Ogbaji Henderson Onah1, Ochuele Dominic Agida2,3, Moses Adondua Abah2,3, Micheal Abimbola Oladosu2,4, Ibeojo Blessing Ugoojo5, Tryphosa Tibile Sojay6, Adaora Chiamaka Ekekwe7 and Olorunda Monday8

 1Department of Genetics and Biotechnology, Faculty of Biological Sciences, University of Calabar, Calabar, Cross River State, Nigeria

2Department of Biochemistry, Faculty of Biosciences, Federal University Wukari, Taraba State, Nigeria

3ResearchHub Nexus Institute, Nigeria

4Department of Biochemistry, Faculty of Basic Medical Sciences, University of Lagos, Lagos State, Nigeria

5Department of Biotechnology, I.M. Sechenov First Moscow State Medical University (Sechenov University)

6Department of Food, Nutrition and Home Sciences, Faculty of Agriculture, Prince Abubakar Audu University, Anyigba, Kogi State, Nigeria

7Department of Community Health and Primary Care, Faculty of Clinical Sciences, University of Lagos, Lagos State, Nigeria.

8Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria

 Received: Oct 28, 2025/ Revised: Nov 29, 2025/Accepted: DEc 2, 2025

() Corresponding Author: : Moses Adondua Abah; m.abah@fuwukari.edu.ng

Abstract

Microbiome research has rapidly transitioned from descriptive ecology to a powerful driver of biotechnological innovation, reshaping approaches to human health, agriculture, industry, and environmental sustainability. Advances in high-throughput sequencing, multi-omics integration, and computational modeling have unraveled the functional complexity of microbial communities, enabling precise characterization of their roles in metabolism, immunity, disease, and ecosystem stability. These insights have catalyzed the emergence of microbiome-based technologies, including next-generation probiotics, engineered microbial consortia, postbiotic therapeutics, and microbiome-guided diagnostics that offer unprecedented opportunities for personalized medicine. Targeted manipulation of plant, animal, and soil microbiomes is increasing crop yield, boosting nutrient efficiency, strengthening disease resistance, and assisting bioremediation techniques that tackle pollution and climate-related issues in agriculture and environmental biotechnology.  Enzymes, metabolites, and artificial microbial communities created from microbiomes are also being used by industrial sectors to produce sustainable biomanufacturing, bioenergy, and circular bioeconomy solutions. Despite these promising developments, there are still significant challenges, including as differences in the microbiome’s composition, a lack of mechanistic understanding, issues with data harmonization, and evolving regulatory and biosafety concerns.  Emerging technologies like organoid co-culture systems, CRISPR-based microbiome editing, and AI-driven ecosystem modeling could eliminate many of these barriers and expedite the transition from discovery to application.  This review outlines current advancements in the main fields of microbiome biotechnology, points out persistent gaps, and recommends important directions for future research.  By combining scientific discoveries with pragmatic perspectives, it provides a forward-looking approach to harnessing microbiome discoveries to solve global health, environmental, and industrial concerns.

Keywords: Microbiome biotechnology, Multi-omics integration, Microbial engineering, Bioremediation, Precision medicine and Synthetic microbial consortia

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How to cite this article

Onah, O. H., Agida, O. D., Abah, M. A., Abimbola, M., Ugoojo, I. B., Sojaye, T. T., Ekekwe, A. C., & Monday, O. (2025). Biotechnological applications of microbiome research: A review of current advances and future prospects. Science Archives, 6(4), 24–40. https://doi.org/10.47587/SA.2025.6401

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