Microbiome-Targeted Therapies in Gastrointestinal Diseases: Clinical Evidence and Emerging Innovations

Lim, ECN; Lim, CED

Microbiome-Targeted Therapies in Gastrointestinal Diseases: Clinical Evidence and Emerging Innovations

Lim, ECN Lim, CED

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Publisher:: MDPI
Publication Type:: Journal Article
Citation:: Acta Microbiologica Hellenica Switzerland, 2025, 70, (3), pp. 36
Issue Date:: 2025-09-01

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Field	Value	Language
dc.contributor.author	Lim, ECN
dc.contributor.author	Lim, CED
dc.date.accessioned	2026-01-13T05:55:18Z
dc.date.available	2026-01-13T05:55:18Z
dc.date.issued	2025-09-01
dc.identifier.citation	Acta Microbiologica Hellenica Switzerland, 2025, 70, (3), pp. 36
dc.identifier.issn	0438-9573
dc.identifier.issn	2813-9054
dc.identifier.uri	http://hdl.handle.net/10453/191747
dc.description.abstract	Microbiome-targeted therapies are redefining gastroenterology by delivering precision interventions that align with the body’s natural microbial ecosystem. This narrative review evaluates evidence for established approaches, probiotics, prebiotics, fecal microbiota transplantation (FMT), and postbiotics, and examines emerging innovations such as engineered probiotics, bacteriophage therapy, and metabolite-based interventions. Cure rates for recurrent Clostridium difficile infection in randomized trials range from 67% to 94%, depending on route and donor protocol, while multi-strain probiotics provide moderate benefits in inflammatory bowel disease. New modalities, including engineered bacteria and defined bacterial consortia, have progressed to Phase 3 trials, with several granted FDA breakthrough therapy designation. Approvals of Rebyota and Vowst mark a pivotal milestone, creating validated regulatory pathways for microbiome therapeutics. Despite progress, challenges remain in protocol standardisation, patient selection, cost-effectiveness, and clinical integration. Over 200 active trials and growing pharmaceutical investment signal a robust pipeline, with applications expanding to oncology, metabolic disorders, and immune modulation. Continued progress depends on validated biomarkers and personalized strategies guided by microbiome profiling. International regulatory harmonization will also be required to ensure safe and equitable adoption. The field is shifting toward working with, rather than against, the body’s microbial ecosystem, offering substantial potential for personalized gastrointestinal disease management.
dc.language	en
dc.publisher	MDPI
dc.relation.ispartof	Acta Microbiologica Hellenica Switzerland
dc.relation.isbasedon	10.3390/amh70030036
dc.rights	info:eu-repo/semantics/openAccess
dc.title	Microbiome-Targeted Therapies in Gastrointestinal Diseases: Clinical Evidence and Emerging Innovations
dc.type	Journal Article
utslib.citation.volume	70
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Science
pubs.organisational-group	University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	open_access	*
dc.rights.license	This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
dc.date.updated	2026-01-13T05:55:17Z
pubs.issue	3
pubs.publication-status	Published
pubs.volume	70
utslib.citation.issue	3

Abstract:

Microbiome-targeted therapies are redefining gastroenterology by delivering precision interventions that align with the body’s natural microbial ecosystem. This narrative review evaluates evidence for established approaches, probiotics, prebiotics, fecal microbiota transplantation (FMT), and postbiotics, and examines emerging innovations such as engineered probiotics, bacteriophage therapy, and metabolite-based interventions. Cure rates for recurrent Clostridium difficile infection in randomized trials range from 67% to 94%, depending on route and donor protocol, while multi-strain probiotics provide moderate benefits in inflammatory bowel disease. New modalities, including engineered bacteria and defined bacterial consortia, have progressed to Phase 3 trials, with several granted FDA breakthrough therapy designation. Approvals of Rebyota and Vowst mark a pivotal milestone, creating validated regulatory pathways for microbiome therapeutics. Despite progress, challenges remain in protocol standardisation, patient selection, cost-effectiveness, and clinical integration. Over 200 active trials and growing pharmaceutical investment signal a robust pipeline, with applications expanding to oncology, metabolic disorders, and immune modulation. Continued progress depends on validated biomarkers and personalized strategies guided by microbiome profiling. International regulatory harmonization will also be required to ensure safe and equitable adoption. The field is shifting toward working with, rather than against, the body’s microbial ecosystem, offering substantial potential for personalized gastrointestinal disease management.

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http://hdl.handle.net/10453/191747