Strain identifier

BacDive ID: 133300

Type strain: Yes

Species: Sphingomonas lutea

Strain Designation: JS5

Strain history: C. N. Seong JS5.

NCBI tax ID(s): 1045317 (species)

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General

@ref: 25055

BacDive-ID: 133300

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

description: Sphingomonas lutea JS5 is an aerobe, Gram-negative bacterium that forms circular colonies and was isolated from freshwater of Juam reservoir.

NCBI tax id

  • NCBI tax id: 1045317
  • Matching level: species

strain history

  • @ref: 67770
  • history: C. N. Seong JS5.

doi: 10.13145/bacdive133300.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas lutea
  • full scientific name: Sphingomonas lutea Lee et al. 2016

@ref: 25055

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas lutea

strain designation: JS5

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.666

colony morphology

  • @ref: 25055
  • colony size: 0.5-1.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

pigmentation

@refproductionname
25055yesCarotenoid pigments
25055noFlexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
25055Reasoner's 2A agar (R2A)yes
25055Marine agar (MA)no
25055PCA (plate-count agar)no
25055TSA (Trypticase soy agar)no
25055NA (nutrient agar)yes

culture temp

@refgrowthtypetemperaturerange
25055positivegrowth10-37
25055positiveoptimum25-30mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
25055positivegrowth6-8
25055positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25055
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
25055no
69481no100
69480no99.895

halophily

  • @ref: 25055
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2505517521(-)-quinic acid-respiration
25055645522-hydroxybutyrate-respiration
25055167632-oxobutanoate-respiration
25055309162-oxoglutarate-respiration
25055286442-oxopentanoate-respiration
25055370543-hydroxybutyrate-respiration
25055182404-hydroxy-L-proline-respiration
25055167244-hydroxybutyrate-respiration
25055181014-hydroxyphenylacetic acid-respiration
2505530089acetate-respiration
2505517128adipate-assimilation
2505515963ribitol-respiration
2505540585alpha-cyclodextrin-respiration
2505517925alpha-D-glucose-assimilation
2505517925alpha-D-glucose-respiration
2505536219alpha-lactose-respiration
2505522599arabinose-assimilation
2505529016arginine-hydrolysis
2505573706bromosuccinate-respiration
2505517126carnitine-respiration
25055casein-hydrolysis
2505562968cellulose-hydrolysis
2505517029chitin-hydrolysis
2505516383cis-aconitate-respiration
2505516947citrate-respiration
2505515570D-alanine-respiration
2505518333D-arabitol-respiration
2505517057cellobiose-respiration
2505515824D-fructose-respiration
2505515895D-galactonic acid lactone-respiration
2505512936D-galactose-assimilation
2505512936D-galactose-respiration
2505518024D-galacturonic acid-respiration
2505530612D-glucarate-respiration
250558391D-gluconate-assimilation
250558391D-gluconate-respiration
2505517784D-glucosaminic acid-respiration
2505515748D-glucuronate-respiration
2505516899D-mannitol-respiration
2505516024D-mannose-respiration
2505527605D-psicose-respiration
2505516523D-serine-respiration
2505517924D-sorbitol-respiration
2505527689decanoate-assimilation
2505523652dextrin-respiration
2505516991dna-hydrolysis
2505517113erythritol-respiration
2505515740formate-respiration
2505528757fructose-builds acid from
2505528260galactose-builds acid from
2505516865gamma-aminobutyric acid-respiration
250555291gelatin-hydrolysis
2505528066gentiobiose-assimilation
2505528066gentiobiose-respiration
2505517234glucose-assimilation
2505517234glucose-builds acid from
2505532323glucuronamide-respiration
2505517754glycerol-respiration
2505528087glycogen-respiration
2505573804glycyl L-aspartic acid-assimilation
2505573804glycyl L-aspartic acid-respiration
2505517368hypoxanthine-hydrolysis
2505517596inosine-respiration
2505517268myo-inositol-respiration
2505517240itaconate-respiration
2505521217L-alaninamide-respiration
2505516977L-alanine-respiration
2505573786L-alanylglycine-respiration
2505530849L-arabinose-respiration
2505517196L-asparagine-respiration
2505529991L-aspartate-respiration
2505518287L-fucose-respiration
2505515971L-histidine-assimilation
2505515971L-histidine-respiration
2505515603L-leucine-respiration
2505515729L-ornithine-respiration
2505517295L-phenylalanine-respiration
2505518183L-pyroglutamic acid-respiration
2505562345L-rhamnose-respiration
2505517115L-serine-respiration
2505516857L-threonine-respiration
2505524996lactate-respiration
2505517716lactose-builds acid from
250556359lactulose-respiration
2505525115malate-assimilation
2505515792malonate-respiration
2505517306maltose-assimilation
2505517306maltose-builds acid from
2505517306maltose-respiration
2505529864mannitol-assimilation
2505529864mannitol-builds acid from
2505537684mannose-assimilation
2505537684mannose-builds acid from
2505528053melibiose-assimilation
2505528053melibiose-respiration
25055320055methyl beta-D-glucopyranoside-respiration
2505551850methyl pyruvate-respiration
2505575146monomethyl succinate-respiration
2505528037N-acetylgalactosamine-respiration
25055506227N-acetylglucosamine-assimilation
25055506227N-acetylglucosamine-respiration
2505517632nitrate-reduction
2505518401phenylacetate-assimilation
2505550048phenylethylamine-respiration
2505532032potassium gluconate-assimilation
2505517272propionate-respiration
2505516634raffinose-respiration
2505526546rhamnose-builds acid from
2505541865sebacic acid-respiration
2505553258sodium citrate-assimilation
2505528017starch-hydrolysis
25055143136succinamate-respiration
2505530031succinate-assimilation
2505530031succinate-respiration
2505517992sucrose-builds acid from
2505517992sucrose-respiration
2505527082trehalose-builds acid from
2505527082trehalose-assimilation
2505527082trehalose-respiration
2505532528turanose-assimilation
2505532528turanose-respiration
2505553423tween 40-assimilation
2505553423tween 40-respiration
2505553426tween 80-hydrolysis
2505553426tween 80-respiration
2505516199urea-hydrolysis
2505527248urocanic acid-respiration
2505515318xanthine-hydrolysis
2505537166xylan-hydrolysis
2505517151xylitol-respiration
2505518222xylose-builds acid from
250558295beta-hydroxybutyrate+respiration
250558295beta-hydroxybutyrate+assimilation
250554853esculin+hydrolysis
2505517203L-proline+respiration
2505573784glycyl-l-glutamate+respiration
2505573784glycyl-l-glutamate+assimilation
2505553424tween 20+hydrolysis
25055620642,3-butanediol+/-respiration
2505514314D-glucose 6-phosphate+/-respiration
2505516000ethanolamine+/-respiration
2505529042glucose 1-phosphate+/-respiration
2505514336glycerol 1-phosphate+/-respiration
2505529985L-glutamate+/-respiration
2505529985L-glutamate+/-assimilation
2505517148putrescine+/-respiration
2505517748thymidine+/-respiration
2505516704uridine+/-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2505516136hydrogen sulfideno
2505535581indoleno

enzymes

@refvalueactivityec
25055acid phosphatase+/-3.1.3.2
25055alkaline phosphatase+3.1.3.1
25055alpha-chymotrypsin-3.4.21.1
25055alpha-fucosidase-3.2.1.51
25055alpha-galactosidase-3.2.1.22
25055alpha-glucosidase-3.2.1.20
25055alpha-mannosidase-3.2.1.24
25055beta-galactosidase-3.2.1.23
25055beta-glucosidase-3.2.1.21
25055beta-glucuronidase-3.2.1.31
25055catalase+1.11.1.6
25055cystine arylamidase-3.4.11.3
25055cytochrome oxidase-1.9.3.1
25055esterase (C 4)+
25055esterase Lipase (C 8)+
25055leucine arylamidase+3.4.11.1
25055lipase (C 14)-
25055N-acetyl-beta-glucosaminidase-3.2.1.52
25055naphthol-AS-BI-phosphohydrolase+/-
25055trypsin-3.4.21.4
25055valine arylamidase+/-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2505511-Methyl C18:1ω7c3.1
    25055C14:02.1
    25055C16:016.4
    25055C16:1ω5c3.9
    25055C16:1ω7c / C16:1ω6c16.3
    25055C17:1ω6c5.2
    25055C18:07.7
    25055C18:1 2OH3.4
    25055C18:1ω7c / C18:1ω6c34.8
    25055C18:1ω9c3
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25055freshwater of Juam reservoirJuam reservoir, Republic of KoreaRepublic of KoreaKORAsia
67770Freshwater of Juam reservoirRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

Sequence information

16S sequences

  • @ref: 25055
  • description: 16S rRNA gene sequence
  • accession: JF922305
  • length: 1428
  • database: ena
  • NCBI tax ID: 1045317

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas lutea KCTC 23642GCA_014396785completencbi1045317
66792Sphingomonas lutea strain KCTC 236421045317.3completepatric1045317
66792Sphingomonas lutea KCTC 236422896432115completeimg1045317
66792Sphingomonas lutea KCTC 23642GCA_021497585chromosomencbi1045317

GC content

  • @ref: 67770
  • GC-content: 64.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.776no
gram-positiveno97.061no
anaerobicno98.668yes
aerobicyes83.287no
halophileno92.179yes
spore-formingno95.573no
thermophileno90.477yes
glucose-utilyes66.109yes
motileno84.478no
glucose-fermentno89.194no

External links

@ref: 25055

culture collection no.: KCTC 23642, JCM 18309, CCTCC AB 2017135

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902188Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir.Lee JH, Kim DI, Kang JW, Seong CNInt J Syst Evol Microbiol10.1099/ijsem.0.0015462016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny35060847Sphingomonas arenae sp. nov., isolated from desert soil.Dong L, Li S, Lian WH, Wei QC, Mohamad OAA, Hozzein WN, Ahmed I, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0051952022Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Sphingomonas/classification/isolation & purificationTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
25055J. H. K. Lee, D. I.,Kang, J. W.,Seong, C. N.Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir10.1099/ijsem.0.001546IJSEM 66: 5493-5499 201627902188
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1