Aug 2026· World Journal of Microbiology & Biotechnology· Vol 42· 0 citations· 139 references
Medicine
TL;DR
The integrated bioinformatics pipeline enabled the reconstruction of 37 medium-to-high-quality metagenome-assembled genomes (MAGs), and recovered 147 BGCs mostly from Pseudomonadota, Actinomycetota, and Acidobacteriota phyla, highlighting the Siwa Oasis as a promising reservoir of unexplored biosynthetic potential and a valuable resource for natural product discovery to address global health challenges.
Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.
William B. Medeiros, Kelly Hidalgo-Martinez, D. D. P. S. Penna et al.· World Journal of Microbiolog...· 0 citations
Antimicrobial resistance (AMR) has been identified as one of the 21st century’s severest global public health crises. AMR led to an estimated 4.95 million deaths in 2019 and will claim 10 million lives a year by 2050 in the absence of targeted interventions. During the same period, the number of novel antibiotics discovered has decreased drastically as many researchers are rediscovering known antibiotics, non-model microorganisms are poorly understood or difficult to culture and antibiotic research and development investment has declined drastically. However, high-throughput whole genome sequencing and the subsequent application of bioinformatics in bacterial and fungal genomes have shown that a numerous of cryptic or silent biosynthetic gene clusters (BGCs) remain latent at ambient laboratory conditions since their genes are transcriptionally inactive. Cryptic BGCs represent a vast source of unique secondary metabolites, many of which may yield novel antibacterial, antifungal, anti-cancer and other potentially valuable natural products. This review discusses the biological relevance of cryptic BGCs, the major limiting factors that restricts their activation and novel strategies that have been employed to activate them and exploit their potential to produce novel natural products. The review focuses on biological approaches including CRISPR-Cas mediation for the activation of cryptic BGCs, promoter engineering, pathway refactoring, and heterologous expression; biochemical strategies such as Osman, OsMAC, Precursor Feeding, Chemical Elicitation, Epigenetic Regulation and Co-cultivation and technology-based strategies such as Genome mining, Microfluidic Cultivation systems, High-Throughput Screening, Metabolomics, Molecular Networking and Artificial Intelligence and Machine Learning based prediction of BGCs and their metabolites. The use of multi-omics technologies combined with synthetic biology to achieve better discovery, characterization and large-scale production of novel natural products is also discussed herein. Finally, we will talk about the ecological significance and evolutionary advantage of cryptic BGCs’ role in interactions between microorganisms, such as competition, communication, symbiosis and environmental adaptability, so as to provide a useful background for accelerating next-generation antibiotics.
Veilumuthu Pattapulavar, Sathiyabama Ramanujam, Avanthi Yellampalli et al.· Frontiers in Bioinformatics· 0 citations
Fermentation of foods and beverages represents one of humanity’s oldest biotechnologies, generating compounds with demonstrated benefits for gut microbiota modulation, immune regulation, and metabolic health. The global rise of non-communicable chronic diseases, including obesity, type 2 diabetes, and chronic inflammation, has intensified the search for microbiome-based interventions, positioning fermented beverages as promising sources of next-generation probiotics and functional microbial consortia. Beverages such as kefir and kombucha, together with traditional Mexican fermented beverages including pozol and pulque, have been subjected to high-depth shotgun metagenomic studies generating high quality genomic resources. Systematic genomic mining efforts aimed at the functional characterization and biotechnological exploitation of these microbial communities, however, remain scarce. Here, we used a bioprospecting pipeline applied to milk-based kefir, kombucha, pozol, and pulque, integrating targeted genomic mining of genes associated with the biosynthesis of B-group vitamins, short-chain fatty acids, natural products, and CAZymes with potential to enhance starch and dietary fiber utilization upon intestinal colonization. Through genome-scale metabolic modeling of metagenome-assembled genomes, we identified microbial candidates predicted as central producers of secondary metabolites involved in pathogen control. We then used these results for the in silico synthetic assembly of a six-member synthetic microbial community predicted to exhibit stable cooperative growth and high metabolic functionality. Cross-feeding analysis revealed iron as one of the most widely shared elements among community members, with Priestia flexa from pozol, serving as a major donor of compounds involved in iron transport and as a stabilizing element within the synthetic community. This approach allows us to design a theoretical highly functional probiotic community, opening new avenues for the systematic exploitation of microbial diversity for biomedical purposes.
Alexandra Trejo-Gaytán, Axel A. Rojero-Hernández, José T. Otero-Pappatheodorou et al.· bioRxiv· 0 citations
Applications across healthcare, environmental science, agriculture, biotechnology, and industry are reviewed with particular emphasis on clinical metagenomic next-generation sequencing (mNGS) for infectious disease diagnostics, antimicrobial resistance (AMR) surveillance, gut microbiome research, and precision medicine.
Ahmed Alsharksi· Razi Medical Journal· 0 citations
Understanding of the metabolic capabilities and genomic landscape of the P. fluorescens species is enhanced, providing a foundation for natural product discovery using bioinformatic approaches.
Sajid Iqbal, Farida Begum· Discover Genetics and Evolut...· 0 citations
