Microbial Bioactives | Online ISSN 2209-2161
Volume 8 Number 1 2025
REVIEWS (Open Access)
Beneficial Microorganisms Allies Role in Human Health, Agriculture, and Environmental Restoration - A Systematic Review
Chandrarohini Saravanan 1, Nor Hazliana Harun 2, Siti Salmah Noordin 2
Microbial Bioactives 8 (1) 1-8 https://doi.org/10.25163/microbbioacts.8110458
Submitted: 21 May 2025 Revised: 15 July 2025 Accepted: 23 July 2025 Published: 24 July 2025
Abstract
Microorganisms are often introduced to us as threats, yet they quietly sustain the foundations of life in ways far more profound than most realize. This systematic review brings together current scientific evidence to explore how beneficial microbes influence human well-being, support agricultural resilience, and help restore ecological balance. Using a structured search across microbiology, biotechnology, and environmental science literature, we synthesized peer-reviewed studies that illuminate the diverse contributions of these microscopic partners. Across the human body, gut microbiota emerge as active collaborators—helping us digest nutrients, regulate immune responses, and even modulate neurochemical pathways linked to mood and cognition. In agriculture, plant–microbe relationships reveal a similar story of cooperation: soil microbes enhance nutrient uptake, strengthen plant defenses, and reduce reliance on chemical inputs, offering a pathway toward more sustainable food production. Environmental studies further highlight how microbes can break down pollutants, neutralize toxins, and revive damaged ecosystems through bioremediation and wastewater treatment processes. The evidence demonstrates that innovations such as probiotics, biofertilizers, and microbial bio-technologies are reshaping how we approach health, farming, and environmental protection. Ultimately, this review emphasizes the importance of shifting public perception—from viewing microbes solely as threats to recognizing them as essential allies. Appreciating these unseen partners allows us to harness their potential in building a healthier, more sustainable, and ecologically balanced future.
Keywords: Beneficial microorganisms; human health; gut microbiota; probiotics; plant–microbe interactions; sustainable agriculture; bioremediation; environmental restoration; microbial biotechnology
References
Austin, H. P., Allen, M. D., Donohoe, B. S., Rorrer, N. A., Kearns, F. L., Silveira, R. L., ... & Beckham, G. T. (2018). Characterization and engineering of a plastic-degrading aromatic polyesterase. Proceedings of the National Academy of Sciences, 115(19), E4350–E4357. https://doi.org/10.1073/pnas.1718804115
Barkay, T., Miller, S. M., & Summers, A. O. (2003). Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiology Reviews, 27(2–3), 355–384. https://doi.org/10.1016/S0168-6445(03)00046-9
Cryan, J. F., & Dinan, T. G. (2012). Mind-altering microorganisms: The impact of the gut microbiota on brain and behavior. Nature Reviews Neuroscience, 13(10), 701–712. https://doi.org/10.1038/nrn3346
Das, N., & Chandran, P. (2011). Microbial degradation of petroleum hydrocarbon contaminants: An overview. Biotechnology Research International, 2011, 1–13. https://doi.org/10.4061/2011/941810
Endersen, L., O'Mahony, J., Hill, C., Ross, R. P., McAuliffe, O., & Coffey, A. (2014). Phage therapy in the food industry. Annual Review of Food Science and Technology, 5, 327–349. https://doi.org/10.1146/annurev-food-030713-092415
Fleet, G. H. (2007). Yeasts in foods and beverages: Impact on product quality and safety. Current Opinion in Biotechnology, 18(2), 170–175. https://doi.org/10.1016/j.copbio.2007.01.010
Frias, J., Doblado, R., Antezana, J. R., & Vidal-Valverde, C. (2017). Fermented pulses: Nutritional value and potential for utilization in food production. Critical Reviews in Food Science and Nutrition, 57(2), 325–338.
Gadd, G. M. (2010). Metals, minerals and microbes: Geomicrobiology and bioremediation. Microbiology, 156(3), 609–643. https://doi.org/10.1099/mic.0.037143-0
Gareau, M. G., Sherman, P. M., & Walker, W. A. (2010). Probiotics and the gut microbiota in intestinal health and disease. Nature Reviews Gastroenterology & Hepatology, 7(9), 503–514. https://doi.org/10.1038/nrgastro.2010.117
Gentry, T. J., Rensing, C., & Pepper, I. L. (2004). New approaches for bioaugmentation as a remediation technology. Critical Reviews in Environmental Science and Technology, 34(5), 447–494. https://doi.org/10.1080/10643380490452362
Hazen, T. C., Dubinsky, E. A., DeSantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh, N., ... & Mason, O. U. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science, 330(6001), 204–208. https://doi.org/10.1126/science.1195979
Hill, C., Guarner, F., Reid, G., Gibson, G. R., Merenstein, D. J., Pot, B., ... & Sanders, M. E. (2014). The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology, 11(8), 506–514. https://doi.org/10.1038/nrgastro.2014.66
Jespersen, L. (2003). Occurrence and taxonomic characteristics of strains of Saccharomyces cerevisiae predominant in African indigenous fermented foods and beverages. FEMS Yeast Research, 3(2), 191–200. https://doi.org/10.1016/S1567-1356(02)00185-X
Kim, D. J., Kim, S. H., & Lee, D. I. (2006). Nitrification of high-strength ammonia wastewater and nitrite accumulation characteristics. Environmental Technology, 27(3), 277–284.
Lovley, D. R., & Coates, J. D. (1997). Bioremediation of metal contamination. Current Opinion in Biotechnology, 8(3), 285–289. https://doi.org/10.1016/S0958-1669(97)80005-5
Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., & Stahl, D. A. (2018). Brock biology of microorganisms (15th ed.). Pearson.
Marco, M. L., Heeney, D., Binda, S., Cifelli, C. J., Cotter, P. D., Foligné, B., ... & Hutkins, R. (2017). Health benefits of fermented foods: Microbiota and beyond. Current Opinion in Biotechnology, 44, 94–102. https://doi.org/10.1016/j.copbio.2016.11.010
Ouwehand, A. C., Salminen, S., & Isolauri, E. (2002). Probiotics: An overview of beneficial effects. Antonie van Leeuwenhoek, 82(1), 279–289. https://doi.org/10.1023/A:1020620607611
Prince, R. C., Gramain, A., & Atlas, R. M. (2010). Bioremediation of marine oil spills. In Oil Spill Science and Technology (pp. 395–412). https://doi.org/10.1007/978-3-540-77587-4_194
Rittmann, B. E., & McCarty, P. L. (2001). Environmental biotechnology: Principles and applications. McGraw-Hill.
Scallan, E., Hoekstra, R. M., Angulo, F. J., Tauxe, R. V., Widdowson, M. A., Roy, S. L., ... & Griffin, P. M. (2011). Foodborne illness acquired in the United States – Major pathogens. Emerging Infectious Diseases, 17(1), 7–15. https://doi.org/10.3201/eid1701.P11101
Settanni, L., & Corsetti, A. (2008). Application of bacteriocins in vegetable food biopreservation. International Journal of Food Microbiology, 121(2), 123–138. https://doi.org/10.1016/j.ijfoodmicro.2007.09.001
Steensels, J., & Verstrepen, K. J. (2014). Taming wild yeast: Potential of conventional and nonconventional yeasts in industrial fermentations. Annual Review of Microbiology, 68, 61–80. https://doi.org/10.1146/annurev-micro-091213-113025
Tamang, J. P., Watanabe, K., & Holzapfel, W. H. (2016). Review: Diversity of microorganisms in global fermented foods and beverages. Frontiers in Microbiology, 7, 377. https://doi.org/10.3389/fmicb.2016.00377
Wilkes, R. A., & Aristilde, L. (2017). Degradation and metabolism of synthetic plastics and associated products by Pseudomonas sp.: Capabilities and challenges. Journal of Applied Microbiology, 123(3), 582–593. https://doi.org/10.1111/jam.13472
Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., ... & Oda, K. (2016). A bacterium that degrades and assimilates poly(ethylene terephthalate). Science, 351(6278), 1196–1199. https://doi.org/10.1126/science.aad6359