Lysobacter aestuarii (KACC 18502, JCM 31130, S2-C)

Name: Lysobacter aestuarii (KACC 18502, JCM 31130, S2-C)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140892

Type strain

Strain Designation S2-C

Culture col. no. KACC 18502 JCM 31130 S2-C

NCBI tax ID(s) 1706195

Special Collections JCM Literature strains

History C. O. Jeon; Chung-Ang Univ., South Korea; S2-C.

Links

Lysobacter aestuarii S2-C is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from An estuary sediment sample.

Gram-negative rod-shaped colony-forming obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 28382

JCM 31130

@ref 20215

Last LPSN update 2026-02-09 11:33:44

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Lysobacter

Species Lysobacter aestuarii

Full scientific name Lysobacter aestuarii Jeong et al. 2016

Synonyms (1)

Marilutibacter aestuarii

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43724	negative	1-1 µm	0.4-0.6 µm	rod-shaped
125438	negative					99

Colony morphology

@ref	Colony color	Colony shape	Medium used
43724	Deep yellow cream	circular	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43724	LB (Luria-Bertani) MEDIUM
43724	Marine agar (MA)
43724	Nutrient agar (NA)
43724	Reasoner's 2A agar (R2A)
43724	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
43724	positive	growth	15-40
43724	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
43724	positive	optimum	6.5-7.5
43724	positive	growth	5.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43724	obligate aerobe
125439	obligate aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
125438		92.5
125439		92.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43724	NaCl	positive	growth	0-7 %(w/v)
43724	NaCl	positive	optimum	0-2 %(w/v)

Observation

43724

ObservationProduces extracellular polysaccharides

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43724	17128 ChEBI	adipate	-	assimilation
43724		casein	+	hydrolysis
43724	17634 ChEBI	D-glucose	+/-	assimilation
43724	16899 ChEBI	D-mannitol	-	assimilation
43724	16024 ChEBI	D-mannose	-	assimilation
43724	27689 ChEBI	decanoate	-	assimilation
43724	4853 ChEBI	esculin	+	hydrolysis
43724	5291 ChEBI	gelatin	+	hydrolysis
43724	30849 ChEBI	L-arabinose	-	assimilation
43724	25115 ChEBI	malate	-	assimilation
43724	17306 ChEBI	maltose	+/-	assimilation
43724	506227 ChEBI	N-acetylglucosamine	+/-	assimilation
43724	17632 ChEBI	nitrate	+	reduction
43724	18401 ChEBI	phenylacetate	-	assimilation
43724	32032 ChEBI	potassium gluconate	-	assimilation
43724	53258 ChEBI	sodium citrate	-	assimilation
43724	28017 ChEBI	starch	-	hydrolysis
43724	53424 ChEBI	tween 20	-	hydrolysis
43724	53426 ChEBI	tween 80	-	hydrolysis
43724	18186 ChEBI	tyrosine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43724	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43724	acid phosphatase	+	3.1.3.2
43724	alkaline phosphatase	+	3.1.3.1
43724	alpha-chymotrypsin	+	3.4.21.1
43724	alpha-fucosidase	-	3.2.1.51
43724	alpha-galactosidase	-	3.2.1.22
43724	alpha-glucosidase	-	3.2.1.20
43724	alpha-mannosidase	-	3.2.1.24
43724	arginine dihydrolase	-	3.5.3.6
43724	beta-galactosidase	-	3.2.1.23
43724	beta-glucosidase	-	3.2.1.21
43724	beta-glucuronidase	-	3.2.1.31
43724	catalase	+	1.11.1.6
43724	cystine arylamidase	-	3.4.11.3
43724	cytochrome oxidase	+	1.9.3.1
43724	esterase (C 4)	+
43724	esterase Lipase (C 8)	+/-
43724	leucine arylamidase	+	3.4.11.1
43724	lipase (C 14)	-
43724	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43724	naphthol-AS-BI-phosphohydrolase	+
43724	trypsin	-	3.4.21.4
43724	urease	-	3.5.1.5
43724	valine arylamidase	+/-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	Entner Doudoroff pathway	100	10 of 10
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	propionate fermentation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	81.91	77 of 94
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	tryptophan metabolism	76.32	29 of 38
66794	glutamate and glutamine metabolism	75	21 of 28
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	histidine metabolism	72.41	21 of 29
66794	alanine metabolism	72.41	21 of 29
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	threonine metabolism	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	vitamin B1 metabolism	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	flavin biosynthesis	66.67	10 of 15
66794	enterobactin biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	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	lipid metabolism	61.29	19 of 31
66794	D-cycloserine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	starch degradation	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	d-xylose degradation	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	vitamin B12 metabolism	44.12	15 of 34
66794	degradation of sugar alcohols	43.75	7 of 16
66794	oxidative phosphorylation	41.76	38 of 91
66794	glycine metabolism	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	ketogluconate metabolism	37.5	3 of 8
66794	degradation of pentoses	35.71	10 of 28
66794	polyamine pathway	34.78	8 of 23
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	carotenoid biosynthesis	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Fatty acid profile

Metadata FA analysis

@ref

43724

Fatty acid	Percentage
C16:0 iso	21.6
C15:0 iso	19.1
C17:1 iso ω9c	11.6
C11:0 iso 3OH	7.1
C15:0 anteiso	6.8
C16:1ω7c-alcohol	5.8
C11:0 iso	5.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43724	An estuary sediment sample	Asan	Republic of Korea	KOR	Asia	36.944	126.99 36.944/126.99
67770	Estuary sediment in Asan		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KT583751 (>99% sequence identity) for Lysobacter from Microbeatlas

Aquatic Samples	37
Soil Samples	34
Animal Samples	15
Plant Samples	3
Total Samples	89

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM654677v1 assembly for Marilutibacter aestuarii JCM 31130	contig	GCA_006546775	1706195.3	2896281107	1706195	46.82

16S sequences

@ref	Description	Accession	Database
43724	Lysobacter sp. S2-C 16S ribosomal RNA gene, partial sequence	KT583751

GC content

@ref	GC-content (mol%)	Method
43724	63.8	Thermal denaturation, fluorometry
67770	63.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lysobacter aestuarii JCM 31130
NCBI: GCA_006546775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.50	no
125439	motility	BacteriaNetⓘ	yes	58.20	no
125439	gram_stain	BacteriaNetⓘ	negative	68.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lysobacter aestuarii strain JCM 31130
PATRIC: 1706195.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	98.32	yes
125438	spore-forming	spore-formingⓘ	no	92.50	no
125438	aerobic	aerobicⓘ	yes	88.85	yes
125438	thermophilic	thermophileⓘ	no	96.82	yes
125438	flagellated	motile2+ⓘ	no	65.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lysobacter penaei sp. nov., isolated from intestinal content of a Pacific white shrimp (Penaeus vannamei).	Xu S, Li A, Zhang MX, Yao Q, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004593	2021
Phylogeny	Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil.	Xu L, Huang XX, Fan DL, Sun JQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003911	2020
Phylogeny	Lysobacter spongiae sp. nov., isolated from spongin.	Choi H, Im WT, Park JS	J Microbiol	10.1007/s12275-018-7462-3	2018
Phylogeny	Lysobacter aestuarii sp. nov., isolated from estuary sediment.	Jeong SE, Lee HJ, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.000884	2016

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 )
#43724	Sang Eun Jeong, Hyo Jung Lee, Che Ok Jeon: Lysobacter aestuarii sp. nov., isolated from estuary sediment. IJSEM 66: 1346 - 1351 2016 ( DOI 10.1099/ijsem.0.000884 , PubMed 26746421 )
#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 .
#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 )

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Lysobacter aestuarii (KACC 18502, JCM 31130, S2-C)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_006546775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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