Strain identifier
BacDive ID: 141165
Type strain:
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)
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
@ref | name | growth | link | composition |
---|---|---|---|---|
44084 | 2xYT | yes | ||
44084 | Reasoner's 2A agar (R2A) | yes | ||
64987 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
44084 | positive | growth | 15-37 | |
44084 | positive | optimum | 28-30 | mesophilic |
64987 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
44084 | positive | growth | 5.0-9.0 | alkaliphile |
44084 | positive | optimum | 6.0-7.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 44084
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 44084
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
44084 | NaCl | positive | growth | 0-6 %(w/v) |
44084 | NaCl | positive | optimum | 4 %(w/v) |
observation
- @ref: 44084
- observation: sphingolipid-producing
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
44084 | 16193 | 3-hydroxybenzoate | - | assimilation |
44084 | 17879 | 4-hydroxybenzoate | - | assimilation |
44084 | 17128 | adipate | - | assimilation |
44084 | 27689 | decanoate | - | assimilation |
44084 | 16899 | D-mannitol | - | assimilation |
44084 | 16988 | D-ribose | - | assimilation |
44084 | 17924 | D-sorbitol | - | assimilation |
44084 | 28087 | glycogen | - | assimilation |
44084 | 17268 | myo-inositol | - | assimilation |
44084 | 17240 | itaconate | - | assimilation |
44084 | 16977 | L-alanine | - | assimilation |
44084 | 18287 | L-fucose | - | assimilation |
44084 | 15971 | L-histidine | - | assimilation |
44084 | 62345 | L-rhamnose | - | assimilation |
44084 | 17115 | L-serine | - | assimilation |
44084 | 24996 | lactate | - | assimilation |
44084 | 25115 | malate | - | assimilation |
44084 | 17306 | maltose | - | assimilation |
44084 | 28053 | melibiose | - | assimilation |
44084 | 18401 | phenylacetate | - | assimilation |
44084 | potassium 2-dehydro-D-gluconate | - | assimilation | |
44084 | potassium 5-dehydro-D-gluconate | - | assimilation | |
44084 | 32032 | potassium gluconate | - | assimilation |
44084 | 17814 | salicin | - | assimilation |
44084 | 32954 | sodium acetate | - | assimilation |
44084 | 53258 | sodium citrate | - | assimilation |
44084 | 62983 | sodium malonate | - | assimilation |
44084 | 9300 | suberic acid | - | assimilation |
44084 | 17992 | sucrose | - | assimilation |
44084 | 27613 | amygdalin | - | builds acid from |
44084 | 18305 | arbutin | - | builds acid from |
44084 | 17057 | cellobiose | - | builds acid from |
44084 | 15963 | ribitol | - | builds acid from |
44084 | 17108 | D-arabinose | - | builds acid from |
44084 | 18333 | D-arabitol | - | builds acid from |
44084 | 15824 | D-fructose | - | builds acid from |
44084 | 28847 | D-fucose | - | builds acid from |
44084 | 12936 | D-galactose | - | builds acid from |
44084 | 17634 | D-glucose | - | builds acid from |
44084 | 16899 | D-mannitol | - | builds acid from |
44084 | 16024 | D-mannose | - | builds acid from |
44084 | 16988 | D-ribose | - | builds acid from |
44084 | 17924 | D-sorbitol | - | builds acid from |
44084 | 16443 | D-tagatose | - | builds acid from |
44084 | 65327 | D-xylose | - | builds acid from |
44084 | 16813 | galactitol | - | builds acid from |
44084 | 17113 | erythritol | - | builds acid from |
44084 | esculin ferric citrate | - | builds acid from | |
44084 | 28066 | gentiobiose | - | builds acid from |
44084 | 17754 | glycerol | - | builds acid from |
44084 | 28087 | glycogen | - | builds acid from |
44084 | 17268 | myo-inositol | - | builds acid from |
44084 | 15443 | inulin | - | builds acid from |
44084 | 18403 | L-arabitol | - | builds acid from |
44084 | 18287 | L-fucose | - | builds acid from |
44084 | 62345 | L-rhamnose | - | builds acid from |
44084 | 17266 | L-sorbose | - | builds acid from |
44084 | 65328 | L-xylose | - | builds acid from |
44084 | 17716 | lactose | - | builds acid from |
44084 | 17306 | maltose | - | builds acid from |
44084 | 6731 | melezitose | - | builds acid from |
44084 | 28053 | melibiose | - | builds acid from |
44084 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
44084 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
44084 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
44084 | 506227 | N-acetylglucosamine | - | builds acid from |
44084 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
44084 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
44084 | 32032 | potassium gluconate | - | builds acid from |
44084 | 16634 | raffinose | - | builds acid from |
44084 | 17814 | salicin | - | builds acid from |
44084 | 28017 | starch | - | builds acid from |
44084 | 17992 | sucrose | - | builds acid from |
44084 | 27082 | trehalose | - | builds acid from |
44084 | 32528 | turanose | - | builds acid from |
44084 | 17151 | xylitol | - | builds acid from |
44084 | 17234 | glucose | - | fermentation |
44084 | 5291 | gelatin | - | hydrolysis |
44084 | 28017 | starch | - | hydrolysis |
44084 | 18186 | tyrosine | - | hydrolysis |
44084 | 37166 | xylan | - | hydrolysis |
44084 | 17632 | nitrate | - | reduction |
44084 | 16301 | nitrite | - | reduction |
44084 | 37054 | 3-hydroxybutyrate | + | assimilation |
44084 | 17634 | D-glucose | + | assimilation |
44084 | 16024 | D-mannose | + | assimilation |
44084 | 30849 | L-arabinose | + | assimilation |
44084 | 17203 | L-proline | + | assimilation |
44084 | 17306 | maltose | + | assimilation |
44084 | 506227 | N-acetylglucosamine | + | assimilation |
44084 | 17272 | propionate | + | assimilation |
44084 | 31011 | valerate | + | assimilation |
44084 | 30849 | L-arabinose | + | builds acid from |
44084 | 85146 | carboxymethylcellulose | + | hydrolysis |
44084 | casein | + | hydrolysis | |
44084 | 4853 | esculin | + | hydrolysis |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
44084 | 28971 | ampicillin | yes | yes | 25 µg/mL | ||
44084 | 27902 | tetracycline | yes | yes | 25 µg/mL | ||
44084 | 28077 | rifampicin | yes | yes | 25 µg/mL | ||
44084 | 17698 | chloramphenicol | yes | yes | 25 µg/mL | ||
44084 | 9215 | spectinomycin | yes | yes | 25 µg/mL | ||
44084 | 100147 | nalidixic acid | yes | yes | 25 µg/mL | ||
44084 | 3393 | carbenicillin | yes | yes | 100 µg/mL | ||
44084 | 24753 | hygromycin | yes | yes | 50 µg/mL | ||
44084 | 6104 | kanamycin | yes | yes | 250 µg/mL |
metabolite production
- @ref: 44084
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
44084 | catalase | + | 1.11.1.6 |
44084 | cytochrome oxidase | + | 1.9.3.1 |
44084 | alkaline phosphatase | + | 3.1.3.1 |
44084 | esterase (C 4) | + | |
44084 | esterase Lipase (C 8) | + | |
44084 | leucine arylamidase | + | 3.4.11.1 |
44084 | valine arylamidase | + | |
44084 | trypsin | + | 3.4.21.4 |
44084 | acid phosphatase | + | 3.1.3.2 |
44084 | naphthol-AS-BI-phosphohydrolase | + | |
44084 | lipase (C 14) | - | |
44084 | cystine arylamidase | - | 3.4.11.3 |
44084 | alpha-chymotrypsin | - | 3.4.21.1 |
44084 | beta-glucuronidase | - | 3.2.1.31 |
44084 | alpha-mannosidase | - | 3.2.1.24 |
44084 | alpha-galactosidase | - | 3.2.1.22 |
44084 | alpha-glucosidase | - | 3.2.1.20 |
44084 | beta-glucosidase | - | 3.2.1.21 |
44084 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
44084 | alpha-fucosidase | - | 3.2.1.51 |
44084 | arginine dihydrolase | - | 3.5.3.6 |
44084 | urease | - | 3.5.1.5 |
44084 | beta-galactosidase | +/- | 3.2.1.23 |
fatty acid profile
fatty acids
@ref fatty acid percentage 44084 C14:0 1.2 44084 C14:0 2OH 7.2 44084 C16:1 8.5 44084 C16:1ω5c 1.8 44084 C16:1ω7t / iso-C15:0 2-OH /C16:1ω7c 7.5 44084 C17:1ω6c 3.2 44084 C18:0 1.7 44084 C18:1ω6c 1.9 44084 C18:1ω7c / C18:1ω9t / C18:1ω12t 66.5 - 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
@ref | sample type | sampling date | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|---|---|
44084 | endophyte of surface-sterilized leaf tissue of Jatropha curcas | 2009-09 | Agrotechnology Experimental Station | Singapore | SGP | Asia | 1.43667 | 103.709 | R2A/Nfb medium | N-free semi-solid medium | 3 days | 30 |
64987 | surface-sterilized stem tissue of the Jatropha curcas L. cultivar (‘B1-2') | Agrotechnology Experimental Station (1° 26' 12'' N 103° 42' 34'' E) | Singapore | SGP | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingomonas jatrophae S5-249 | GCA_900113315 | contig | ncbi | 1166337 |
66792 | Sphingomonas jatrophae S5-249 | 2654588199 | draft | img | 1166337 |
GC content
@ref | GC-content | method |
---|---|---|
44084 | 68.5 | genome sequence analysis |
64987 | 66.9 | sequence analysis |
External links
@ref: 64987
culture collection no.: DSM 27345, KACC 17593
straininfo link
- @ref: 96875
- straininfo: 405139
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29087271 | Sphingomonas 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 L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002434 | 2017 | Bacterial 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/chemistry | Enzymology |
Phylogeny | 32416739 | Sphingomonas montanisoli sp. nov., isolated from mountain soil. | Xu Z, Zhang Y, Muhammad Y, Wang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004187 | 2020 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | 10.1099/ijsem.0.004332 | |||
44084 | Munusamy Madhaiyan, Tan Hian Hwee Alex, Hayoung Cho, Soo-Jin Kim, Hang-Yeon Weon, Soon-Wo Kwon, William B. Whitman and Lianghui Ji | Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L. | 10.1099/ijsem.0.002434 | IJSEM 67: 5150-5158 2017 | 29087271 | |
64987 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27345 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27345) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
96875 | Reimer, 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 identifiers | 10.60712/SI-ID405139.1 |