Pharmacomicrobiomics: The Intersection of Gut Microbiome and Pharmacology 

By Jeannie Gorman, MS, CCN  | July 29, 2025

 

As microbiome science advances, the gut’s microbial ecosystem is gaining recognition as a major influence on how the body responds to medications. No longer viewed as a passive bystander, these trillions of microbes can shape drug efficacy, side effects, and disease progression. Ongoing research in this area is helping move us closer to precision medicine, where microbial analysis is integrated with genetic, phenotypic, and lifestyle data to guide personalized treatment. 

Pharmacomicrobiomics, the study of microbiome-drug interactions, shows that microbes alter drug absorption, metabolism, efficacy, and toxicity. Two key mechanisms govern these effects: bioaccumulation, where microbes sequester drugs and reduce their availability; and biotransformation, where microbial enzymes modify drugs into active, inactive, or toxic forms. These bidirectional influences position the gut microbiota as active contributors to pharmacologic outcomes. 

Emerging evidence shows that nearly 25% of non-antibiotic medications alter the gut microbiota, disrupting microbial diversity and ecosystem functions for weeks to months, or longer. Such changes can affect systemic immunity, inflammation, glucose metabolism, and overall homeostasis, particularly with chronic polypharmacy. Several widely used medications illustrate this point: 

  • Proton Pump Inhibitors (PPIs): Increase intestinal pH and alter bile acid profiles, encouraging overgrowth of Clostridium difficile and Enterococcus spp. 
  • Metformin (Glucophage): A first-line diabetes therapy, enriches beneficial short-chain fatty acid–producing taxa (e.g. Akkermansia muciniphila, Bifidobacterium spp.) but can also increase Escherichia coli, contributing to GI side effects. Farup et al. (2018) introduced the idea of “good” dysbiosis, suggesting the microbial shift due to metformin may be associated with a health conferring pattern. 
  • Non-steroidal anti-inflammatories (NSAIDs): Compromise gut barrier integrity, decrease microbial diversity, and elevate pro-inflammatory signals. 
  • Antipsychotics (e.g., olanzapine, risperidone): Increase Firmicutes phylum while suppressing Bifidobacterium spp. and Lactobacillus spp. resulting in changes associated with metabolic dysfunction. 
  • Statins (HMG-CoA reductase inhibitors): Influence microbial enzyme activity and bile acid pathways, altering drug metabolism and trimethylamine N-oxide (TMAO) production. 
  • Selective serotonin reuptake inhibitors (SSRIs): Broad spectrum antimicrobial effects; due to lipophilic nature, SSRIs disrupt membrane activity causing cellular leakage and oxidative stress. 
  • Birth Control Pills (BCPs): one study showed the age of onset of contraceptive use and the gut microbiome profile may determine susceptibility to mood-related side effects.

It’s essential to assess medications not only by their therapeutic goals and systemic effects, but also by their unintended impact on the gut microbiome. Stool testing offers valuable insights into host–microbe interactions, guiding pharmacobiologic decisions with a personalized approach. As microbiome profiling becomes more accessible, integrating these data into electronic health records and prescribing platforms could help identify individuals at greater risk for gut-related drug reactions. Including microbiome considerations in clinical trials may enhance prediction of individual drug responses and uncover novel biomarkers of safety and efficacy. This evolving field of pharmacomicrobiomics is positioned to reshape pharmacology, reinforcing the important foundations for personalized microbiome-aware medicine. 


 

References

  1. Torres-Carrillo, N., Martínez-López, E., Torres-Carrillo, N. M., López-Quintero, A., Moreno-Ortiz, J. M., González-Mercado, A., & Gutiérrez-Hurtado, I. A. (2023). Pharmacomicrobiomics and Drug–Infection Interactions: The Impact of Commensal, Symbiotic and Pathogenic Microorganisms on a Host Response to Drug Therapy. International Journal of Molecular Sciences, 24(23), 17100. https://doi.org/10.3390/ijms242317100
  2. Maier, L. et al. (2018). Extensive impact of non-antibiotic drugs on human gut bacteria. Nature, 555(7698), 623–628. https://doi.org/10.1038/nature25979
  3. Imhann, F. et al. (2016). Proton pump inhibitors affect the gut microbiome. Gut, 65(5), 740–748. https://doi.org/10.1136/gutjnl-2015-310376
  4. Gao, Y., Zhao, T., Lv, N. et al. (2024). Metformin-induced changes of the gut microbiota in patients with type 2 diabetes mellitus: results from a prospective cohort study. Endocrine, 85, 1178–1192. https://doi.org/10.1007/s12020-024-03828-x
  5. Wang, C.-Y., Wen, Q.-F., Wang, Q.-Q., Kuang, X., Dong, C., Deng, Z.-X., & Guo, F.-B. (2022). Discovery of drug candidates for specific human disease based on natural products of gut microbes. Frontiers in Microbiology, 13, 896740. https://doi.org/10.3389/fmicb.2022.896740
  6. Rogers, M.A.M., & Aronoff, D.M. (2016). The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clinical Microbiology and Infection, 22(2), 178.e1–178.e9. https://doi.org/10.1016/j.cmi.2015.10.003
  7. Yang, Y., Long, Y., Kang, D. et al. (2021). Effect of Bifidobacterium on olanzapine-induced body weight and appetite changes in patients with psychosis. Psychopharmacology, 238, 2449–2457. https://doi.org/10.1007/s00213-021-05866-z
  8. Tomizawa, Y., Yoshida, T., Nagai, K., Watanabe, K., & Kaneko, S. Effect of psychotropic medication on gut microbiota in patients with depression and anxiety: A prospective study. International Journal of Neuropsychopharmacology, 24(2), 97–105. https://doi.org/10.1093/ijnp/pyaa099
  9. Liu, D. (Ed.). (2023). Statins - From Lipid-Lowering Benefits to Pleiotropic Effects. IntechOpen. https://doi.org/10.5772/intechopen.1001540
  10. Zimmermann, M. et al. (2019). Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature, 570(7762), 462–467. https://doi.org/10.1038/s41586-019-1291-3
  11. Wu, G.D. et al. (2020). The gut microbiome in cardiometabolic disease: The potential of prebiotic and probiotic therapy. Cell Host & Microbe, 27(3), 339–350. https://doi.org/10.1016/j.chom.2020.02.009
  12. Farup, P. G., Aasbrenn, M., & Valeur, J. (2018). Separating “good” from “bad” faecal dysbiosis – evidence from two cross-sectional studies. BMC Obesity, 5, Article 30.
  13. Noronha, A., Modamio, J., Jarosz, Y., et al. (2019). The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research, 47(D1), D614–D624. https://doi.org/10.1093/nar/gky992
  14. Kheloui S, Smith A, Ismail N. Combined oral contraceptives and mental health: Are adolescence and the gut-brain axis the missing links? Front Neuroendocrinol. 2023 Jan;68:101041. doi: 10.1016/j.yfrne.2022.101041. Epub 2022 Oct 14. PMID: 36244525.
 

Hidden in Plain Sight: Identifying and Addressing Metal Exposures in Daily Life

Presented by Julia Malkowski, ND, DC |  August 6, 2025 at 12 PM Pacific

Do your patients reach for green powders, cosmetics, or other seemingly harmless products each day? These everyday choices may be silently contributing to their toxic metal burden.

Join Dr. Julia Malkowski of Doctor's Data for a dynamic live presentation exploring common and often overlooked sources of metal exposure in modern life. She'll weave in historical context, highlight key detoxification systems and provide practical insights into assessing metal exposures. Attendees will walk away with a clear understanding of identifying everyday metal exposures with potential for extraordinary health impact.


Learning Objectives:

  • Identify common and often-overlooked sources of toxic metal exposure in modern life, including water, cosmetics, and food products
  • Differentiate testing modalities for assessing metal burden: urine, blood, stool, and hair, and their clinical applications
  • In a case series format, interpret metal exposure patterns in the context of symptom presentation
  • Develop foundational clinical strategies to reduce exposure and support detoxification using evidence-based tools.


 
 

Functional Testing Considerations for the Peri-Menopausal Female

Presented by Lylen Ferris, ND | September 3, 2025 at 12 PM Pacific

Peri-menopause, which can begin as early as the mid-30s, is a complex transitional phase marked by symptoms such as hot flashes, insomnia, fatigue, mood changes, and cognitive issues. Effective care depends on accurate patient intake and comprehensive lab assessments, which guide personalized treatment plans. While many patients benefit from lifestyle changes and basic hormone support, others require deeper investigation into physiological imbalances. Optimizing disease prevention adds another layer of complexity, making advanced testing and holistic strategies-including hormone panels, GI and HPA axis assessments, and trauma-informed care-essential for long-term wellness.



Learning Objectives:

  • Articulate stats and symptoms associated with the peri-menopausal transition.
  • Examine pathologies that are more prevalent in menopause and what can be done to decrease risk beginning in the peri-menopausal years.
  • Summarize conventional labs and considerations that should not be overlooked.
  • Discuss various functional labs and considerations for this population, based on current symptoms and disease prevention, that will optimize health during the peri-menopausal years and beyond.

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Serum Steroid Hormone Testing Enough Evidence to Challenge the Status Quo? | 01/04/2024


Feeding the Microbiome for Optimal Health - Got Beans? | 11/28/2023

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Disclaimer: All information given about health conditions, treatment, products, and dosages are for educational purposes only and do not constitute medical advice.

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