Strain identifier

BacDive ID: 133127

Type strain: Yes

Species: Sphingobacterium thermophilum

Strain Designation: CKTN2

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

NCBI tax ID(s): 768534 (species)

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General

@ref: 25081

BacDive-ID: 133127

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

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

NCBI tax id

  • NCBI tax id: 768534
  • Matching level: species

strain history

@refhistory
67770S. Yabe CKTN2.
67771<- S Yabe, kennan Eisei Kogyo, Co., Ltd., Japan

doi: 10.13145/bacdive133127.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium thermophilum
  • full scientific name: Sphingobacterium thermophilum Yabe et al. 2013

@ref: 25081

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium thermophilum

strain designation: CKTN2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
25081negative0.9-1.4 µm0.4-0.5 µmrod-shapedno
30702negative2.05 µm1.05 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 25081
  • colony size: 2.0-3.3 mm
  • colony color: pale yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: NA (HiMedia)

pigmentation

  • @ref: 30702
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 25081
  • name: NA (HiMedia)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25081positivegrowth25-50
25081positivegrowth20-42
30702positivegrowth20-50
30702positiveoptimum42.5thermophilic
67770positivegrowth45thermophilic
67771positivegrowth45thermophilic

culture pH

@refabilitytypepHPH range
25081positivegrowth7.0-8.0
25081positivegrowth6.0-8.0
30702positivegrowth5.9-8.8alkaliphile
30702positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30702aerobe
67771aerobe

spore formation

  • @ref: 30702
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
25081NaClpositivegrowth0-3.0 %
30702NaClpositivegrowth0-5 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25081645522-hydroxybutyrate-respiration
25081167632-oxobutanoate-respiration
25081286442-oxopentanoate-respiration
25081182404-hydroxy-L-proline-respiration
2508130089acetate-respiration
2508117128adipate-assimilation
2508140585alpha-cyclodextrin-respiration
2508117925alpha-D-glucose-respiration
2508122599arabinose-assimilation
2508117057cellobiose-respiration
2508116947citrate-assimilation
2508116947citrate-respiration
2508118333D-arabitol-respiration
2508115824D-fructose-respiration
2508112936D-galactose-respiration
2508118024D-galacturonic acid-respiration
250818391D-gluconate-respiration
2508117784D-glucosaminic acid-respiration
2508114314D-glucose 6-phosphate-respiration
2508116899D-mannitol-respiration
2508116024D-mannose-respiration
2508127605D-psicose-respiration
2508117924D-sorbitol-respiration
2508127689decanoate-assimilation
2508123652dextrin-respiration
2508117234glucose-fermentation
2508117234glucose-assimilation
2508129042glucose 1-phosphate-respiration
2508132323glucuronamide-respiration
2508117754glycerol-respiration
2508114336glycerol 1-phosphate-respiration
2508128087glycogen-respiration
2508173804glycyl L-aspartic acid-respiration
2508130849L-arabinose-respiration
2508117196L-asparagine-respiration
2508129991L-aspartate-respiration
2508118287L-fucose-respiration
2508115729L-ornithine-respiration
2508117115L-serine-respiration
2508124996lactate-respiration
2508117716lactose-respiration
250816359lactulose-respiration
2508117306maltose-respiration
2508117306maltose-assimilation
2508129864mannitol-assimilation
2508137684mannose-assimilation
2508128053melibiose-respiration
25081320055methyl beta-D-glucopyranoside-respiration
2508128037N-acetylgalactosamine-respiration
25081506227N-acetylglucosamine-respiration
25081506227N-acetylglucosamine-assimilation
2508173784glycyl-l-glutamate-respiration
2508117632nitrate-reduction
2508118401phenylacetate-assimilation
2508132032potassium gluconate-assimilation
2508117272propionate-respiration
2508116634raffinose-respiration
2508117992sucrose-respiration
2508126986threonine-respiration
2508127082trehalose-respiration
2508127897tryptophan-energy source
25081167632-oxobutanoate+respiration
25081286442-oxopentanoate+respiration
25081182404-hydroxy-L-proline+respiration
2508130089acetate+respiration
2508140585alpha-cyclodextrin+respiration
2508117925alpha-D-glucose+respiration
2508115824D-fructose+respiration
2508112936D-galactose+respiration
250814853esculin+builds acid from
2508128066gentiobiose+respiration
2508117234glucose+assimilation
2508128087glycogen+respiration
2508130849L-arabinose+respiration
2508117196L-asparagine+respiration
2508129991L-aspartate+respiration
2508129985L-glutamate+respiration
2508115729L-ornithine+respiration
2508117203L-proline+respiration
2508117115L-serine+respiration
2508124996lactate+respiration
2508117716lactose+respiration
250816359lactulose+respiration
2508117306maltose+assimilation
2508117306maltose+respiration
2508128053melibiose+respiration
25081320055methyl beta-D-glucopyranoside+respiration
2508175146monomethyl succinate+respiration
25081506227N-acetylglucosamine+assimilation
25081506227N-acetylglucosamine+respiration
2508173784glycyl-l-glutamate+respiration
2508117272propionate+respiration
2508117992sucrose+respiration
2508126986threonine+respiration
2508127082trehalose+respiration
2508132528turanose+respiration
3070215963ribitol+carbon source
3070217057cellobiose+carbon source
3070233984fucose+carbon source
3070228260galactose+carbon source
3070217234glucose+carbon source
3070217754glycerol+carbon source
3070217716lactose+carbon source
3070217306maltose+carbon source
3070237684mannose+carbon source
3070228053melibiose+carbon source
30702506227N-acetylglucosamine+carbon source
3070216634raffinose+carbon source
3070217814salicin+carbon source
3070217992sucrose+carbon source
3070227082trehalose+carbon source
307024853esculin+hydrolysis
3070217632nitrate+reduction

metabolite production

  • @ref: 25081
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitemethylred-testindole test
2508117234glucose-
2508135581indole-

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
25081food-waste compostTaichungTaiwanTWNAsianutrient agar (NA; HiMedia)2 days30standard serial dilution-to-extinction plating technique
67770Manure compost produced by a field-scale composter which is used for the treatment of livestock excreta
67771From manure compost produced by a field-scale composter which is used for the treatment of livestock excreta(Hazaka systemHazaka Plant Kogyo)JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Food production#Food
#Engineered#Waste#Domestic waste

taxonmaps

  • @ref: 69479
  • File name: preview.99_40874.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_19008;97_23567;98_29780;99_40874&stattab=map
  • Last taxonomy: Sphingobacterium thermophilum subclade
  • 16S sequence: AB563783
  • Sequence Identity:
  • Total samples: 1887
  • soil counts: 309
  • aquatic counts: 321
  • animal counts: 1123
  • plant counts: 134

Sequence information

16S sequences

  • @ref: 30702
  • description: Sphingobacterium thermophilum gene for 16S rRNA, partial sequence, strain: CKTN2
  • accession: AB563783
  • length: 1461
  • database: nuccore
  • NCBI tax ID: 768534

GC content

@refGC-contentmethod
2508134.5high performance liquid chromatography (HPLC)
3070240.3

External links

@ref: 25081

culture collection no.: JCM 17858, KCTC 23708

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22904214Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost.Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.042481-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Manure/microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purificationGenetics
Phylogeny27498829Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, Aslam ZInt J Syst Evol Microbiol10.1099/ijsem.0.0013702016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginsenosides/*metabolism, Panax/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27666956Sphingobacterium 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 CCInt J Syst Evol Microbiol10.1099/ijsem.0.0015172016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedID_cross_reference
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25081W. 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. 201310.1099/ijsem.0.001517IJSEM 66: 5336-5344 201627666956
30702Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127033
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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 betahttps://microbeatlas.org/