Microbiome-Driven Therapeutics: From Gut Health to Precision Medicine
<p>Gut microbiota and disease connections (Created in <a href="https://BioRender.com" target="_blank">https://BioRender.com</a>).</p> "> Figure 2
<p>Gut microbiota restoration through fecal microbiota transplantation (FMT) in patients with <span class="html-italic">Clostridioides difficile</span> infection (Created in <a href="https://BioRender.com" target="_blank">https://BioRender.com</a>).</p> ">
Abstract
:1. Introduction
2. Microbiome and Disease Connections
2.1. Gastrointestinal Disorders
2.1.1. Irritable Bowel Syndrome (IBS)
2.1.2. Inflammatory Bowel Disease (IBD)
2.2. Metabolic Disorders
2.3. Mental Health
2.4. Immune-Mediated Diseases
2.5. Cardiovascular Diseases
2.6. Cancer
3. Current Microbiome-Driven Therapies
3.1. Fecal Microbiome Transplantation
3.2. Probiotics, Prebiotics, and Synbiotics
3.3. Microbial Metabolite-Based Therapies
3.4. Emerging Microbiome Editing Therapeutics
4. Microbiome-Based Drug Development
4.1. Microbiome as a Drug Target and Modulator
4.2. Engineered Microbiomes
5. Challenges and Limitations
5.1. Individual Microbiome Variation
5.2. Mechanistic Gaps in Microbiome Research
5.3. Regulatory and Ethical Considerations
6. Future Directions
7. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Disorder | Associated Bacterial Strains | Alterations | Clinical Implications | References |
---|---|---|---|---|
Irritable Bowel Syndrome (IBS) | Bifidobacterium spp., Lactobacillus genera (e.g., Lacticaseibacillus, Limosilactobacillus), Methanobrevibacter smithii, Escherichia coli | Decreased Bifidobacterium and members of the reclassified Lactobacillus genera; increased Methanobrevibacter and E. coli. | Increased gas production, altered motility, and inflammation. | [83] |
Inflammatory Bowel Disease (IBD) | Faecalibacterium prausnitzii, Roseburia spp., Eubacterium rectale, Akkermansia muciniphila, Escherichia coli | Depletion of anti-inflammatory species (F. prausnitzii, Roseburia); overgrowth of pathogenic E. coli. | Loss of gut barrier integrity, chronic inflammation. | [84] |
Clostridioides difficile Infection | Clostridioides difficile, reduced Bacteroidetes and Firmicutes diversity | Overgrowth due to disrupted microbiota (e.g., post-antibiotics). | Severe diarrhea and colitis. | [84] |
Helicobacter pylori Infection | Helicobacter pylori | Colonizes the stomach lining, reduces protective microbial diversity. | Gastritis, ulcers, increased gastric cancer risk. | [85] |
Colorectal Cancer (CRC) | Fusobacterium nucleatum, Bacteroides fragilis, Escherichia coli | Enrichment of F. nucleatum and B. fragilis. | Promotes tumorigenesis via inflammation and DNA damage. | [86] |
Diverticulitis | Bacteroides fragilis, Escherichia coli, Enterococcus spp. | Altered microbial diversity, increased inflammation. | Pain, fever, abscess formation. | [87] |
Metabolic Disorders | Akkermansia muciniphila, Bacteroidetes spp., Firmicutes spp. | Reduced Akkermansia; altered Firmicutes/Bacteroidetes ratio. | Obesity, insulin resistance, increased inflammation. | [88] |
Celiac Disease | Bifidobacterium spp., members of the reclassified Lactobacillus genera (e.g., Lacticaseibacillus, Limosilactobacillus), increased Enterobacteriaceae. | Reduced beneficial bacteria; increased pathogenic strains. | Triggers inflammatory responses in the gut. | [89,90] |
Autism Spectrum Disorders (ASD) | Bacteroides spp., Clostridium spp., Prevotella spp. | Decreased Prevotella; increased Clostridium. | Altered gut–brain axis signaling, behavioral symptoms. | [91,92] |
Cardiovascular Diseases | Members of the reclassified Lactobacillus genera (e.g., Lacticaseibacillus, Limosilactobacillus), Bifidobacterium spp., Firmicutes | Increased trimethylamine-N-oxide (TMAO)-producing species. | Links to atherosclerosis and hypertension. | [93,94] |
Aspect | Microbial Metabolite Based Therapies | Probiotic Treatment |
---|---|---|
Definition | Utilizes metabolites produced by gut microbiota (e.g., SCFAs) to exert therapeutic effects [126]. | Involves the administration of live microorganisms that confer health benefits when consumed in adequate amounts [127]. |
Mechanism | Directly modulates host signaling via metabolites, influencing immune responses and gut health [126,127]. | Restores or maintains a healthy gut microbiota, inhibiting pathogenic bacteria and enhancing mucosal barrier function [127]. |
Efficacy in Disease Treatment | Effective for conditions like IBD, metabolic disorders, and neurological conditions through targeted action [126]. | Variable efficacy; beneficial for gastrointestinal disorders like diarrhea and IBD, but effectiveness can be strain-specific [127]. |
Advantages | Provides targeted therapy; may overcome limitations of probiotics related to colonization and individual microbiomes [126]. | Generally safe; can restore gut flora balance effectively in many individuals [127]. |
Limitation | Less research on long-term effects; potential need for personalized approaches based on specific metabolites. | Variable efficacy based on strain and individual microbiome composition; may pose risks for immunocompromised individuals. |
Safety Profile | Generally low toxicity; fewer risks associated with live organisms. | Safe for most; caution advised in immunocompromised individuals or those with severe underlying conditions. |
Administration | Can be administered as stable compounds (e.g., supplements). | Requires viable organisms; may have storage and viability issues. |
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Yaqub, M.O.; Jain, A.; Joseph, C.E.; Edison, L.K. Microbiome-Driven Therapeutics: From Gut Health to Precision Medicine. Gastrointest. Disord. 2025, 7, 7. https://doi.org/10.3390/gidisord7010007
Yaqub MO, Jain A, Joseph CE, Edison LK. Microbiome-Driven Therapeutics: From Gut Health to Precision Medicine. Gastrointestinal Disorders. 2025; 7(1):7. https://doi.org/10.3390/gidisord7010007
Chicago/Turabian StyleYaqub, Muneer Oladipupo, Aashika Jain, Chinedu Eucharia Joseph, and Lekshmi K. Edison. 2025. "Microbiome-Driven Therapeutics: From Gut Health to Precision Medicine" Gastrointestinal Disorders 7, no. 1: 7. https://doi.org/10.3390/gidisord7010007
APA StyleYaqub, M. O., Jain, A., Joseph, C. E., & Edison, L. K. (2025). Microbiome-Driven Therapeutics: From Gut Health to Precision Medicine. Gastrointestinal Disorders, 7(1), 7. https://doi.org/10.3390/gidisord7010007