Over recent years, studies on microbiota research and synthetic biology have explored novel approaches microbial manipulation for therapeutic purposes. However, fragmented information is available on this aspect with key insights scattered across various disciplines such as molecular biology, genetics, bioengineering, and medicine. This review aims to the transformative potential of synthetic biology in advancing microbiome research and therapies, with significant implications for healthcare, agriculture, and environmental sustainability. By merging computer science, engineering, and biology, synthetic biology allows for precise design and modification of biological systems via cutting edge technologies like CRISPR/Cas9 gene editing, metabolic engineering, and synthetic oligonucleotide synthesis, thus paving the way for targeted treatments such as personalized probiotics and engineered microorganisms. The review will also highlight the vital role of gut microbiota in disorders caused by its dysbiosis and suggesting microbiota-based therapies and innovations such as biosensors for real-time gut health monitoring, non-invasive diagnostic tools, and automated bio foundries for better outcomes. Moreover, challenges including genetic stability, environmental safety, and robust regulatory frameworks will be discussed to understand the importance of ongoing research to ensure safe and effective microbiome interventions.

The growing threat of antimicrobial resistance (AMR) has underlined the need for a sustained supply of novel antimicrobial agents. Endophyte microorganism that reside within plant tissues as symbionts have been the source of potential antimicrobial substances. However, many novel and potent antimicrobials are yet to be discovered from these endophytes. The present study investigates the potential of endophytic fungi as a source of novel bioactive chemicals with antibacterial capabilities. These fungi synthesize secondary metabolites such as polyketides and peptides via polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) pathways. Notable substances, like prenylated indole alkaloids and fumaric acid, have shown promising antibacterial and antifungal properties against multidrug-resistant infectious agents. This review also emphasizes the symbiotic link between endophytes and their host plants, which is critical for secondary metabolite production. The study focuses on the significance of isolation methods for endophytes and proposes their use in for sustainable agriculture, bioremediation, and medicine. Future research combining endophytic biodiversity analysis with next-generation sequencing (NGS) and nanotechnology could provide novel techniques for combating AMR and contributing to sustainability across multiple industries.

Endophytic microorganisms, including bacterial and fungal species, establish symbiotic relationships within plant tissues, contributing to plant growth, nutrient acquisition, and stress resilience. In this review, multiple roles of endophyte-plant interactions have been discussed. Endophytes aid in nitrogen fixation for plants, enhance nutrient solubilization and uptake, control the attack of phytopathogens on plants, and help the plants to tolerate environmental stresses. The molecular mechanisms of these interactions, uncovered by the advancements in genomics, metabolomics, and microbiome engineering, reveal novel bioactive compounds and metabolic pathways that can improve crop resilience. The integration of multi-omics technologies and functional validation holds great potential for sustainable agriculture, offering new strategies for formulating effective biostimulants, bioinoculants, and biocontrol agents to improve crop health, agricultural productivity, and nutritional quality.

The human body functions as a complex ecosystem, hosting trillions of microbes that collectively form the microbiome, pivotal in immune system regulation. The host-microbe immunological axis maintains homeostasis and influences key physiological processes, including metabolism, epithelial integrity, and neural function. Recent advancements in microbiome-based therapeutics, including probiotics, prebiotics and fecal microbiota transplantation, offer promising strategies for immune modulation. Microbial therapies leveraging microbial metabolites and engineered bacterial consortia are emerging as novel therapeutic strategies. However, significant challenges remain, including individual microbiome variability, the complexity of host-microbe interactions, and the need for precise mechanistic insights. This review comprehensively examines the host microbiota immunological interactions, elucidating its mechanisms, therapeutic potential, and the future directions of microbiome-based immunomodulation in human health. It will also critically evaluate challenges, limitations, and future directions for microbiome-based precision medicine.

Endophytic fungi are an important component that colonizes in healthy tissues of living plants and can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. Their huge diversity and particular habituation, they can provide a good area for research in the field of making new medicines and novel drug-like molecules. Because of the impact of endophytes on host plant by enhancing their growth or increasing their fitness, also making them tolerant to abiotic and biotic stresses and holding the secondary metabolites, endophytes are gaining attention as a subject for research. This review aims to comprehend the contribution and uses of endophytes and relationships between endophytic fungi and their host medicinal plants.