Name: Sphingobacterium thermophilum CKTN2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133127

Type strain:

Species: Sphingobacterium thermophilum

Strain Designation: CKTN2

Culture col. no.: JCM 17858, KCTC 23708

Strain history: <- S Yabe, kennan Eisei Kogyo, Co., Ltd., Japan

NCBI tax ID(s): 768534 (species)

Section

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

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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium thermophilum**
	Full Scientific Name (PNU)	Sphingobacterium thermophilum Yabe et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #25081]	Gram stain	negative
[Ref.: #25081]	Cell length	0.9-1.4 µm
[Ref.: #25081]	Cell width	0.4-0.5 µm
[Ref.: #25081]	Cell shape	rod-shaped
[Ref.: #25081]	Motility	no

[Ref.: #30702]	Gram stain	negative
[Ref.: #30702]	Cell length	2.05 µm
[Ref.: #30702]	Cell width	1.05 µm
[Ref.: #30702]	Cell shape	rod-shaped
[Ref.: #30702]	Motility	no

[Ref.: #67771]	Gram stain	negative

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Motility	no

[Ref.: #25081]	Colony size	2.0-3.3 mm
[Ref.: #25081]	Colony color	pale yellow
[Ref.: #25081]	Colony shape	circular
[Ref.: #25081]	Incubation period	2 days
[Ref.: #25081]	Cultivation medium used	NA (HiMedia)

[Ref.: #30702]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25081]

Culture medium

NA (HiMedia)

[Ref.: #25081]

Culture medium growth

		Temperature
[Ref.: #25081]	growth	25-50 °C
[Ref.: #25081]	growth	20-42 °C
[Ref.: #30702]	growth	20-50 °C
[Ref.: #30702]	optimum	42.5 °C
[Ref.: #67770]	growth	45 °C
[Ref.: #67771]	growth	45 °C

[Ref.: #30702]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #67771]	Temperature range	thermophilic

		pH	pH range
[Ref.: #30702]	optimum	7
[Ref.: #25081]	growth	7.0-8.0
[Ref.: #25081]	growth	6.0-8.0
[Ref.: #30702]	growth	5.9-8.8	alkaliphile

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30702]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #30702]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25081]		NaCl		growth	0-3.0	%
[Ref.: #30702]		NaCl		growth	0-5	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25081]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #25081]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #25081]	2-oxobutanoate ChEBI	+	respiration
[Ref.: #25081]	2-oxopentanoate ChEBI	-	respiration
[Ref.: #25081]	2-oxopentanoate ChEBI	+	respiration
[Ref.: #25081]	4-hydroxy-L-proline ChEBI	-	respiration
[Ref.: #25081]	4-hydroxy-L-proline ChEBI	+	respiration
[Ref.: #25081]	acetate ChEBI	-	respiration
[Ref.: #25081]	acetate ChEBI	+	respiration
[Ref.: #25081]	adipate ChEBI	-	assimilation
[Ref.: #25081]	alpha-cyclodextrin ChEBI	-	respiration
[Ref.: #25081]	alpha-cyclodextrin ChEBI	+	respiration
[Ref.: #25081]	alpha-D-glucose ChEBI	-	respiration
[Ref.: #25081]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #25081]	arabinose ChEBI	-	assimilation
[Ref.: #25081]	cellobiose ChEBI	-	respiration
[Ref.: #30702]	cellobiose ChEBI	+	carbon source
[Ref.: #25081]	citrate ChEBI	-	assimilation
[Ref.: #25081]	citrate ChEBI	-	respiration
[Ref.: #25081]	D-arabitol ChEBI	-	respiration
[Ref.: #25081]	D-fructose ChEBI	-	respiration
[Ref.: #25081]	D-fructose ChEBI	+	respiration
[Ref.: #25081]	D-galactose ChEBI	-	respiration
[Ref.: #25081]	D-galactose ChEBI	+	respiration
[Ref.: #25081]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #25081]	D-gluconate ChEBI	-	respiration
[Ref.: #25081]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #25081]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #25081]	D-mannitol ChEBI	-	respiration
[Ref.: #25081]	D-mannose ChEBI	-	respiration
[Ref.: #25081]	D-psicose ChEBI	-	respiration
[Ref.: #25081]	D-sorbitol ChEBI	-	respiration
[Ref.: #25081]	decanoate ChEBI	-	assimilation
[Ref.: #25081]	dextrin ChEBI	-	respiration
[Ref.: #25081]	esculin ChEBI	+	builds acid from
[Ref.: #30702]	esculin ChEBI	+	hydrolysis
[Ref.: #30702]	fucose ChEBI	+	carbon source
[Ref.: #30702]	galactose ChEBI	+	carbon source
[Ref.: #25081]	gentiobiose ChEBI	+	respiration
[Ref.: #25081]	glucose ChEBI	-	fermentation
[Ref.: #25081]	glucose ChEBI	-	assimilation
[Ref.: #25081]	glucose ChEBI	+	assimilation
[Ref.: #30702]	glucose ChEBI	+	carbon source
[Ref.: #25081]	glucose 1-phosphate ChEBI	-	respiration
[Ref.: #25081]	glucuronamide ChEBI	-	respiration
[Ref.: #25081]	glycerol ChEBI	-	respiration
[Ref.: #30702]	glycerol ChEBI	+	carbon source
[Ref.: #25081]	glycerol 1-phosphate ChEBI	-	respiration
[Ref.: #25081]	glycogen ChEBI	-	respiration
[Ref.: #25081]	glycogen ChEBI	+	respiration
[Ref.: #25081]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #25081]	glycyl-l-glutamate ChEBI	-	respiration
[Ref.: #25081]	glycyl-l-glutamate ChEBI	+	respiration
[Ref.: #25081]	L-arabinose ChEBI	-	respiration
[Ref.: #25081]	L-arabinose ChEBI	+	respiration
[Ref.: #25081]	L-asparagine ChEBI	-	respiration
[Ref.: #25081]	L-asparagine ChEBI	+	respiration
[Ref.: #25081]	L-aspartate ChEBI	-	respiration
[Ref.: #25081]	L-aspartate ChEBI	+	respiration
[Ref.: #25081]	L-fucose ChEBI	-	respiration
[Ref.: #25081]	L-glutamate ChEBI	+	respiration
[Ref.: #25081]	L-ornithine ChEBI	-	respiration
[Ref.: #25081]	L-ornithine ChEBI	+	respiration
[Ref.: #25081]	L-proline ChEBI	+	respiration
[Ref.: #25081]	L-serine ChEBI	-	respiration
[Ref.: #25081]	L-serine ChEBI	+	respiration
[Ref.: #25081]	lactate ChEBI	-	respiration
[Ref.: #25081]	lactate ChEBI	+	respiration
[Ref.: #25081]	lactose ChEBI	-	respiration
[Ref.: #25081]	lactose ChEBI	+	respiration
[Ref.: #30702]	lactose ChEBI	+	carbon source
[Ref.: #25081]	lactulose ChEBI	-	respiration
[Ref.: #25081]	lactulose ChEBI	+	respiration
[Ref.: #25081]	maltose ChEBI	-	respiration
[Ref.: #25081]	maltose ChEBI	-	assimilation
[Ref.: #25081]	maltose ChEBI	+	assimilation
[Ref.: #25081]	maltose ChEBI	+	respiration
[Ref.: #30702]	maltose ChEBI	+	carbon source
[Ref.: #25081]	mannitol ChEBI	-	assimilation
[Ref.: #25081]	mannose ChEBI	-	assimilation
[Ref.: #30702]	mannose ChEBI	+	carbon source
[Ref.: #25081]	melibiose ChEBI	-	respiration
[Ref.: #25081]	melibiose ChEBI	+	respiration
[Ref.: #30702]	melibiose ChEBI	+	carbon source
[Ref.: #25081]	methyl beta-D-glucopyranoside ChEBI	-	respiration
[Ref.: #25081]	methyl beta-D-glucopyranoside ChEBI	+	respiration
[Ref.: #25081]	monomethyl succinate ChEBI	+	respiration
[Ref.: #25081]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #25081]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #25081]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25081]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #25081]	N-acetylglucosamine ChEBI	+	respiration
[Ref.: #30702]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #25081]	nitrate ChEBI	-	reduction
[Ref.: #30702]	nitrate ChEBI	+	reduction
[Ref.: #25081]	phenylacetate ChEBI	-	assimilation
[Ref.: #25081]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25081]	propionate ChEBI	-	respiration
[Ref.: #25081]	propionate ChEBI	+	respiration
[Ref.: #25081]	raffinose ChEBI	-	respiration
[Ref.: #30702]	raffinose ChEBI	+	carbon source
[Ref.: #30702]	ribitol ChEBI	+	carbon source
[Ref.: #30702]	salicin ChEBI	+	carbon source
[Ref.: #25081]	sucrose ChEBI	-	respiration
[Ref.: #25081]	sucrose ChEBI	+	respiration
[Ref.: #30702]	sucrose ChEBI	+	carbon source
[Ref.: #25081]	threonine ChEBI	-	respiration
[Ref.: #25081]	threonine ChEBI	+	respiration
[Ref.: #25081]	trehalose ChEBI	-	respiration
[Ref.: #25081]	trehalose ChEBI	+	respiration
[Ref.: #30702]	trehalose ChEBI	+	carbon source
[Ref.: #25081]	tryptophan ChEBI	-	energy source
[Ref.: #25081]	turanose ChEBI	+	respiration
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #25081]		indole ChEBI

	Physiological tests	Metabolite	Methylred-test	Indole test
[Ref.: #25081]		glucose ChEBI	-
[Ref.: #25081]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #25081]	acid phosphatase	+	3.1.3.2
[Ref.: #30702]	acid phosphatase	+	3.1.3.2
[Ref.: #25081]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30702]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25081]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #25081]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25081]	alpha-galactosidase	+	3.2.1.22
[Ref.: #25081]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25081]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25081]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25081]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25081]	beta-galactosidase	+	3.2.1.23
[Ref.: #25081]	beta-glucosidase	+	3.2.1.21
[Ref.: #25081]	beta-glucosidase	-	3.2.1.21
[Ref.: #25081]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25081]	catalase	+	1.11.1.6
[Ref.: #30702]	catalase	+	1.11.1.6
[Ref.: #25081]	chymotrypsin	+	3.4.4.5
[Ref.: #25081]	cystine arylamidase	+	3.4.11.3
[Ref.: #25081]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25081]	esterase	-
[Ref.: #25081]	esterase (C 4)	+
[Ref.: #25081]	esterase lipase (C 8)	+
[Ref.: #25081]	gelatinase	-
[Ref.: #25081]	leucine arylamidase	+	3.4.11.1
[Ref.: #25081]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25081]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25081]	trypsin	+	3.4.21.4
[Ref.: #25081]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25081]	urease	-	3.5.1.5
[Ref.: #30702]	urease	+	3.5.1.5
[Ref.: #25081]	valine arylamidase	+
	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.: #25081]	Sample type/isolated from	food-waste compost
[Ref.: #25081]	Geographic location (country and/or sea, region)	Taichung
[Ref.: #25081]	Country	Taiwan
[Ref.: #25081]	Country ISO 3 Code	TWN
[Ref.: #25081]	Continent	Asia
[Ref.: #25081]	Enrichment culture	nutrient agar (NA; HiMedia)
[Ref.: #25081]	Enrichment culture duration	2 days
[Ref.: #25081]	Enrichment culture temperature	30 ̊C
[Ref.: #25081]	Isolation/enrichment procedure	standard serial dilution-to-extinction plating technique

[Ref.: #67770]	Sample type/isolated from	Manure compost produced by a field-scale composter which is used for the treatment of livestock excreta

[Ref.: #67771]	Sample type/isolated from	From manure compost produced by a field-scale composter which is used for the treatment of livestock excreta(Hazaka system
[Ref.: #67771]	Geographic location (country and/or sea, region)	Hazaka Plant Kogyo)
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Food production	#Food
#Engineered	#Waste	#Domestic waste

What are isolation sources categories?

[Ref.: #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

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.: #30702]	Sphingobacterium thermophilum gene for 16S rRNA, partial sequence, strain: CKTN2	AB563783	1461	GenBank	768534 tax ID

[Ref.: #25081]	GC-content	34.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30702]	GC-content	40.3 mol%

Availability in culture collections External links

[Ref.: #25081]

Culture collection no.

JCM 17858, KCTC 23708

[Ref.: #20218]

Associated Passport(s) in StrainInfo

886906, 886907, 886908

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*

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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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 )

#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 (see below)

#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 .

#27033

IJSEM 1584 2013 ( DOI 10.1099/ijs.0.042481-0 , PubMed 22904214 )

* These data were automatically processed and therefore are not curated

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