Lacibacter nakdongensis (SS2-56, KCTC 52160, JCM 31372)

Name: Lacibacter nakdongensis (SS2-56, KCTC 52160, JCM 31372)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133331

Type strain

Strain Designation SS2-56

Culture col. no. SS2-56 KCTC 52160 JCM 31372 BCRC 81229

NCBI tax ID(s) 1843099

Special Collections JCM KCTC Literature strains

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Lacibacter nakdongensis SS2-56 is an aerobe, Gram-negative, motile prokaryote that forms circular colonies and was isolated from surface sediment.

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

Name and taxonomic classification

SI-ID 27080

KCTC 52160,JCM 31372

@ref 20215

Last LPSN update 2025-12-16 10:01:45

Domain Pseudomonadati

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Lacibacter

Species Lacibacter nakdongensis

Full scientific name Lacibacter nakdongensis Han et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
25190	negative	1.6-3.8 µm	0.4-0.5 µm	rod-shaped
67771				rod-shaped	gliding
67771	negative

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
25190	orange	circular	2 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
25190	nutrient agar (NA)
25190	Reasoner's 2A agar (R2A)
25190	tryptic soy agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
25190	positive	growth	15.0-37.0
25190	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
25190	positive	optimum	7
25190	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
25190	aerobe
67771	aerobe

Spore formation

@ref	Spore formation
25190
67771

Halophily

@ref	Salt	Tested relation	Concentration
25190	NaCl	maximum	0 %

Observation

@ref	Observation
67770	quinones: MK-7
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25190	16763 ChEBI	2-oxobutanoate	-	carbon source
25190	30916 ChEBI	2-oxoglutarate	-	carbon source
25190	17128 ChEBI	adipate	-	carbon source
25190	17925 ChEBI	alpha-D-glucose	+	carbon source
25190	36219 ChEBI	alpha-lactose	+	carbon source
25190	27613 ChEBI	amygdalin	+	builds acid from
25190	18305 ChEBI	arbutin	+	builds acid from
25190	17968 ChEBI	butyrate	-	carbon source
25190	85146 ChEBI	carboxymethylcellulose	-	degradation
25190		casein	-	degradation
25190	17057 ChEBI	cellobiose	+	builds acid from
25190	17057 ChEBI	cellobiose	+	carbon source
25190	16947 ChEBI	citrate	-	carbon source
25190	15570 ChEBI	D-alanine	-	carbon source
25190	17108 ChEBI	D-arabinose	-	builds acid from
25190	18333 ChEBI	D-arabitol	-	builds acid from
25190	18333 ChEBI	D-arabitol	-	carbon source
25190	15824 ChEBI	D-fructose	-	carbon source
25190	28847 ChEBI	D-fucose	-	builds acid from
25190	12936 ChEBI	D-galactose	+	carbon source
25190	17634 ChEBI	D-glucose	+	builds acid from
25190	14314 ChEBI	D-glucose 6-phosphate	-	carbon source
25190	62318 ChEBI	D-lyxose	-	builds acid from
25190	16899 ChEBI	D-mannitol	-	builds acid from
25190	16899 ChEBI	D-mannitol	+	carbon source
25190	16024 ChEBI	D-mannose	+	builds acid from
25190	16024 ChEBI	D-mannose	+	carbon source
25190	16988 ChEBI	D-ribose	-	builds acid from
25190	17924 ChEBI	D-sorbitol	-	builds acid from
25190	17924 ChEBI	D-sorbitol	-	carbon source
25190	65327 ChEBI	D-xylose	-	builds acid from
25190	65327 ChEBI	D-xylose	+	builds acid from
25190	16991 ChEBI	dna	-	degradation
25190	17113 ChEBI	erythritol	-	builds acid from
25190	4853 ChEBI	esculin	-	builds acid from
25190	4853 ChEBI	esculin	+	hydrolysis
25190	5291 ChEBI	gelatin	+	hydrolysis
25190	28066 ChEBI	gentiobiose	+	builds acid from
25190	28066 ChEBI	gentiobiose	+	carbon source
25190	24265 ChEBI	gluconate	+	carbon source
25190	17234 ChEBI	glucose	-	fermentation
25190	17234 ChEBI	glucose	+	carbon source
25190	17754 ChEBI	glycerol	-	builds acid from
25190	17754 ChEBI	glycerol	-	carbon source
25190	28087 ChEBI	glycogen	-	carbon source
25190	28087 ChEBI	glycogen	+	builds acid from
25190	73804 ChEBI	glycyl L-aspartic acid	-	carbon source
25190	17368 ChEBI	hypoxanthine	-	degradation
25190	15443 ChEBI	inulin	+	builds acid from
25190	16977 ChEBI	L-alanine	-	carbon source
25190	30849 ChEBI	L-arabinose	-	carbon source
25190	17196 ChEBI	L-asparagine	-	carbon source
25190	18287 ChEBI	L-fucose	-	builds acid from
25190	18287 ChEBI	L-fucose	-	carbon source
25190	29985 ChEBI	L-glutamate	+	carbon source
25190	15603 ChEBI	L-leucine	-	carbon source
25190	17203 ChEBI	L-proline	+	carbon source
25190	62345 ChEBI	L-rhamnose	-	carbon source
25190	62345 ChEBI	L-rhamnose	+	builds acid from
25190	16857 ChEBI	L-threonine	+	carbon source
25190	65328 ChEBI	L-xylose	-	builds acid from
25190	24996 ChEBI	lactate	-	carbon source
25190	17716 ChEBI	lactose	+	builds acid from
25190	6359 ChEBI	lactulose	+	carbon source
25190	25115 ChEBI	malate	-	carbon source
25190	15792 ChEBI	malonate	-	carbon source
25190	17306 ChEBI	maltose	-	builds acid from
25190	17306 ChEBI	maltose	+	builds acid from
25190	17306 ChEBI	maltose	+	carbon source
25190	6731 ChEBI	melezitose	+	builds acid from
25190	28053 ChEBI	melibiose	+	builds acid from
25190	28053 ChEBI	melibiose	+	carbon source
25190	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
25190	43943 ChEBI	methyl alpha-D-mannoside	+	builds acid from
25190	320055 ChEBI	methyl beta-D-glucopyranoside	+	carbon source
25190	51850 ChEBI	methyl pyruvate	+	carbon source
25190	75146 ChEBI	monomethyl succinate	+	carbon source
25190	17268 ChEBI	myo-inositol	-	carbon source
25190	28037 ChEBI	N-acetylgalactosamine	-	carbon source
25190	506227 ChEBI	N-acetylglucosamine	+	builds acid from
25190	506227 ChEBI	N-acetylglucosamine	+	carbon source
25190	17632 ChEBI	nitrate	-	reduction
25190	16301 ChEBI	nitrite	-	reduction
25190	18401 ChEBI	phenylacetate	-	carbon source
25190	16634 ChEBI	raffinose	-	carbon source
25190	16634 ChEBI	raffinose	+	builds acid from
25190	17814 ChEBI	salicin	+	builds acid from
25190	28017 ChEBI	starch	-	degradation
25190	28017 ChEBI	starch	+	builds acid from
25190	30031 ChEBI	succinate	-	carbon source
25190	17992 ChEBI	sucrose	+	builds acid from
25190	17992 ChEBI	sucrose	+	carbon source
25190	27082 ChEBI	trehalose	+	builds acid from
25190	27082 ChEBI	trehalose	+	carbon source
25190	27897 ChEBI	tryptophan	-	energy source
25190	32528 ChEBI	turanose	+	builds acid from
25190	32528 ChEBI	turanose	+	carbon source
25190	53423 ChEBI	tween 40	-	carbon source
25190	53426 ChEBI	tween 80	-	carbon source
25190	18186 ChEBI	tyrosine	+	degradation
25190	15318 ChEBI	xanthine	-	degradation
25190	17151 ChEBI	xylitol	-	builds acid from
25190	17151 ChEBI	xylitol	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25190	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25190	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25190	acid phosphatase	-	3.1.3.2
25190	alkaline phosphatase	+	3.1.3.1
25190	alpha-chymotrypsin	+	3.4.21.1
25190	alpha-fucosidase	+	3.2.1.51
25190	alpha-galactosidase	+	3.2.1.22
25190	alpha-glucosidase	+	3.2.1.20
25190	arginine dihydrolase	-	3.5.3.6
25190	beta-galactosidase	+	3.2.1.23
25190	catalase	+	1.11.1.6
25190	cystine arylamidase	+	3.4.11.3
25190	cytochrome oxidase	+	1.9.3.1
25190	esterase (C 4)	+
25190	esterase Lipase (C 8)	+
25190	leucine arylamidase	+	3.4.11.1
25190	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25190	naphthol-AS-BI-phosphohydrolase	+
25190	trypsin	+	3.4.21.4
25190	tryptophan deaminase	-	4.1.99.1
25190	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

25190

Fatty acid	Percentage
C15:0 iso	47.6
C17:0 iso 3OH	13.8
C15:1 iso G	7.2
C16:1ω6c / C16:1ω7c	7
C16:0	5.5
C15:0 anteiso	4.2
C15:0 iso 3OH	2.4
C13:0 iso	2.2
C16:0 iso	2.1
C17:0 iso	1.2
C16:0 iso 3OH	1.1
C16:0 3OH	1
C14:0	1
C12:0	0.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure	Latitude	Longitude
25190	surface sediment	Nakdong River	Republic of Korea	KOR	Asia	R2A agar (BD)	14 days	25	serially diluted with 1/4 strength Ringer solution (per litre: NaCl 2.25 g, KCl 0.105 g, CaCl2 0.12 g, NaHCO3 0.05 g) and suitable ten-fold dilutions
67770	Sediment of the Nakdong River in Sangju-si		Republic of Korea	KOR	Asia
67771	From surface sediment, Nakdong River	Sanju-si	Republic of Korea	KOR	Asia					36.44	128.257 36.44/128.257

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25190	Lacibacter nakdongensis strain SS2-56 16S ribosomal RNA gene, partial sequence	KU341406	1450		1843099

GC content

@ref	GC-content (mol%)	Method
25190	43.8	Thermal denaturation, fluorometry
67771	43.8
67770	43.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lacibacter luteus sp. nov., isolated from a freshwater river.	Sheu SY, Chen TY, Kwon SW, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003926	2020
Phylogeny	Lacibacter nakdongensis sp. nov., isolated from river sediment.	Han JH, Baek K, Lee MH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001631	2017

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 )
#25190	J. H. B. Han, K.,Lee, M. H.: Lacibacter nakdongensis sp. nov., isolated from river sediment. IJSEM 67: 352 - 356 2017 ( DOI 10.1099/ijsem.0.001631 , PubMed 27902234 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Lacibacter nakdongensis (SS2-56, KCTC 52160, JCM 31372)

Name and taxonomic classification