Name: Limibaculum halophilum KCTC 52187
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140769

Type strain:

Species: Limibaculum halophilum

Culture col. no.: KCTC 52187, NBRC 112522, DSM 108279, CAU 1123

Strain history: <- Wonyong Kim, Chung-Ang Univ.

NCBI tax ID(s): 1902428 (species)

SI-ID 403089

DSM 108279

Special Collections

Section

Limibaculum halophilum KCTC 52187 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from reclaimed land mud.

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

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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Limibaculum*
	Species	**Limibaculum halophilum**
	Full Scientific Name (LPSN)	Limibaculum halophilum Shin et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43547]	Gram stain	negative

[Ref.: #43547]	Cell length	1.2-1.9 µm

[Ref.: #43547]	Cell width	0.6-1.3 µm

[Ref.: #43547]	Cell shape	rod-shaped

[Ref.: #43547]	Motility	no

[Ref.: #43547]	Colony size	0.2-0.3 mm
[Ref.: #43547]	Colony color	cream coloured
[Ref.: #43547]	Colony shape	circular
[Ref.: #43547]	Incubation period	3 days
[Ref.: #43547]	Cultivation medium used	MA agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43547]

Culture medium

Marine agar (MA)

[Ref.: #43547]

Culture medium growth

[Ref.: #64912]

Culture medium

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

[Ref.: #64912]

Culture medium growth

[Ref.: #64912]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64912]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #43547]	growth	20-40 °C
[Ref.: #43547]	optimum	37 °C
[Ref.: #64912]	growth	30 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #43547]			optimum	7.5
[Ref.: #43547]			growth	6.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43547]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #43547]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43547]		NaCl		growth	0-7	%(w/v)
[Ref.: #43547]		NaCl		optimum	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43547]	adipate ChEBI	-	assimilation
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43547]	casein	-	hydrolysis
[Ref.: #43547]	citrate ChEBI	+	hydrolysis
[Ref.: #43547]	D-arabitol ChEBI	+	carbon source
[Ref.: #43547]	D-arabitol ChEBI	+	energy source
[Ref.: #43547]	D-fructose ChEBI	-	carbon source
[Ref.: #43547]	D-fructose ChEBI	-	energy source
[Ref.: #43547]	D-galactose ChEBI	-	carbon source
[Ref.: #43547]	D-galactose ChEBI	-	energy source
[Ref.: #43547]	D-glucose ChEBI	-	carbon source
[Ref.: #43547]	D-glucose ChEBI	-	energy source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #43547]	D-mannitol ChEBI	-	assimilation
[Ref.: #43547]	D-mannitol ChEBI	-	carbon source
[Ref.: #43547]	D-mannitol ChEBI	-	energy source
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #43547]	D-mannose ChEBI	-	assimilation
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	D-ribose ChEBI	-	carbon source
[Ref.: #43547]	D-ribose ChEBI	-	energy source
[Ref.: #43547]	D-tagatose ChEBI	+	carbon source
[Ref.: #43547]	D-tagatose ChEBI	+	energy source
[Ref.: #43547]	D-xylose ChEBI	-	carbon source
[Ref.: #43547]	D-xylose ChEBI	-	energy source
[Ref.: #43547]	decanoate ChEBI	-	assimilation
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #43547]	gelatin ChEBI	+	hydrolysis
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	L-arabinose ChEBI	-	assimilation
[Ref.: #43547]	L-arabinose ChEBI	-	carbon source
[Ref.: #43547]	L-arabinose ChEBI	-	energy source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	L-fucose ChEBI	+	carbon source
[Ref.: #43547]	L-fucose ChEBI	+	energy source
[Ref.: #43547]	lactose ChEBI	-	carbon source
[Ref.: #43547]	lactose ChEBI	-	energy source
[Ref.: #43547]	malate ChEBI	-	assimilation
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	maltose ChEBI	-	assimilation
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #43547]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #43547]	phenylacetate ChEBI	-	assimilation
[Ref.: #43547]	potassium 5-dehydro-D-gluconate	+	carbon source
[Ref.: #43547]	potassium 5-dehydro-D-gluconate	+	energy source
[Ref.: #43547]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43547]	sodium citrate ChEBI	+	assimilation
[Ref.: #43547]	sodium pyruvate ChEBI	-	hydrolysis
[Ref.: #43547]	starch ChEBI	-	hydrolysis
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #43547]	urea ChEBI	-	hydrolysis
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43547]	xylitol ChEBI	+	carbon source
[Ref.: #43547]	xylitol ChEBI	+	energy source
	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.: #43547]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #43547]	cystine arylamidase	+	3.4.11.3
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #43547]	esterase (C 4)	+
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #43547]	esterase Lipase (C 8)	+
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #43547]	leucine arylamidase	+	3.4.11.1
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #43547]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #43547]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #43547]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43547]

Fatty acid	Percentage
C18:1ω7c	73.6
11-methyl C18:1ω7c	8.7
C16:0	6.5
C12:1 3OH	3.4
C18:0	1.9
C10:0 3OH	1.7
C16:1ω7c / C16:1ω6c	1.2
unknown 18.846 / C19:1ω6c / cyclo-C19:	1.1
C18:1ω9c	0.7

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.: #64912]	24771	+	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	not determinedn.d.

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.: #64912]	14113	-	-	-	-	-	+	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #43547]	Sample type/isolated from	reclaimed land mud
[Ref.: #43547]	Geographic location (country and/or sea, region)	Modo
[Ref.: #43547]	Country	Republic of Korea
[Ref.: #43547]	Country ISO 3 Code	KOR
[Ref.: #43547]	Continent	Asia
[Ref.: #43547]	Geographic location	37.5360°/126.4140°

[Ref.: #64912]	Sample type/isolated from	Soil of reclaimed land
[Ref.: #64912]	Geographic location (country and/or sea, region)	Modo (37° 32' 12.28'' N, 126° 24' 51.47'' E)
[Ref.: #64912]	Country	Republic of Korea
[Ref.: #64912]	Country ISO 3 Code	KOR
[Ref.: #64912]	Continent	Asia
[Ref.: #64912]	Geographic location	37.5367°/126.4140°

[Ref.: #67771]	Sample type/isolated from	From soil of reclaim land
[Ref.: #67771]	Geographic location (country and/or sea, region)	Modo, Incheon
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX774334 (>99% sequence identity) for Limibaculum halophilum subclade from Microbeatlas

Aquatic Samples	201
Soil Samples	131
Animal Samples	33
Plant Samples
Total Samples	365

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

[Ref.: #64912]

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.: #64912]	Limibaculum halophilum strain CAU 1123 16S ribosomal RNA gene, partial sequence	KX774334	1403	GenBank ENA	1902428 tax ID

[Ref.: #43547]

GC-content

71.1 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #64912]

Culture collection no.

KCTC 52187, NBRC 112522, DSM 108279, CAU 1123

[Ref.: #96786]

SI-ID 403089

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Algiphilus acroporae sp. nov. and Coraliihabitans acroporae gen. nov. sp. nov., isolated from scleractinian coral Acropora digitifera.	Sun H, Zheng H, Liao B, Chen B, Li A, Xiao B	Int J Syst Evol Microbiol	10.1099/ijsem.0.005321	2022	*
Phylogeny	Thermohalobaculum xanthum gen. nov., sp. nov., a moderately thermophilic bacterium isolated from mangrove sediment.	Pan X, Li Z, Li F, Huang Y, Wang Q, Huang S, Hu W, Jiang M	Antonie Van Leeuwenhoek	10.1007/s10482-021-01641-4	2021	*
Phylogeny	Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae.	Shin YH, Kim JH, Suckhoom A, Kantachote D, Kim W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002200	2017	*
Phylogeny	Limibaculum sediminis sp. nov., isolated from mangrove sediment.	Huang Y, Liu L, Li J, Pan J, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.005580	2022	*

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 )

#43547

Yong Ho Shin, Jong-Hwa Kim, Ampaitip Suckhoom, Duangporn Kantachote, Wonyong Kim: Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae. IJSEM 67: 3812 - 3818 2017 ( DOI 10.1099/ijsem.0.002200 , PubMed 28879850 )

#64912

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108279

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#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 .

#96786

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-ID403089.1 )

* These data were automatically processed and therefore are not curated

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