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The rhizosphere, a thin soil zone around the roots, is a hotspot for microbial activity, making it a crucial component of the soil ecosystem. Secondary metabolites produced by rhizospheric<jats:italic>Sphingomonas sanguinis<\/jats:italic>DM have sparked significant curiosity in investigating their possible biological impacts.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>A bacterial strain has been isolated from the rhizosphere of<jats:italic>Datura metel<\/jats:italic>. The bacterium\u2019s identification, fermentation, and working up have been outlined. The ethyl acetate fraction of the propagated culture media of<jats:italic>Sphingomonas sanguinis<\/jats:italic>DM was fractioned and purified using various chromatographic techniques. The characterization of the isolated compounds was accomplished through the utilization of various spectroscopic techniques, such as UV, MS, 1D, and 2D-NMR. Furthermore, the evaluation of their antimicrobial activity was conducted using the agar well diffusion method, while cytotoxicity was assessed using the MTT test.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The extract from<jats:italic>Sphingomonas sanguinis<\/jats:italic>DM provided two distinct compounds: n-dibutyl phthalic acid (<jats:bold>1<\/jats:bold>) and Bis (2-methyl heptyl) phthalate (<jats:bold>2<\/jats:bold>) within its ethyl acetate fraction. Furthermore, the 16S rRNA gene sequence of<jats:italic>Sphingomonas sanguinis<\/jats:italic>DM has been registered under the NCBI GenBank database with the accession number PP422198. The bacterial extract exhibited its effect against gram-positive bacteria, inhibiting<jats:italic>Streptococcus mutans<\/jats:italic>(12.6\u2009\u00b1\u20090.6\u00a0mm) and<jats:italic>Staphylococcus aureus<\/jats:italic>(10.6\u2009\u00b1\u20090.6\u00a0mm) compared to standard antibiotics. Conversely, compound<jats:bold>1<\/jats:bold>showed a considerable effect against phytopathogenic fungi such as<jats:italic>Alternaria alternate<\/jats:italic>(56.3\u2009\u00b1\u200910.6\u00a0mm) and<jats:italic>Fusarium oxysporum<\/jats:italic>(21.3\u2009\u00b1\u20091.5\u00a0mm) with a MIC value of 17.5\u00a0\u00b5g\/mL. However, it was slightly active against<jats:italic>Klebsiella pneumonia<\/jats:italic>(11.0\u2009\u00b1\u20091.0\u00a0mm). Furthermore, compound<jats:bold>2<\/jats:bold>was the most active metabolite, having a significant antimicrobial efficacy against<jats:italic>Rhizoctonia solani<\/jats:italic>(63.6\u2009\u00b1\u20091.1\u00a0mm),<jats:italic>Pseudomonas aeruginosa<\/jats:italic>(16.7\u2009\u00b1\u20090.6\u00a0mm), and<jats:italic>Alternaria alternate<\/jats:italic>(20.3\u2009\u00b1\u20090.6\u00a0mm) with MIC value at 15\u00a0\u00b5g\/mL. In addition, compound<jats:bold>2<\/jats:bold>exhibited the most potency against hepatocellular (HepG-2) and skin (A-431) carcinoma cell lines with IC<jats:sub>50<\/jats:sub>values of 107.16\u00a0\u00b5g\/mL and 111.36\u00a0\u00b5g\/mL, respectively.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p><jats:italic>Sphingomonas sanguinis<\/jats:italic>DM, a rhizosphere bacterium of<jats:italic>Datura metel<\/jats:italic>, was studied for its phytochemical and biological characteristics, resulting in the identification of two compounds with moderate antimicrobial and cytotoxic activities.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12906-024-04482-6","type":"journal-article","created":{"date-parts":[[2024,5,25]],"date-time":"2024-05-25T13:02:00Z","timestamp":1716642120000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel"],"prefix":"10.1186","volume":"24","author":[{"given":"Mohamed A.","family":"Awad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sherif F.","family":"Hammad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samir F.","family":"El-Mashtoly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bahig","family":"El-Deeb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hesham S. 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