Name: Lysobacter spongiicola DSM 21749
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17492

Type strain:

Species: Lysobacter spongiicola

Culture col. no.: DSM 21749, JCM 14760, KMM 329, NRIC 0728, KCTC 23742

Strain history: M. Uchino <-- L. A. Romanenko KMM 329.

NCBI tax ID(s): 1122188 (strain), 435289 (species)

Section

Lysobacter spongiicola DSM 21749 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sponge .

Gram-negative
motile
rod-shaped
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter spongiicola**
	Full Scientific Name (LPSN)	Lysobacter spongiicola Romanenko et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32371]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #32371]	Cell length	1.4 µm

[Ref.: #32371]	Cell width	0.55 µm

[Ref.: #32371]	Cell shape	rod-shaped

[Ref.: #32371]	Motility	yes

[Ref.: #32371]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15912]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #15912]

Culture medium growth

[Ref.: #15912]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15912]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15912]	growth	28 °C
[Ref.: #32371]	growth	05-41 °C
[Ref.: #32371]	optimum	26.5 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #15912]	Temperature range	mesophilic
[Ref.: #32371]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32371]			optimum	7.5
[Ref.: #32371]			growth	5.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32371]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32371]		NaCl		growth	0-6	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32371]		ribitol ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32371]	acid phosphatase	+	3.1.3.2
[Ref.: #32371]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32371]	catalase	+	1.11.1.6
[Ref.: #32371]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32371]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	oxidative phosphorylation	34.07	31 of 91
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	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.: #15912]	Sample type/isolated from	sponge (Pachastrella sp.)
[Ref.: #15912]	Host species	Pachastrella
[Ref.: #15912]	Geographic location (country and/or sea, region)	Philippine Sea at a water depth of 750 m
[Ref.: #15912]	Country	Philippines
[Ref.: #15912]	Country ISO 3 Code	PHL
[Ref.: #15912]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sponge specimen (Pachastrella sp.) collected from the Philippine Sea at a water depth of 750 m
[Ref.: #67770]	Host species	Pachastrella sp.
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Porifera (Sponges)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB299978 (>99% sequence identity) for Lysobacter spongiicola subclade from Microbeatlas

Aquatic Samples	161
Soil Samples	356
Animal Samples	117
Plant Samples	48
Total Samples	682

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

[Ref.: #15912]

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.: #15912]	Lysobacter spongiicola gene for 16S ribosomal RNA, partial sequence, strain: KMM 329	AB299978	1516	ENA	435289 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Lysobacter spongiicola DSM 21749	GCA_900167055	contig	GenBank	1122188 tax ID
[Ref.: #66792]	Lysobacter spongiicola DSM 21749 strain DSM 21749	1122188.5	wgs	PATRIC	1122188 tax ID	*
[Ref.: #66792]	Lysobacter spongiicola DSM 21749	2568526003	draft	JGI IMG/M	1122188 tax ID	*

[Ref.: #15912]	GC-content	69 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #32371]	GC-content	69 mol%
[Ref.: #67770]	GC-content	69 mol%	high performance liquid chromatography (HPLC)

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: Lysobacter spongiicola DSM 21749 strain DSM 21749 PATRIC: 1122188.5
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lysobacter spongiicola DSM 21749 strain DSM 21749 PATRIC: 1122188.5
[Ref.: #69480]	motile	yes	81.255	no
[Ref.: #69480]	flagellated	no	77.96	no
[Ref.: #69480]	gram-positive	no	98.427	no
[Ref.: #69480]	anaerobic	no	98.481	no
[Ref.: #69480]	aerobic	yes	91.075	yes
[Ref.: #69480]	halophile	no	90.714	no
[Ref.: #69480]	spore-forming	no	95.549	no
[Ref.: #69480]	thermophile	no	98.554	no
[Ref.: #69480]	glucose-util	yes	81.94	no
[Ref.: #69480]	glucose-ferment	no	93.422	no

Availability in culture collections External links

[Ref.: #15912]

Culture collection no.

DSM 21749, JCM 14760, KMM 329, NRIC 0728, KCTC 23742

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysobacter chengduensis sp. nov. Isolated from the Air of Captive Ailuropoda melanoleuca Enclosures in Chengdu, China.	Wen C, Xi L, She R, Zhao S, Hao Z, Luo L, Liao H, Chen Z, Han G, Cao S, Wu R, Yan Q, Hou R	Curr Microbiol	10.1007/s00284-015-0921-8	2016	*
Phylogeny	Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.	Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CX	Int J Syst Evol Microbiol	10.1099/ijs.0.024448-0	2010	*
Phylogeny	Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge.	Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.65391-0	2008	*
Phylogeny	Lysobacter selenitireducens sp. nov., isolated from river sediment.	Mao S, Li S, Guo B, Mu W, Hou X, Liu H, Wei S, Liu A, Kong L, Chen Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005550	2022	*

References

#15912

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21749

#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 )

#32371

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 #28599 (see below)

#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;

#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 )

#28599

IJSEM 370 2008 ( DOI 10.1099/ijs.0.65391-0 , PubMed 18218933 )

* These data were automatically processed and therefore are not curated

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Lysobacter spongiicola DSM 21749 strain DSM 21749

Lysobacter spongiicola DSM 21749 strain DSM 21749

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