Lysinibacillus contaminans (DSM 25560, CCM 8383, CIP 110362)

Name: Lysinibacillus contaminans (DSM 25560, CCM 8383, CIP 110362)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23760

Type strain

Strain Designation FSt3A

Culture col. no. DSM 25560 CCM 8383 CIP 110362 CCUG 62186 FSt3A

NCBI tax ID(s) 1293441

Special Collections DSMZ CCUG CIP Literature strains

History 2012, P. Kämpfer, J. Liebig Univ., Giessen, Germany: strain Fst3A <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; FSt 3 A CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain Fst3A

Links

Lysinibacillus contaminans FSt3A is an aerobe, spore-forming, mesophilic prokaryote that was isolated from surface water; strain was isolated from an agar plate as a contaminant of a Enterobacter sp. strain.

spore-forming Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 390749

CCM 8383,DSM 25560,CIP 110362,CCUG 62186

@ref 20215

Last LPSN update 2026-02-09 11:23:48

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Caryophanaceae

Genus Lysinibacillus

Species Lysinibacillus contaminans

Full scientific name Lysinibacillus contaminans Kämpfer et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Motility	Cell shape
31005	positive	2.5 µm	0.9 µm
118737					rod-shaped

Pigmentation

31005

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
39842	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
21167	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
118737	CIP Medium 566	Medium recipe at CIP
118737	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21167	positive	growth	30	mesophilic
31005	positive	growth	15-45
31005	positive	optimum	30	mesophilic
39842	positive	growth	25	mesophilic
62792	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31005	positive	optimum	7.5
31005	positive	growth	6.5-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31005	aerobe
62792	aerobe
118737	obligate aerobe
125439	facultative anaerobe	93.4

Spore formation

31005

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31005	NaCl	positive	growth	01-07 %
31005	NaCl	positive	optimum	1 %

Murein

@ref	Murein short key	Type
21167	A11.31	A4alpha L-Lys-D-Asp

Observation

31005

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
118737	17632 ChEBI	nitrate	-	reduction
118737	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118737	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31005	catalase	+	1.11.1.6
118737	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31005	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
31005	gelatinase	+
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118737	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
31005	urease	+	3.5.1.5
118737	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	vitamin B1 metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	valine 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	peptidoglycan biosynthesis	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
66794	heme metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	flavin biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B12 metabolism	76.47	26 of 34
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	NAD metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	purine metabolism	65.96	62 of 94
66794	histidine metabolism	65.52	19 of 29
66794	lysine metabolism	64.29	27 of 42
66794	proline metabolism	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	tryptophan metabolism	60.53	23 of 38
66794	arachidonate biosynthesis	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	polyamine pathway	56.52	13 of 23
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	ascorbate metabolism	54.55	12 of 22
66794	pentose phosphate pathway	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	starch degradation	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	lactate fermentation	50	2 of 4
66794	glutathione metabolism	50	7 of 14
66794	degradation of sugar acids	48	12 of 25
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	glycogen metabolism	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cholesterol biosynthesis	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	metabolism of disaccharids	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	CMP-KDO biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	allantoin degradation	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118737	-	-	+	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Contaminant
#Environmental	#Aquatic	#Surface water
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
21167	surface water; strain was isolated from an agar plate as a contaminant of a Enterobacter sp. strain	Enterobacter	Giessen	Germany	DEU	Europe
62792			Wuppertal	Germany	DEU	Europe	2000
118737	Environment, Surface water		Wuppertal	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KC254732 (>99% sequence identity) for Lysinibacillus contaminans subclade from Microbeatlas

Aquatic Samples	34
Soil Samples	214
Animal Samples	163
Plant Samples	3
Total Samples	414

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21167	1	Risk group (German classification)
118737	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	ASM127894v1 assembly for Lysinibacillus contaminans DSM 25560	scaffold	GCA_001278945	1293441.3	2648501842	1293441	59.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21167	Lysinibacillus contaminans strain FSt3A 16S ribosomal RNA gene, partial sequence	KC254732	1435		1293441

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lysinibacillus contaminans DSM 25560
NCBI: GCA_001278945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.00	no
125439	motility	BacteriaNetⓘ	yes	68.90	no
125439	gram_stain	BacteriaNetⓘ	variable	69.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lysinibacillus contaminans DSM 25560
NCBI: GCA_001278945.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.16	no
125438	anaerobic	anaerobicⓘ	no	93.57	yes
125438	aerobic	aerobicⓘ	yes	73.85	no
125438	spore-forming	spore-formingⓘ	yes	83.35	no
125438	thermophilic	thermophileⓘ	no	94.81	no
125438	flagellated	motile2+ⓘ	yes	78.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability.	Wu X, Zhou H, Li L, Wang E, Zhou X, Gu Y, Wu X, Shen L, Zeng W.	Microorganisms	10.3390/microorganisms8050716	2020
Transcriptome	Partial rpoB Gene Sequencing Identification and Probiotic Potential of Floricoccus penangensis ML061-4 Isolated from Assam Tea (Camellia sinensis var. assamica).	Rungsirivanich P, Inta A, Tragoolpua Y, Thongwai N.	Sci Rep	10.1038/s41598-019-52979-9	2019
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

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 )
#21167	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25560
#27335	IJSEM 3148 2013 ( DOI 10.1099/ijs.0.049593-0 , PubMed 23435244 )
#31005	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 #27335
#39842	; Curators of the CIP;
#62792	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62186
#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 )
#68382	Automatically annotated from API zym .
#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 .
#118737	Collection of Institut Pasteur ; Curators of the CIP; CIP 110362
#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 )

Rate our new design

Content

About us

Lysinibacillus contaminans (DSM 25560, CCM 8383, CIP 110362)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001278945

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media