Sphingobacterium thermophilum (CKTN2, JCM 17858, KCTC 23708)

Name: Sphingobacterium thermophilum (CKTN2, JCM 17858, KCTC 23708)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133127

Type strain

Strain Designation CKTN2

Culture col. no. CKTN2 JCM 17858 KCTC 23708

NCBI tax ID(s) 768534

Special Collections JCM KCTC Literature strains

History S. Yabe CKTN2. <- S Yabe, kennan Eisei Kogyo, Co., Ltd., Japan

Links

Sphingobacterium thermophilum CKTN2 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from food-waste compost.

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

Name and taxonomic classification

SI-ID 27631

KCTC 23708,JCM 17858

@ref 20215

Last LPSN update 2026-02-09 11:31:52

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium thermophilum

Full scientific name Sphingobacterium thermophilum Yabe et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
25081	negative	0.9-1.4 µm	0.4-0.5 µm	rod-shaped
30702	negative	2.05 µm	1.05 µm	rod-shaped
67771				rod-shaped
67771	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25081	2.0-3.3 mm	pale yellow	circular	2 days	NA (HiMedia)

Pigmentation

30702

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth
25081	NA (HiMedia)

Culture temp

@ref	Growth	Type	Temperature (°C)
25081	positive	growth	25-50
25081	positive	growth	20-42
30702	positive	growth	20-50
30702	positive	optimum	42.5
67770	positive	growth	45
67771	positive	growth	45

Culture pH

@ref	Ability	Type	PH	PH range
30702	positive	optimum	7
25081	positive	growth	7.0-8.0
25081	positive	growth	6.0-8.0
30702	positive	growth	5.9-8.8	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30702	aerobe
67771	aerobe

Spore formation

30702

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25081	NaCl	positive	growth	0-3.0 %
30702	NaCl	positive	growth	0-5 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25081	64552 ChEBI	2-hydroxybutyrate	-	respiration
25081	16763 ChEBI	2-oxobutanoate	-	respiration
25081	16763 ChEBI	2-oxobutanoate	+	respiration
25081	28644 ChEBI	2-oxopentanoate	-	respiration
25081	28644 ChEBI	2-oxopentanoate	+	respiration
25081	18240 ChEBI	4-hydroxy-L-proline	-	respiration
25081	18240 ChEBI	4-hydroxy-L-proline	+	respiration
25081	30089 ChEBI	acetate	-	respiration
25081	30089 ChEBI	acetate	+	respiration
25081	17128 ChEBI	adipate	-	assimilation
25081	40585 ChEBI	alpha-cyclodextrin	-	respiration
25081	40585 ChEBI	alpha-cyclodextrin	+	respiration
25081	17925 ChEBI	alpha-D-glucose	-	respiration
25081	17925 ChEBI	alpha-D-glucose	+	respiration
25081	22599 ChEBI	arabinose	-	assimilation
25081	17057 ChEBI	cellobiose	-	respiration
30702	17057 ChEBI	cellobiose	+	carbon source
25081	16947 ChEBI	citrate	-	assimilation
25081	16947 ChEBI	citrate	-	respiration
25081	18333 ChEBI	D-arabitol	-	respiration
25081	15824 ChEBI	D-fructose	-	respiration
25081	15824 ChEBI	D-fructose	+	respiration
25081	12936 ChEBI	D-galactose	-	respiration
25081	12936 ChEBI	D-galactose	+	respiration
25081	18024 ChEBI	D-galacturonic acid	-	respiration
25081	8391 ChEBI	D-gluconate	-	respiration
25081	17784 ChEBI	D-glucosaminic acid	-	respiration
25081	14314 ChEBI	D-glucose 6-phosphate	-	respiration
25081	16899 ChEBI	D-mannitol	-	respiration
25081	16024 ChEBI	D-mannose	-	respiration
25081	27605 ChEBI	D-psicose	-	respiration
25081	17924 ChEBI	D-sorbitol	-	respiration
25081	27689 ChEBI	decanoate	-	assimilation
25081	23652 ChEBI	dextrin	-	respiration
25081	4853 ChEBI	esculin	+	builds acid from
30702	4853 ChEBI	esculin	+	hydrolysis
30702	33984 ChEBI	fucose	+	carbon source
30702	28260 ChEBI	galactose	+	carbon source
25081	28066 ChEBI	gentiobiose	+	respiration
25081	17234 ChEBI	glucose	-	fermentation
25081	17234 ChEBI	glucose	-	assimilation
25081	17234 ChEBI	glucose	+	assimilation
30702	17234 ChEBI	glucose	+	carbon source
25081	29042 ChEBI	glucose 1-phosphate	-	respiration
25081	32323 ChEBI	glucuronamide	-	respiration
25081	17754 ChEBI	glycerol	-	respiration
30702	17754 ChEBI	glycerol	+	carbon source
25081	14336 ChEBI	glycerol 1-phosphate	-	respiration
25081	28087 ChEBI	glycogen	-	respiration
25081	28087 ChEBI	glycogen	+	respiration
25081	73804 ChEBI	glycyl L-aspartic acid	-	respiration
25081	73784 ChEBI	glycyl-l-glutamate	-	respiration
25081	73784 ChEBI	glycyl-l-glutamate	+	respiration
25081	30849 ChEBI	L-arabinose	-	respiration
25081	30849 ChEBI	L-arabinose	+	respiration
25081	17196 ChEBI	L-asparagine	-	respiration
25081	17196 ChEBI	L-asparagine	+	respiration
25081	29991 ChEBI	L-aspartate	-	respiration
25081	29991 ChEBI	L-aspartate	+	respiration
25081	18287 ChEBI	L-fucose	-	respiration
25081	29985 ChEBI	L-glutamate	+	respiration
25081	15729 ChEBI	L-ornithine	-	respiration
25081	15729 ChEBI	L-ornithine	+	respiration
25081	17203 ChEBI	L-proline	+	respiration
25081	17115 ChEBI	L-serine	-	respiration
25081	17115 ChEBI	L-serine	+	respiration
25081	24996 ChEBI	lactate	-	respiration
25081	24996 ChEBI	lactate	+	respiration
25081	17716 ChEBI	lactose	-	respiration
25081	17716 ChEBI	lactose	+	respiration
30702	17716 ChEBI	lactose	+	carbon source
25081	6359 ChEBI	lactulose	-	respiration
25081	6359 ChEBI	lactulose	+	respiration
25081	17306 ChEBI	maltose	-	respiration
25081	17306 ChEBI	maltose	-	assimilation
25081	17306 ChEBI	maltose	+	assimilation
25081	17306 ChEBI	maltose	+	respiration
30702	17306 ChEBI	maltose	+	carbon source
25081	29864 ChEBI	mannitol	-	assimilation
25081	37684 ChEBI	mannose	-	assimilation
30702	37684 ChEBI	mannose	+	carbon source
25081	28053 ChEBI	melibiose	-	respiration
25081	28053 ChEBI	melibiose	+	respiration
30702	28053 ChEBI	melibiose	+	carbon source
25081	320055 ChEBI	methyl beta-D-glucopyranoside	-	respiration
25081	320055 ChEBI	methyl beta-D-glucopyranoside	+	respiration
25081	75146 ChEBI	monomethyl succinate	+	respiration
25081	28037 ChEBI	N-acetylgalactosamine	-	respiration
25081	506227 ChEBI	N-acetylglucosamine	-	respiration
25081	506227 ChEBI	N-acetylglucosamine	-	assimilation
25081	506227 ChEBI	N-acetylglucosamine	+	assimilation
25081	506227 ChEBI	N-acetylglucosamine	+	respiration
30702	506227 ChEBI	N-acetylglucosamine	+	carbon source
25081	17632 ChEBI	nitrate	-	reduction
30702	17632 ChEBI	nitrate	+	reduction
25081	18401 ChEBI	phenylacetate	-	assimilation
25081	32032 ChEBI	potassium gluconate	-	assimilation
25081	17272 ChEBI	propionate	-	respiration
25081	17272 ChEBI	propionate	+	respiration
25081	16634 ChEBI	raffinose	-	respiration
30702	16634 ChEBI	raffinose	+	carbon source
30702	15963 ChEBI	ribitol	+	carbon source
30702	17814 ChEBI	salicin	+	carbon source
25081	17992 ChEBI	sucrose	-	respiration
25081	17992 ChEBI	sucrose	+	respiration
30702	17992 ChEBI	sucrose	+	carbon source
25081	26986 ChEBI	threonine	-	respiration
25081	26986 ChEBI	threonine	+	respiration
25081	27082 ChEBI	trehalose	-	respiration
25081	27082 ChEBI	trehalose	+	respiration
30702	27082 ChEBI	trehalose	+	carbon source
25081	27897 ChEBI	tryptophan	-	energy source
25081	32528 ChEBI	turanose	+	respiration

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25081	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Methylred-test	Indole test
25081	17234 ChEBI	glucose	-
25081	35581 ChEBI	indole		-

Enzymes

@ref	Value	Activity	Ec
25081	acid phosphatase	+	3.1.3.2
30702	acid phosphatase	+	3.1.3.2
25081	alkaline phosphatase	+	3.1.3.1
30702	alkaline phosphatase	+	3.1.3.1
25081	alpha-chymotrypsin	+	3.4.21.1
25081	alpha-fucosidase	-	3.2.1.51
25081	alpha-galactosidase	+	3.2.1.22
25081	alpha-glucosidase	+	3.2.1.20
25081	alpha-glucosidase	-	3.2.1.20
25081	alpha-mannosidase	-	3.2.1.24
25081	arginine dihydrolase	-	3.5.3.6
25081	beta-galactosidase	+	3.2.1.23
25081	beta-glucosidase	+	3.2.1.21
25081	beta-glucosidase	-	3.2.1.21
25081	beta-glucuronidase	-	3.2.1.31
25081	catalase	+	1.11.1.6
30702	catalase	+	1.11.1.6
25081	chymotrypsin	+	3.4.4.5
25081	cystine arylamidase	+	3.4.11.3
25081	cytochrome oxidase	+	1.9.3.1
25081	esterase	-
25081	esterase (C 4)	+
25081	esterase lipase (C 8)	+
25081	gelatinase	-
25081	leucine arylamidase	+	3.4.11.1
25081	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25081	naphthol-AS-BI-phosphohydrolase	+
25081	trypsin	+	3.4.21.4
25081	tryptophan deaminase	-	4.1.99.1
25081	urease	-	3.5.1.5
30702	urease	+	3.5.1.5
25081	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting
#Engineered	#Food production	#Food
#Engineered	#Waste	#Domestic waste

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
25081	food-waste compost	Taichung	Taiwan, Province of China	TWN	Asia	nutrient agar (NA; HiMedia)	2 days	30	standard serial dilution-to-extinction plating technique
67770	Manure compost produced by a field-scale composter which is used for the treatment of livestock excreta
67771	From manure compost produced by a field-scale composter which is used for the treatment of livestock excreta(Hazaka system	Hazaka Plant Kogyo)	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB563783 (>99% sequence identity) for Sphingobacterium thermophilum subclade from Microbeatlas

Aquatic Samples	321
Soil Samples	309
Animal Samples	1123
Plant Samples	134
Total Samples	1887

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954167v1 assembly for Sphingobacterium thermophilum JCM 17858	scaffold	GCA_039541675	768534	50.47

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30702	Sphingobacterium thermophilum gene for 16S rRNA, partial sequence, strain: CKTN2	AB563783	1461		768534

GC content

@ref	GC-content (mol%)	Method
25081	34.5	high performance liquid chromatography (HPLC)
30702	40.3

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacteriumthermophilum Yabe et al. 2013.	Lai WA, Hameed A, Liu YC, Hsu YH, Lin SY, Young CC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001517	2016
Phylogeny	Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost.	Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.042481-0	2012
Phylogeny	Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.	Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, Aslam Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001370	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 )
#25081	W. A. H. Lai, A.,Liu, Y. C.,Hsu, Y. H.,Lin, S. Y.,Young, C. C.: Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium thermophilum Yabe et al. 2013. IJSEM 66: 5336 - 5344 2016 ( DOI 10.1099/ijsem.0.001517 , PubMed 27666956 )
#27033	IJSEM 1584 2013 ( DOI 10.1099/ijs.0.042481-0 , PubMed 22904214 )
#30702	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 #27033
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sphingobacterium thermophilum (CKTN2, JCM 17858, KCTC 23708)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_039541675

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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