Bioassay- and metabolomics-guided screening of bioactive soil actinomycetes from the ancient city of Ihnasia, Egypt

Abstract

Literature surveys, taxonomical differences, and bioassay results have been utilized in the discovery of new natural products to aid in Actinomycetes isolate-selection. However, no or less investigation have been done on establishing the differences in metabolomic profiles of the isolated microorganisms. The study aims to utilise bioassay- and metabolomics-guided tools that included dereplication study and multivariate analysis of the NMR and mass spectral data of microbial extracts to assist the selection of isolates for scaling-up the production of antimicrobial natural products. A total of 58 actinomycetes were isolated from different soil samples collected from Ihnasia City, Egypt and screened for their antimicrobial activities against indicator strains that included Bacillus subtilis, Escherichia coli, methicillin-resistant Staphylococcus aureus and Candida albicans. A number of 25 isolates were found to be active against B. subtilis and/or to at least one of the tested indicator strains. Principal component analyses showed chemical uniqueness for four outlying bioactive actinomycetes extracts. In addition, Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) and dereplication study led us to further select two outlying anti-MRSA active isolates MS.REE.13 and 22 for scale-up work. MS.REE.13 and 22 exhibited zones of inhibition at 19 and 13 mm against MRSA, respectively. A metabolomics-guided approach provided the steer to target the bioactive metabolites (P<0.01) present in a crude extract or fraction even at nanogram levels but it was a challenge that such low-yielding bioactive natural products would be feasible to isolate. Validated to occur only on the active side of OPLS-DA loadings plot, the isolated compounds exhibited medium to weak antibiotic activity with MIC values between 250 and 800 μM. Two new compounds, P_24306 (C10H13N2) and N_12799 (C18H32O3) with MICs of 795 and 432 μM, were afforded from the scale-up of MS.REE. 13 and 22, respectively.

Isolation and optimized production of putative antimicrobial compounds from Egyptian soil isolate Streptomyces sp. MS. 10

“…1 H-1 H COSY and 1 H- 13 C HMBC experiments confirmed the presence of saturated FA as major bioactive compound in fraction 8 (Fig. S5 and Fig.…”

“…S5 and Fig. S6), while all carbons-protons assignments were done by 1 H- 13 C HSQC experiment (Fig. S7).…”

“…MS. 10 was recovered from a superficial soil layer sample collected from Ihnasia City in Beni-Suef Governorate, Egypt. It was isolated on International Streptomyces Project (ISP) 4 agar using the soil dilution plate technique, as previously described [13,14].…”

The gut microbial diversity of colon cancer patients and the clinical significance

“…It also play the role of metabolism and the storage of food residues. However, the residue and some acids, phenols, and other carcinogens produced by metabolism can be the pathogen for intestinal [17][18][19]. Thus, the integrity of the barrier for the intestinal, as well as the immune system, etc., would be invaded and destroyed, and the risk of exposure would increase [20][21][22].…”

Metabolomics: towards acceleration of antibacterial plant-based leads discovery

“…Metabolomics is suitable to explore food, especially a plant-based food, for the presence of pharmacologically active secondary metabolites (Adebo et al 2017;Silva et al 2019). When combined with bioactivity studies, particularly with bioactivityguided isolation, it enables fast tracking and identification of molecules with desired biological potential (Sebak et al 2019).…”