Biotherapy Strategies for Modulating the Gut Microbiome to Prevent and Treat Infectious Diseases

Nwankwu Chinaza Marycynthia¹, Adolalom Obinna Tony², Abiodun Michael Bolade³, Ochuele Dominic Agida^4,5, Moses Adondua Abah^4,5 and Micheal Oladosu Abimbola^5,6

¹Department: Biology Education, Faculty of Education, University of Nigeria, Nsukka, Nsukka, Enugu State, Nigeria

²Department of Medicine and Surgery, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria

³Department of Medicine and Surgery, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria

⁴Department of Biochemistry, Faculty of Biosciences, Federal University Wukari, Taraba State, Nigeria

⁵ResearchHub Nexus Institute, Nigeria

⁶Department of Chemical Sciences, Faculty of Science, Anchor University, Ayobo, Lagos State, Nigeria

(✉) Corresponding Author: Nwankwu Chinaza Marycynthia; nwankwujane@gmail.com

Received: Aug 2, 2026/ Revised: Sept 15 2026/Accepted: Sept 17, 2026

Highlights

Gut microbiome modulation supports intestinal homeostasis and pathogen resistance.
Probiotics, prebiotics, synbiotics, and FMT offer promising biotherapeutic approaches.
Live biotherapeutic products and defined microbial consortia provide targeted microbiome modulation.
Microbiome-derived metabolites can strengthen the intestinal barrier and regulate host immunity.
Clinical applications are most established for Clostridioides difficile infection.
Precision microbiome profiling may enable personalized and more predictable therapies.

Abstract

The gut microbiome plays a central role in maintaining intestinal homeostasis, regulating host immunity, and providing colonization resistance against invading pathogens. Disruption of this microbial ecosystem can facilitate pathogen colonization, antimicrobial resistance, impaired barrier function, and increased susceptibility to infectious diseases. Consequently, therapeutic strategies that restore or selectively modify the gut microbiome have emerged as promising complements to conventional antimicrobial approaches. This narrative review examines current biotherapy strategies for modulating the gut microbiome to prevent and treat infectious diseases, with emphasis on their mechanisms, therapeutic applications, clinical evidence, and translational challenges. Major approaches include probiotics, prebiotics and synbiotics, fecal microbiota transplantation, live biotherapeutic products, defined microbial consortia, and postbiotics or microbiome-derived metabolites. These interventions may enhance colonization resistance through competitive exclusion of pathogens, production of antimicrobial metabolites, restoration of microbial diversity, reinforcement of intestinal barrier integrity, and modulation of host immune responses. Their applications are particularly established in Clostridioides difficile infection, while emerging evidence supports potential benefits against multidrug-resistant bacterial colonization, enteric infections, and selected viral, fungal, and parasitic diseases. Despite promising therapeutic outcomes, variability in microbiome composition, treatment response, safety, formulation, manufacturing, and regulatory requirements continues to limit widespread clinical implementation. Advances in precision microbiome profiling, engineered microbial therapeutics, and personalized interventions may improve efficacy and therapeutic predictability. Overall, microbiome-targeted biotherapies represent an evolving strategy for infection prevention and treatment, with substantial potential to complement antimicrobial therapy and contribute to more sustainable approaches to infectious-disease management.

Keywords: Gut microbiome, biotherapy, probiotics, fecal microbiota transplantation, infectious diseases and microbiome modulation

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How to cite this article

Marycythia, N. C., Tony, A. O., Bolade, A. M., Agida, O. D., Abah, M. A., & Abimbola, M. O. (2026). Biotherapy strategies for modulating the gut microbiome to prevent and treat infectious diseases. Microbial Science Archives, 6(3), 76–91. https://doi.org/10.47578/MSA.2026.6302

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