Name: Lysobacter antibioticus 3C
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17474

Type strain:

Species: Lysobacter antibioticus

Strain Designation: 3C

Culture col. no.: DSM 2044, ATCC 29479, NBRC 100085, VKM B-2273, CCUG 55583, LMG 8760, HAMBI 1957, Ly a2, UASM 3C

Strain history: <- H. Reichenbach, Ly a2 <- P. Christensen, UASM 3C <- F.D. Cook (Sorangium sp. 3C)

NCBI tax ID(s): 84531 (species)

SI-ID 3550

LMG 8760, ATCC 29479, CCRC 11653, DSM 2044, NCIB 10773, NCIMB 10773, CECT 4280, VKM B-2273, NBRC 100085, HAMBI 1957, BCRC 11653, KCTC 12129

Other strains from Lysobacter antibioticus

L. antibioticus DSM 2045, ATCC 29480, Ly a1, UASM ...

Section

Lysobacter antibioticus 3C is a mesophilic bacterium that was isolated from soil.

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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter antibioticus**
	Full Scientific Name (LPSN)	Lysobacter antibioticus Christensen and Cook 1978 (Approved Lists 1980)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #686]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #686]

Culture medium growth

[Ref.: #686]

Culture medium link

Medium recipe at MediaDive

[Ref.: #686]

Culture medium composition

expand / minimize

[Ref.: #686]

Culture medium

CY-AGAR (DSMZ Medium 67)

[Ref.: #686]

Culture medium growth

[Ref.: #686]

Culture medium link

Medium recipe at MediaDive

[Ref.: #686]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #686]			growth	30 °C

[Ref.: #686]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #686]

Name of produced compound

myxin

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #686]	23350	+	-	-	-	-	+	+	+	-	-	+	-	+	+	-	-	-	-	-	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	tryptophan metabolism	78.95	30 of 38
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		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.: #686]	Sample type/isolated from	soil
[Ref.: #686]	Geographic location (country and/or sea, region)	Ontario, Ottawa
[Ref.: #686]	Country	Canada
[Ref.: #686]	Country ISO 3 Code	CAN
[Ref.: #686]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB019582 (>99% sequence identity) for Lysobacter from Microbeatlas

Aquatic Samples	1340
Soil Samples	9924
Animal Samples	1424
Plant Samples	3890
Total Samples	16578

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

[Ref.: #686]

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.: #686]	Lysobacter antibioticus gene for 16S rRNA, partial sequence	AB019582	1495	ENA	84531 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lysobacter antibioticus ATCC 29479	GCA_001442535	complete	GenBank	84531 tax ID	*
[Ref.: #66792]	Lysobacter antibioticus strain ATCC 29479	84531.7	complete	PATRIC	84531 tax ID	*
[Ref.: #66792]	Lysobacter antibioticus ATCC 29479	2687453248	complete	JGI IMG/M	84531 tax ID	*

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 antibioticus ATCC 29479 NCBI: GCA_001442535.1
[Ref.: #69480]	flagellated	no	94.811	no
[Ref.: #69480]	gram-positive	no	98.201	no
[Ref.: #69480]	anaerobic	no	99.487	no
[Ref.: #69480]	aerobic	yes	95.291	no
[Ref.: #69480]	halophile	no	96.443	no
[Ref.: #69480]	spore-forming	no	93.897	no
[Ref.: #69480]	glucose-util	yes	91.468	no
[Ref.: #69480]	motile	no	60.852	no
[Ref.: #69480]	thermophile	no	99.147	yes
[Ref.: #69480]	glucose-ferment	no	90.354	no

Availability in culture collections External links

[Ref.: #686]

Culture collection no.

DSM 2044, ATCC 29479, NBRC 100085, VKM B-2273, CCUG 55583, LMG 8760, HAMBI 1957, Ly a2, UASM 3C

[Ref.: #86470]	SI-ID 3550	*
[Ref.: #86471]	SI-ID 410514	*

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Comparative resistomic analyses of Lysobacter species with high intrinsic multidrug resistance.	Yu M, Zhao Y	J Glob Antimicrob Resist	10.1016/j.jgar.2019.05.008	2019	*
Phylogeny	Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov.	Miess H, van Trappen S, Cleenwerck I, De Vos P, Gross H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001329	2016	*
Metabolism	Identification of an Anti-MRSA Cyclic Lipodepsipeptide, WBP-29479A1, by Genome Mining of Lysobacter antibioticus.	Sang M, Wang H, Shen Y, Rodrigues de Almeida N, Conda-Sheridan M, Li S, Li Y, Du L	Org Lett	10.1021/acs.orglett.9b02333	2019	*
Phylogeny	Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.	Chen W, Zhao YL, Cheng J, Zhou XK, Salam N, Fang BZ, Li QQ, Hozzein WN, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0704-7	2016	*
Phylogeny	Lysobacter soli sp. nov., isolated from soil of a ginseng field.	Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.016428-0	2009	*
Phylogeny	Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea.	Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64473-0	2007	*
Phylogeny	Lysobacter koreensis sp. nov., isolated from a ginseng field.	Lee JW, Im WT, Kim MK, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.63955-0	2006	*

References

#686	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2044

#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 )

#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 )

#68369

Automatically annotated from API 20NE .

#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) .

#86470

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-ID3550.1 )

#86471

* These data were automatically processed and therefore are not curated

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Lysobacter antibioticus ATCC 29479

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