Microbiome Engineering: Exploring Probiotic and Synthetic Biology Approaches for Health and Industry

Authors

  • Abdol Ghaffar Ebadi Researcher and Faculty member, Jouybar branch, Islamic Azad University, Jouybar, Iran
  • Yaira Rakhmetova Department of Biotechnology, Faculty of Biology and Biotechnology, Al Farabi Kazakh National University, Almaty, Kazakhstan.
  • Hamdia Yousif Issa Department of Biology, College of Science, University of Zakho, Duhok, Iraq.
  • Muhammad Yasir Naeem Department of Agronomy, Animals, Food, Natural Resources and the Environment (DAFNAE), University of Padua, Italy.
  • Zeliha Selamoglu

DOI:

https://doi.org/10.1071/ejmbs.v5i2.38

Keywords:

Microbiome engineering, Probiotics, Synthetic biology, CRISPR, Industrial biotechnology

Abstract

Microbiome engineering is a ground-breaking field with profound implications for human health, agriculture, and industrial biotechnology. By leveraging probiotics and synthetic biology, scientists are able to manage microbial communities to achieve optimal disease prevention, industrial process optimization, and environmental sustainability. In spite of excellent advances, challenges in the fields of biosafety, functionality, and regulatory strategies remain. This review highlights present developments in microbiome engineering, namely genetically engineered probiotics and synthetic biology-driven microbial manipulation. The purpose is to highlight their therapeutic, industrial, and direction for research work. Engineered probiotics are being engineered for the treatment of gastrointestinal disorders, metabolic diseases, and immune system modulation, with implications to animal health and sustainable food production. Synthetic biology tools, including CRISPR-based genome editing and synthetic microbial consortia, have enabled precise genetic manipulations, enhancing the functional abilities of microbial communities. These advancements are revolutionizing biomanufacturing, environmental remediation, and biofuel production. Nevertheless, with such developments, there are still huge challenges, including scepticism about ecological risks, ethics, and the formulation of robust regulatory policies to guarantee effective and safe uses. Microbiome engineering holds immense potential to transform healthcare, industry, and environmental science. The combination of AI-powered microbiome analytics, personalized medicine approaches, and advanced biotechnology tools will further accelerate the momentum of this field. However, overcoming biosafety challenges and establishing effective regulatory frameworks will be crucial to scaling up laboratory breakthroughs to real-world applications. The future task must be focused on the creation of rigorous safety paradigms, microbial stability maximization, and personalized microbiome targeting for maximum efficacy. A multidisciplinary approach is crucial to unlocking the full potential of microbiome engineering for global health and industrial sustainability.

References

Azad, M. A. K., Sarker, M., Li, T., Yin, J. (2018). Probiotic species in the modulation of gut microbiota: An overview. Biomedicine and Pharmacotherapy, 111, 153–167.

Babaee, M., Ebadi, A. G. (2016). Study of intellectual property laws in Iranian pharmacology and drug industries. Journal of Pure and Applied Microbiology, 10(1), 333–337.

Chen, H., Alcaine, S. D. (2021). Engineering probiotics as therapeutics for the gut microbiota. Trends in Microbiology, 29(4), 329–337.

Chen, W., Zhang, J., Wang, Y., et al. (2020). Genetically engineered probiotics for treatment of metabolic disorders. Bioscience, Biotechnology, and Biochemistry, 84(5), 939–948.

Gupta, R., Singh, V., Kumar, A., et al. (2020). Engineered probiotics for targeted therapy in gastrointestinal diseases. Journal of Microbiome Research, 8(1), 55–67.

Heinemann, J. A., Panke, S. (2006). Synthetic biology—putting engineering back into biology. BioEssays, 28(8), 741–742.

Kim, S., Lee, S., Han, J., et al. (2019). Probiotic engineering for gut health and cancer prevention. Cancer Prevention Research, 12(2), 131–139.

LeBlanc, J. G., Chain, L., Van Hieu, T., et al. (2021). Engineered probiotics for human health and disease prevention. Journal of Applied Microbiology, 131(4), 1167–1181.

Markowiak, P., Śliżewska, K. (2018). The role of probiotics, prebiotics and synbiotics in animal nutrition. Gut Pathogens, 10, 21.

O'Toole, P. W., Marchesi, J. R., Hill, C. (2017). Next-generation probiotics: The spectrum from probiotics to live biotherapeutics. Nature Reviews Microbiology, 15(11), 827–838.

Park, S. J., Kim, H. J., Yim, H. S., et al. (2019). Lactobacillus-based probiotics in the treatment of gastrointestinal disorders. International Journal of Food Sciences and Nutrition, 70(3), 335–343.

Patel, N., Zhao, X., Wong, P., et al. (2019). Microbial therapeutics in cancer: A synthetic biology perspective. Bioengineering and Translational Medicine, 4(2), 221–237.

Patel, R., Kim, D., Zhang, W. (2021). Regulatory challenges in engineered probiotic applications. Microbial Biotechnology Reports, 9(2), 112–128.

Sağlıker, H. A., Darici, C. (2005). Nutrient dynamics of Olea europaea L. growing on soils derived from two different parent materials in the eastern Mediterranean region (Turkey). Turkish Journal of Botany, 29(4), 255-262.

Sağliker, H. A., Darici, C. (2007). Nutrient contents of Pinus brutia Ten.(Pinaceae) and Pistacia terebinthus L.(Anacardiaceae) growing on marl and conglomerate substrata in the Eastern Mediterranean. Turkish Journal of Botany, 31(1), 11-17.

Smith, A., Jones, B., Taylor, C. (2020). Ethical and safety concerns in microbiome engineering. Journal of Synthetic Biology, 18(4), 233–245.

Smith, J. J., Parker, D., Kim, H., et al. (2022). Synthetic biology and metabolic engineering for sustainable biofuel production. Biotechnology Advances, 40, 107594.

Torres, M. D., Wang, Y., Chen, J., et al. (2021). Advances in CRISPR-based synthetic biology for microbiome engineering. Trends in Biotechnology, 39(3), 345–360.

Van Pijkeren, J. P., Britton, R. A. (2019). Engineering probiotics for therapeutic applications in humans and animals. Current Opinion in Biotechnology, 61, 160–167.

Wilson, G., Chen, Y., Alvarez, L. (2019). Stability and adaptation issues in synthetic microbiome engineering. Advances in Microbial Research, 14(1), 67–82.

Yaşar, S., Sağlıker, H. A., Darıcı, C. (2009). Doğu Akdeniz Bölgesinde (Adana) Yetişen Dört Odunsu Bitkinin Bazı Toprak Ve Yaprak Özellikleri İle Sabit Yağ Oranları. TÜBAV Bilim Dergisi, 2(2), 157-161.

Zhang, F., Zeng, Z., Han, M., Wang, J. (2020). Synthetic microbial communities: Promising applications in industrial and environmental biotechnology. Trends in Biotechnology, 38(8), 795–814.

Zhang, W., Zhou, L., Zhang, L., et al. (2021). Microbiome engineering for waste biodegradation and environmental sustainability. Applied Microbiology and Biotechnology, 105(6), 2447–2460.

Zhao, Y., Liu, X., Zhang, Y., et al. (2022). Probiotic-based antimicrobial strategies in livestock: Enhancements and challenges. Journal of Animal Science and Biotechnology, 13, 25–39.

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Published

2026-01-07

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Section

Review Article

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