Name: Lysobacter defluvii DSM 18482
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17490

Type strain:

Species: Lysobacter defluvii

Culture col. no.: DSM 18482, CCUG 53152, CIP 109615, IMMIB APB-9

Strain history: CIP <- 2007, CCUG <- 2006, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB APB-9

NCBI tax ID(s): 1385515 (strain), 391738 (species)

SI-ID 308619

CCUG 53152, DSM 18482, CIP 109615

Section

Lysobacter defluvii DSM 18482 is an aerobe, Gram-negative, motile bacterium that was isolated from municipal land fill.

Gram-negative
motile
rod-shaped
aerobe
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter defluvii**
	Full Scientific Name (LPSN)	Lysobacter defluvii Yassin et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32101]	Gram stain	negative
[Ref.: #118870]	Gram stain	negative

[Ref.: #32101]	Cell length	1.5 µm

[Ref.: #32101]	Cell shape	rod-shaped
[Ref.: #118870]	Cell shape	rod-shaped

[Ref.: #32101]	Motility	yes
[Ref.: #118870]	Motility	no

[Ref.: #32101]	Flagellum arrangement	gliding

[Ref.: #32101]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37789]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #37789]

Culture medium growth

[Ref.: #37789]

Culture medium composition

expand / minimize

[Ref.: #118870]

Culture medium

CIP Medium 40

[Ref.: #118870]

Culture medium growth

[Ref.: #118870]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #118870]

Culture medium

CIP Medium 72

[Ref.: #118870]

Culture medium growth

[Ref.: #118870]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #32101]	growth	22-37 °C
[Ref.: #32101]	optimum	29.5 °C
[Ref.: #37789]	growth	30 °C
[Ref.: #59812]	growth	22-42 °C

[Ref.: #32101]	Temperature range	mesophilic
[Ref.: #37789]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32101]	Oxygen tolerance	aerobe
[Ref.: #59812]	Oxygen tolerance	aerobe
[Ref.: #118870]	Oxygen tolerance	obligate aerobe

[Ref.: #32101]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32101]		NaCl		growth	0-6	%
[Ref.: #32101]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32101]	gelatin ChEBI	+	carbon source
[Ref.: #118870]	nitrate ChEBI	-	reduction
[Ref.: #118870]	nitrite ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118870]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32101]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32101]	catalase	+	1.11.1.6
[Ref.: #118870]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32101]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #32101]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118870]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118870]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118870]	12001	-	+	-	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	threonine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	heme metabolism	42.86	6 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	oxidative phosphorylation	34.07	31 of 91
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7555]	Sample type/isolated from	municipal land fill
[Ref.: #7555]	Geographic location (country and/or sea, region)	Udupi, Karnataka state
[Ref.: #7555]	Country	India
[Ref.: #7555]	Country ISO 3 Code	IND
[Ref.: #7555]	Continent	Asia

[Ref.: #59812]	Sample type/isolated from	Municipal land fill waiste
[Ref.: #59812]	Sampling date	2005
[Ref.: #59812]	Geographic location (country and/or sea, region)	Karnataka state,Udupi
[Ref.: #59812]	Country	India
[Ref.: #59812]	Country ISO 3 Code	IND
[Ref.: #59812]	Continent	Asia

[Ref.: #118870]	Sample type/isolated from	Environment, Soil, municipal landfill site
[Ref.: #118870]	Country	India
[Ref.: #118870]	Country ISO 3 Code	IND
[Ref.: #118870]	Continent	Asia
[Ref.: #118870]	Isolation date	2005
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Landfill

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM283465 (>99% sequence identity) for Lysobacter defluvii subclade from Microbeatlas

Aquatic Samples	178
Soil Samples	176
Animal Samples	295
Plant Samples	51
Total Samples	700

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

[Ref.: #7555]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118870]	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.: #7555]	Lysobacter defluvii partial 16S rRNA gene, type strain IMMIB APB-9T	AM283465	1509	ENA	1385515 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lysobacter defluvii IMMIB APB-9 = DSM 18482	GCA_000423325	scaffold	GenBank	1385515 tax ID	*
[Ref.: #66792]	Lysobacter defluvii IMMIB APB-9 = DSM 18482	GCA_000769985	contig	GenBank	1385515 tax ID	*
[Ref.: #66792]	Lysobacter defluvii DSM 18482	1122186.3	wgs	PATRIC	1385515 tax ID	*
[Ref.: #66792]	Lysobacter defluvii IMMIB APB-9 = DSM 18482	1385515.3	wgs	PATRIC	1385515 tax ID	*
[Ref.: #66792]	Lysobacter defluvii DSM 18482	2524614664	draft	JGI IMG/M	1385515 tax ID	*

[Ref.: #32101]

GC-content

67.1 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lysobacter defluvii IMMIB APB-9 = DSM 18482 DSM 18482 NCBI: GCA_000423325.1
[Ref.: #69480]	motile	yes	82.696	no
[Ref.: #69480]	flagellated	no	86.784	yes
[Ref.: #69480]	gram-positive	no	98.635	no
[Ref.: #69480]	anaerobic	no	98.33	yes
[Ref.: #69480]	aerobic	yes	88.69	yes
[Ref.: #69480]	halophile	no	90.173	no
[Ref.: #69480]	spore-forming	no	95.382	yes
[Ref.: #69480]	glucose-util	yes	78.555	no
[Ref.: #69480]	thermophile	no	95.827	yes
[Ref.: #69480]	glucose-ferment	no	91.524	no

Availability in culture collections External links

[Ref.: #7555]

Culture collection no.

DSM 18482, CCUG 53152, CIP 109615, IMMIB APB-9

[Ref.: #86488]

SI-ID 308619

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysobacter defluvii sp. nov., isolated from municipal solid waste.	Yassin AF, Chen WM, Hupfer H, Siering C, Kroppenstedt RM, Arun AB, Lai WA, Shen FT, Rekha PD, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.64966-0	2007	*

References

#7555

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18482

#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 )

#32101

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 #28346 (see below)

#37789 ; Curators of the CIP;
#59812 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53152

#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 .

#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) .

#86488

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-ID308619.1 )

#118870 Collection of Institut Pasteur ; Curators of the CIP; CIP 109615

#28346

IJSEM 1131 2007 ( DOI 10.1099/ijs.0.64966-0 , PubMed 17473271 )

* These data were automatically processed and therefore are not curated

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Lysobacter defluvii IMMIB APB-9 = DSM 18482 DSM 18482

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