A direct examination of microbial specialized metabolites associated with ocean sediments from Baffin Bay and the Gulf of Maine
Arshad Ali Shaikh, Joost T. P. Verhoeven, Rupesh K. Sinha, Suzanne C. Dufour, and Kapil Tahlan
Abstract: Specialized metabolites produced by microorganisms found in ocean sediments display a wide range of clinically relevant bioactivities, including antimicrobial, anticancer, antiviral, and anti-inflammatory. Due to limitations in our ability to culture many benthic microorganisms under laboratory conditions, their potential to produce bioactive compounds remains underexplored. However, the advent of modern mass spectrometry technologies and data analysis methods for chemical structure prediction has aided in the discovery of such metabolites from complex mixtures. In this study, ocean sediments were collected from Baffin Bay (Canadian Arctic) and the Gulf of Maine for untargeted metabolomics using mass spectrometry. A direct examination of prepared organic extracts identified 1468 spectra, of which ∼45% could be annotated using in silico analysis methods. A comparable number of spectral features were detected in sediments collected from both locations, but 16S rRNA gene sequencing revealed a significantly more diverse bacterial community in samples from Baffin Bay. Based on spectral abundance, 12 specialized metabolites known to be associated with bacteria were selected for discussion. The application of metabolomics directly on marine sediments provides an avenue for culture-independent detection of metabolites produced under natural settings. The strategy can help prioritize samples for novel bioactive metabolite discovery using traditional workflows.
Significance: The work is focused on the exploration of untapped bioactive compounds from ocean sediments, with potential contributions to drug discovery. Untargeted metabolomics was used to identify specialized metabolites directly from sediments, avoiding the need for traditional cultivation methods. Bioactive compounds, including antimicrobial and anticancer agents, were revealed through this approach, demonstrating the oceans as a valuable source of new therapeutics. The biodiversity of marine microorganisms, particularly in the Arctic, is emphasized, and further exploration of extreme environments for novel metabolites with pharmaceutical potential is encouraged.
Significance: The work is focused on the exploration of untapped bioactive compounds from ocean sediments, with potential contributions to drug discovery. Untargeted metabolomics was used to identify specialized metabolites directly from sediments, avoiding the need for traditional cultivation methods. Bioactive compounds, including antimicrobial and anticancer agents, were revealed through this approach, demonstrating the oceans as a valuable source of new therapeutics. The biodiversity of marine microorganisms, particularly in the Arctic, is emphasized, and further exploration of extreme environments for novel metabolites with pharmaceutical potential is encouraged.
Double-Edged Nanobiotic Platform with Protean Functionality: Leveraging the Synergistic Antibacterial Activity of a Food-Grade Peptide to Mitigate Multidrug-Resistant Bacterial Pathogens
Piyush Kumar, Arshad Ali Shaikh, Pardeep Kumar, Vivek Kumar Gupta, Rajat Dhyani, Tarun Kumar Sharma, Ajmal Hussain, Krishnakant Gangele, Krishna Mohan, Poluri Korasapati, Nageswara Rao, Ravinder Kumar Malik, Ranjana Pathania and Naveen Kumar Navani
Abstract: While persistent efforts are being made to develop a novel arsenal against bacterial pathogens, the development of such materials remains a formidable challenge. One such strategy is to develop a multimodel antibacterial agent which will synergistically combat bacterial pathogens, including multidrug-resistant bacteria. Herein, we used pediocin, a class IIa bacteriocin, to decorate Ag° and developed a double-edged nanoplatform (Pd-SNPs) that inherits intrinsic properties of both antibacterial moieties, which engenders strikingly high antibacterial potency against a broad spectrum of bacterial pathogens including the ESKAPE category without displaying adverse cytotoxicity. The enhanced antimicrobial activity of Pd-SNPs is due to their higher affinity with the bacterial cell wall, which allows Pd-SNPs to penetrate the outer membrane, inducing membrane depolarization and the disruption of membrane integrity. Bioreporter assays revealed the upregulation of cpxP, degP, and sosX genes, triggering the burst of reactive oxygen species which eventually cause bacterial cell death. Pd-SNPs prevented biofilm formation, eradicated established biofilms, and inhibited persister cells. Pd-SNPs display unprecedented advantages because they are heat-resistant, retain antibacterial activity in human serum, and alleviate vancomycin intermediate Staphylococcus aureus (VISA) infection in the mouse model. In addition, Pd-SNPs wrapped in biodegradable nanofibers mitigated Listeria monocytogenes in cheese samples. Collectively, Pd-SNPs exhibited excellent biocompatibility and in vivo therapeutic potency without allowing foreseeable resistance acquisition by pathogens. These findings underscore new avenues for using a potent biocompatible nanobiotic platform to combat a wide range of bacterial pathogens.
Significance: The work presents the development of a novel antibacterial nanobiotic system, which effectively combats multidrug-resistant bacterial pathogens. The pediocin-capped silver nanoparticles (Pd-SNPs) were created that combined the antimicrobial properties of both pediocin and silver. These nanoparticles showed potent antibacterial activity against a broad spectrum of bacterial pathogens, including those resistant to multiple drugs, without causing toxicity to mammalian cells. Furthermore, Pd-SNPs prevented biofilm formation and eradicated persister cells, addressing major challenges in combating antibiotic-resistant bacteria. This work opens new avenues for using biocompatible nanomaterials to tackle resistant infections in clinical and food safety applications.
Significance: The work presents the development of a novel antibacterial nanobiotic system, which effectively combats multidrug-resistant bacterial pathogens. The pediocin-capped silver nanoparticles (Pd-SNPs) were created that combined the antimicrobial properties of both pediocin and silver. These nanoparticles showed potent antibacterial activity against a broad spectrum of bacterial pathogens, including those resistant to multiple drugs, without causing toxicity to mammalian cells. Furthermore, Pd-SNPs prevented biofilm formation and eradicated persister cells, addressing major challenges in combating antibiotic-resistant bacteria. This work opens new avenues for using biocompatible nanomaterials to tackle resistant infections in clinical and food safety applications.
Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus
Arshad Ali Shaikh, Louis-Felix Nothias, Santosh K. Srivastava, Pieter C. Dorrestein and Kapil Tahlan
Abstract: Bacterial specialized metabolites are of immense importance because of their medicinal, industrial, and agricultural applications. Streptomyces clavuligerus is a known producer of such compounds; however, much of its metabolic potential remains unknown, as many associated biosynthetic gene clusters are silent or expressed at low levels. The overexpression of ribosome recycling factor (frr) and ribosome engineering (induced rpsL mutations) in other Streptomyces spp. has been reported to increase the production of known specialized metabolites. Therefore, we used an overexpression strategy in combination with untargeted metabolomics, molecular networking, and in silico analysis to annotate 28 metabolites in the current study, which have not been reported previously in S. clavuligerus. Many of the newly described metabolites are commonly found in plants, further alluding to the ability of S. clavuligerus to produce such compounds under specific conditions. In addition, the manipulation of frr and rpsL led to different metabolite production profiles in most cases. Known and putative gene clusters associated with the production of the observed compounds are also discussed. This work suggests that the combination of traditional strain engineering and recently developed metabolomics technologies together can provide rapid and cost-effective strategies to further speed up the discovery of novel natural products.
Significance: The significance of the work lies in its exploration of novel methods to activate and enhance the production of specialized metabolites in Streptomyces clavuligerus. By applying ribosome engineering techniques, such as overexpressing ribosomal proteins and creating specific mutations, the study successfully identified 28 previously unreported metabolites. This approach not only expands the known biosynthetic potential of S. clavuligerus but also demonstrates the efficacy of combining traditional strain engineering with modern metabolomics technologies. The findings offer valuable insights for accelerating the discovery of novel natural products, which could have important applications in medicine, industry, and agriculture.
Significance: The significance of the work lies in its exploration of novel methods to activate and enhance the production of specialized metabolites in Streptomyces clavuligerus. By applying ribosome engineering techniques, such as overexpressing ribosomal proteins and creating specific mutations, the study successfully identified 28 previously unreported metabolites. This approach not only expands the known biosynthetic potential of S. clavuligerus but also demonstrates the efficacy of combining traditional strain engineering with modern metabolomics technologies. The findings offer valuable insights for accelerating the discovery of novel natural products, which could have important applications in medicine, industry, and agriculture.
Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism
Nader F. AbuSara*, Brandon M. Piercey*, Marcus A. Moore*, Arshad Ali Shaikh*, Louis-Félix Nothias, Santosh K Srivastava, Pablo Cruz-Morales, Pieter C Dorrestein, Francisco Barona-Gómez and Kapil Tahlan (*Co-first-author)
Abstract: Clavulanic acid is a bacterial specialized metabolite, which inhibits certain serine β-lactamases, enzymes that inactivate β-lactam antibiotics to confer resistance. Due to this activity, clavulanic acid is widely used in combination with penicillin and cephalosporin (β-lactam) antibiotics to treat infections caused by β-lactamase-producing bacteria. Clavulanic acid is industrially produced by fermenting Streptomyces clavuligerus, as large-scale chemical synthesis is not commercially feasible. Other than S. clavuligerus, Streptomyces jumonjinensis and Streptomyces katsurahamanus also produce clavulanic acid along with cephamycin C, but information regarding their genome sequences is not available. In addition, the Streptomyces contain many biosynthetic gene clusters thought to be “cryptic,” as the specialized metabolites produced by them are not known. Therefore, we sequenced the genomes of S. jumonjinensis and S. katsurahamanus, and examined their metabolomes using untargeted mass spectrometry along with S. clavuligerus for comparison. We analyzed the biosynthetic gene cluster content of the three species to correlate their biosynthetic capacities, by matching them with the specialized metabolites detected in the current study. It was recently reported that S. clavuligerus can produce the plant-associated metabolite naringenin, and we describe more examples of such specialized metabolites in extracts from the three Streptomyces species. Detailed comparisons of the biosynthetic gene clusters involved in clavulanic acid (and cephamycin C) production were also performed, and based on our analyses, we propose the core set of genes responsible for producing this medicinally important metabolite.
Significance: The work enhances our understanding of the biosynthetic pathways involved in the production of clavulanic acid, a key β-lactamase inhibitor used in antibiotic therapies. By sequencing the genomes of Streptomyces jumonjinensis and Streptomyces katsurahamanus and comparing them to Streptomyces clavuligerus, the study identifies specialized metabolite gene clusters (BGCs) involved in the production of both clavulanic acid and cephamycin C. This research provides valuable insights into the metabolic capabilities of these organisms and highlights the potential for discovering novel metabolites from cryptic BGCs. The findings contribute to the development of improved industrial production strains and the discovery of new antibiotics, addressing the ongoing challenge of antibiotic resistance.
Significance: The work enhances our understanding of the biosynthetic pathways involved in the production of clavulanic acid, a key β-lactamase inhibitor used in antibiotic therapies. By sequencing the genomes of Streptomyces jumonjinensis and Streptomyces katsurahamanus and comparing them to Streptomyces clavuligerus, the study identifies specialized metabolite gene clusters (BGCs) involved in the production of both clavulanic acid and cephamycin C. This research provides valuable insights into the metabolic capabilities of these organisms and highlights the potential for discovering novel metabolites from cryptic BGCs. The findings contribute to the development of improved industrial production strains and the discovery of new antibiotics, addressing the ongoing challenge of antibiotic resistance.