Strain identifier

BacDive ID: 141165

Type strain: Yes

Species: Sphingomonas jatrophae

Strain Designation: S5-249

Strain history: <- M. Madhaiyan, Temasek Life Sciences Laboratory, Univ. Singapore; S5-249

NCBI tax ID(s): 1166337 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 64987

BacDive-ID: 141165

DSM-Number: 27345

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

description: Sphingomonas jatrophae S5-249 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from endophyte of surface-sterilized leaf tissue of Jatropha curcas.

NCBI tax id

  • NCBI tax id: 1166337
  • Matching level: species

strain history

  • @ref: 64987
  • history: <- M. Madhaiyan, Temasek Life Sciences Laboratory, Univ. Singapore; S5-249

doi: 10.13145/bacdive141165.20230509.8.1

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 jatrophae
  • full scientific name: Sphingomonas jatrophae Madhaiyan et al. 2017

@ref: 64987

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas jatrophae

full scientific name: Sphingomonas jatrophae Madhaiyan et al. 2017

strain designation: S5-249

type strain: yes

Morphology

cell morphology

  • @ref: 44084
  • gram stain: negative
  • cell length: 1.8-2.1 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 44084
  • colony size: 1.1-1.4 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: 2xYT

multimedia

  • @ref: 64987
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27345.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
440842xYTyes
44084Reasoner's 2A agar (R2A)yes
64987R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
44084positivegrowth15-37
44084positiveoptimum28-30mesophilic
64987positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
44084positivegrowth5.0-9.0alkaliphile
44084positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 44084
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 44084
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
44084NaClpositivegrowth0-6 %(w/v)
44084NaClpositiveoptimum4 %(w/v)

observation

  • @ref: 44084
  • observation: sphingolipid-producing

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44084161933-hydroxybenzoate-assimilation
44084178794-hydroxybenzoate-assimilation
4408417128adipate-assimilation
4408427689decanoate-assimilation
4408416899D-mannitol-assimilation
4408416988D-ribose-assimilation
4408417924D-sorbitol-assimilation
4408428087glycogen-assimilation
4408417268myo-inositol-assimilation
4408417240itaconate-assimilation
4408416977L-alanine-assimilation
4408418287L-fucose-assimilation
4408415971L-histidine-assimilation
4408462345L-rhamnose-assimilation
4408417115L-serine-assimilation
4408424996lactate-assimilation
4408425115malate-assimilation
4408417306maltose-assimilation
4408428053melibiose-assimilation
4408418401phenylacetate-assimilation
44084potassium 2-dehydro-D-gluconate-assimilation
44084potassium 5-dehydro-D-gluconate-assimilation
4408432032potassium gluconate-assimilation
4408417814salicin-assimilation
4408432954sodium acetate-assimilation
4408453258sodium citrate-assimilation
4408462983sodium malonate-assimilation
440849300suberic acid-assimilation
4408417992sucrose-assimilation
4408427613amygdalin-builds acid from
4408418305arbutin-builds acid from
4408417057cellobiose-builds acid from
4408415963ribitol-builds acid from
4408417108D-arabinose-builds acid from
4408418333D-arabitol-builds acid from
4408415824D-fructose-builds acid from
4408428847D-fucose-builds acid from
4408412936D-galactose-builds acid from
4408417634D-glucose-builds acid from
4408416899D-mannitol-builds acid from
4408416024D-mannose-builds acid from
4408416988D-ribose-builds acid from
4408417924D-sorbitol-builds acid from
4408416443D-tagatose-builds acid from
4408465327D-xylose-builds acid from
4408416813galactitol-builds acid from
4408417113erythritol-builds acid from
44084esculin ferric citrate-builds acid from
4408428066gentiobiose-builds acid from
4408417754glycerol-builds acid from
4408428087glycogen-builds acid from
4408417268myo-inositol-builds acid from
4408415443inulin-builds acid from
4408418403L-arabitol-builds acid from
4408418287L-fucose-builds acid from
4408462345L-rhamnose-builds acid from
4408417266L-sorbose-builds acid from
4408465328L-xylose-builds acid from
4408417716lactose-builds acid from
4408417306maltose-builds acid from
440846731melezitose-builds acid from
4408428053melibiose-builds acid from
44084320061methyl alpha-D-glucopyranoside-builds acid from
4408443943methyl alpha-D-mannoside-builds acid from
4408474863methyl beta-D-xylopyranoside-builds acid from
44084506227N-acetylglucosamine-builds acid from
44084potassium 2-dehydro-D-gluconate-builds acid from
44084potassium 5-dehydro-D-gluconate-builds acid from
4408432032potassium gluconate-builds acid from
4408416634raffinose-builds acid from
4408417814salicin-builds acid from
4408428017starch-builds acid from
4408417992sucrose-builds acid from
4408427082trehalose-builds acid from
4408432528turanose-builds acid from
4408417151xylitol-builds acid from
4408417234glucose-fermentation
440845291gelatin-hydrolysis
4408428017starch-hydrolysis
4408418186tyrosine-hydrolysis
4408437166xylan-hydrolysis
4408417632nitrate-reduction
4408416301nitrite-reduction
44084370543-hydroxybutyrate+assimilation
4408417634D-glucose+assimilation
4408416024D-mannose+assimilation
4408430849L-arabinose+assimilation
4408417203L-proline+assimilation
4408417306maltose+assimilation
44084506227N-acetylglucosamine+assimilation
4408417272propionate+assimilation
4408431011valerate+assimilation
4408430849L-arabinose+builds acid from
4408485146carboxymethylcellulose+hydrolysis
44084casein+hydrolysis
440844853esculin+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4408428971ampicillinyesyes25 µg/mL
4408427902tetracyclineyesyes25 µg/mL
4408428077rifampicinyesyes25 µg/mL
4408417698chloramphenicolyesyes25 µg/mL
440849215spectinomycinyesyes25 µg/mL
44084100147nalidixic acidyesyes25 µg/mL
440843393carbenicillinyesyes100 µg/mL
4408424753hygromycinyesyes50 µg/mL
440846104kanamycinyesyes250 µg/mL

metabolite production

  • @ref: 44084
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44084catalase+1.11.1.6
44084cytochrome oxidase+1.9.3.1
44084alkaline phosphatase+3.1.3.1
44084esterase (C 4)+
44084esterase Lipase (C 8)+
44084leucine arylamidase+3.4.11.1
44084valine arylamidase+
44084trypsin+3.4.21.4
44084acid phosphatase+3.1.3.2
44084naphthol-AS-BI-phosphohydrolase+
44084lipase (C 14)-
44084cystine arylamidase-3.4.11.3
44084alpha-chymotrypsin-3.4.21.1
44084beta-glucuronidase-3.2.1.31
44084alpha-mannosidase-3.2.1.24
44084alpha-galactosidase-3.2.1.22
44084alpha-glucosidase-3.2.1.20
44084beta-glucosidase-3.2.1.21
44084N-acetyl-beta-glucosaminidase-3.2.1.52
44084alpha-fucosidase-3.2.1.51
44084arginine dihydrolase-3.5.3.6
44084urease-3.5.1.5
44084beta-galactosidase+/-3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44084C14:01.2
    44084C14:0 2OH7.2
    44084C16:18.5
    44084C16:1ω5c1.8
    44084C16:1ω7t / iso-C15:0 2-OH /C16:1ω7c7.5
    44084C17:1ω6c3.2
    44084C18:01.7
    44084C18:1ω6c1.9
    44084C18:1ω7c / C18:1ω9t / C18:1ω12t66.5
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 30
  • incubation time: 2
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
44084endophyte of surface-sterilized leaf tissue of Jatropha curcas2009-09Agrotechnology Experimental StationSingaporeSGPAsia1.43667103.709R2A/Nfb mediumN-free semi-solid medium3 days30
64987surface-sterilized stem tissue of the Jatropha curcas L. cultivar (‘B1-2')Agrotechnology Experimental Station (1° 26' 12'' N 103° 42' 34'' E)SingaporeSGPAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Leaf (Phyllosphere)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 64987
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64987
  • description: Sphingomonas jatrophae strain S5-249 16S ribosomal RNA gene, partial sequence
  • accession: JQ660172
  • length: 1412
  • database: ena
  • NCBI tax ID: 1166337

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas jatrophae S5-249GCA_900113315contigncbi1166337
66792Sphingomonas jatrophae S5-2492654588199draftimg1166337

GC content

@refGC-contentmethod
4408468.5genome sequence analysis
6498766.9sequence analysis

External links

@ref: 64987

culture collection no.: DSM 27345, KACC 17593

straininfo link

  • @ref: 96875
  • straininfo: 405139

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29087271Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.Madhaiyan M, Alex THH, Cho H, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji LInt J Syst Evol Microbiol10.1099/ijsem.0.0024342017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Jatropha/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Singapore, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryEnzymology
Phylogeny32416739Sphingomonas montanisoli sp. nov., isolated from mountain soil.Xu Z, Zhang Y, Muhammad Y, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0041872020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
44084Munusamy Madhaiyan, Tan Hian Hwee Alex, Hayoung Cho, Soo-Jin Kim, Hang-Yeon Weon, Soon-Wo Kwon, William B. Whitman and Lianghui JiSphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.10.1099/ijsem.0.002434IJSEM 67: 5150-5158 201729087271
64987Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27345Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27345)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
96875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405139.1