formation	BacteriaNetⓘ	yes	59.18	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lysinibacillus composti strain DSM 24785
PATRIC: 720633.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	61.60	yes
125438	anaerobic	anaerobicⓘ	no	91.88	yes
125438	spore-forming	spore-formingⓘ	yes	86.99	no
125438	aerobic	aerobicⓘ	yes	81.54	no
125438	thermophilic	thermophileⓘ	no	92.15	yes
125438	flagellated	motile2+ⓘ	yes	83.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures.	Gupta RS, Patel S.	Front Microbiol	10.3389/fmicb.2019.02821	2019
	Lysinibacillus composti sp. nov., isolated from compost	Hayat R, Ahmed I, Paek J, Sin Y, Ehsan M, Iqbal M, Yokota A, Chang YH.	Ann Microbiol	10.1007/s13213-013-0747-1	2014
Phylogeny	Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean.	Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang Q	J Microbiol	10.1007/s12275-019-8709-3	2019

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 )
#21165	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24785
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 )

Content

About us

Lysinibacillus composti (DSM 24785, JCM 18777, KCTC 13796)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016908465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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