Kirk E. Hevener, PharmD, PhD

It is well known that orally administered drugs can affect the gut microbiome, resulting in dysbiosis-mediated adverse effects.

 A common example is antibiotic-associated diarrhea. Less understood is the effect that gut bacteria can have on therapeutic drugs, primarily their systemic availability and subsequent drug levels. Although microbial biotransformation of drugs has been previously documented in a small number of cases, such as the conversion of sulfasalazine by gut bacteria into its active moieties, results from a recent study showed that gut organisms can alter drug availability by biotransformation on a significantly broader scale than previously expected.

These findings and those of other related studies have played a significant role in the emergence of a new field of personalized medicine known as pharmacomicrobiomics, which has a strong potential to complement pharmacogenomics, metabolomics, and other personalized medicine disciplines.

In a recent publication, Klünemann and colleagues demonstrated that in addition to the biotransformation of therapeutic drugs, gut bacteria can bioaccumulate therapeutic drugs 

 The authors showed that the sequestering of therapeutic drugs by gut bacteria had the primary effect of reducing drug availability and, interestingly, a secondary effect of changing bacterial metabolite production. The secondary effect can lead to changes in the gut bacteria composition and potentially result in altered drug adverse effects and drug mode of action. The authors investigated bacteria-drug interactions using 15 structurally diverse drugs and 25 unique strains of gut bacteria totaling 375 bacteria-drug pairs. The depletion of drug from the culture media was measured by ultraperformance liquid chromatography with ultraviolet detection after 48 hours of anaerobic growth. Postgrowth drug concentrations from the culture supernatant were compared with drug concentrations from total culture extracts, which included the bacterial cells, to track the fate of the depleted drugs. The investigators identified 70 bacteria-drug interactions, of which 29 were previously unknown. Approximately half the newly identified interactions involved intracellular storage of the drug without chemical modification. Nuclear magnetic resonance and liquid chromatography–mass spectrometry studies were used to confirm these results. The authors also tested for bacterial growth alterations by the studied drugs and identified 30 inhibitory drug-bacteria interactions, but only 3 also involved altered drug concentrations. The authors concluded that bacteria-drug and drug-bacteria interactions, although prevalent, appear to be largely independent.

To investigate the mechanism by which bacteria were able to bioaccumulate the drugs, the authors performed a series of follow-up studies using the drug duloxetine, which several bacterial species were shown to have accumulated. Using a chemically activated duloxetine analogue, the investigators performed a “click chemistry” pull-down assay to identify several metabolic bacterial enzymes that bound to the drug. Thermal proteome profiling studies with nonmodified drug were used to confirm these results, demonstrating that intracellular protein binding, in this case to metabolic enzymes, was the mechanism for bacterial accumulation of duloxetine. The authors went on to show that duloxetine bioaccumulation in gut bacteria shifted the overall gut bacterial community composition by altering the bacterial metabolite secretion and inducing metabolic cross-feeding, which was consistent with duloxetine binding to metabolic enzymes. These results are important because they demonstrate that human-targeted drugs can alter microbial gut communities by inhibiting direct bacterial growth and by creating bacterial cross-feeding opportunities. Lastly, the authors showed that drug bioaccumulation by bacteria can affect host response by studying duloxetine bioaccumulation using 

as a model system. They followed animal movement as a behavioral readout for duloxetine in the presence and absence of bioaccumulating bacterial species and showed that the duloxetine-bioaccumulating strains attenuated the effect of the drug on the host.

These results further demonstrate the critical role that the gut microbiome can potentially play in altering human drug therapeutic response. The ability of drugs to alter the microbiome directly by antibacterial activity and indirectly via altered metabolic cross-feeding, and the ability of bacteria to alter drug availability by both biotransformation and bioaccumulation, highlight the need for and the importance of pharmacomicrobiomics in therapeutic approaches to personalized medicine. 

The findings of this study, although demonstrative, are limited by the small sample sizes of both drugs and gut bacteria in the study. Further, the mechanism of bioaccumulation of other drugs by gut bacteria may differ from that identified here for duloxetine. Overall, the results suggest that a broader scale mapping of the interactions between drugs and human gut bacteria is needed along with studies of gut bacteria interactions with drugs in the broader context of the microbiome versus the individual gut-bacteria pairs studied here.



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A new study demonstrated that gut organisms can alter drug availability by biotransformation on a significantly broader scale than previously expected.

Bioaccumulation of Drugs by Human Gut Bacteria Can Affect Drug Availability

Microbiome transplantation has been a controversial topic since the introduction of fecal microbiome transplantation (FMT) for the treatment of recurrent 

 infections. While this treatment modality may be considered unconventional, multiple FMT trials have reported favorable outcomes, with some studies showing up to 100% 

 Four-year follow-up studies of FMT-treated patients showed significantly improved bowel habits and decreased gastrointestinal tract symptoms compared to antibiotic therapy, which indicates that the long-term effects can prove to be beneficial.

 Given the reported efficacy and safety profile of FMT, researchers have begun investigating a potential role for the procedure in the management of other disease states believed to be affected by the microbiome, including inflammatory bowel disease and depression.

 A natural progression in the research of microbiome transplantation for the treatment and prevention of chronic disease is to study the role of microbiome transplantation at other sites of human colonization. A recent study by Lev-Sagie and colleagues reported the benefit of vaginal microbiome transplantation (VMT) for the treatment of recurrent bacterial vaginosis (BV).

 Their results are striking and are likely to spur a significant amount of further research in this area.

The authors reported a prospective, non-randomized trial of 5 women with intractable BV, defined as having high relapse of symptoms and overall negative impact on patients’ quality of life. The subjects were given VMTs from healthy donors and evaluated for improvement in symptoms. Before the transplantation, all patients were treated with an intravaginal antibiotic regimen that previously allowed symptom-free intervals. The process of the transplantation included transferring vaginal fluids collected from healthy donors’ vaginal fornices to the patients with intractable BV. The patients had weekly follow-up appointments for the first month, during which remission was defined as having disappearance of symptoms, normalization of all Amsel criteria,

-dominated vaginal microbiome. Patients A and B were reported to have immediate improvement after a single transplant. Patient C and D were reported to have microscopic findings consistent with BV and a recurrence of symptoms, respectively; however, after another VMT trial, they were able to achieve full remission. Patient E was reported to have a partial symptomatic improvement after a second VMT procedure. No adverse events were reported for any of the 5 patients.  

While VMT appears to be a promising potential treatment option for women who suffer from refractory bacterial vaginosis, the study was limited by the low number of recruited patients, patient-physician blinding, and randomization; therefore, its applicability to general practice is still uncertain. Follow-up studies with greater numbers of patients and placebo controls should be performed to assess the full efficacy of this treatment. Future studies should also assess potential risks, including transmission of multidrug-resistant pathogens, induction of other diseases, and long-term side effects. Notwithstanding this, the findings of this study are of strong clinical interest because they suggest a potential avenue for BV treatment in patients who have exhausted other medical and pharmacologic options. The potential impact is significant as bacterial vaginosis affects nearly 30% of the female population every year.

Of the 21.2 million affected women, a subset further develops recurrent disease, which typically requires chronic antibiotic suppressive therapy, further driving high relapse rates. This study by Lev-Sagie and colleagues shows that microbiome transplantation is a promising frontier in treating intractable bacterial vaginosis by targeting the root cause, a dysbiosis which leads to eruption of disease. Of the 5 patients who suffered from the negative impacts of recurrent disease, 4 patients achieved full remission with no pharmacologic interventions after the transplant. More importantly, none of the patients experienced side effects. This procedure may offer a potential therapeutic alternative to safeguard patients from chronic antibiotic use and its sequalae, particularly in the era where multi-drug resistant pathogens are becoming more common.

Microbiome transplantation presents an attractive treatment option for chronic and recurrent infections such as 

and bacterial vaginosis. Furthermore, this study suggests that VMT may be applied to other recurrent infections which are the result of a dysregulated microbiome, such as chronic yeast or urinary tract infections and also a potential role for microbiome transplantation in other areas of human colonization associated with chronic infection such as the oral cavity and the skin.

Nasritdinova is a current third-year student at UTHSC College of Pharmacy in Nashville, TN. Her clinical interests include critical care, infectious diseases, and public health, particularly in underserved populations.

Hevener is an assistant professor of pharmaceutical sciences at University of Tennessee College of Pharmacy. His research focuses on the characterization and validation of narrow-spectrum antibacterial drug targets. He is a member of Contagion®’s Editorial Advisory Board. He is also an active member of the Society of Infectious Diseases Pharmacists.

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A recent study reported the benefit of vaginal microbiome transplantation for the treatment of recurrent bacterial vaginosis.

Vaginal Microbiome Transplantation Effective in Intractable Bacterial Vaginosis

 Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. 

. 2019 Jun;570(7762):462-467. doi: 10.1038/s41586-019-1291-3.

There is an increasing awareness of the potential role that the gut microbiota can play in drug metabolism, drug exposure, and drug action. Orally administered drugs typically encounter gut microorganisms prior to absorption and recent studies have shown that, in some cases, these bacteria possess drug-metabolizing capabilities that can significantly influence clinical drug exposure, activity, and toxicity. Examples of such include the metabolism of omeprazole by gut anaerobes,

 microbiota-mediated metabolism of lovastatin precipitated by antibiotic co-administration,

 and the reduction of digoxin by a specific gut organism.

 This has led to the emergence of a new field of study that has strong potential to inform personalized medicine—pharmacomicrobiomics.

 Defined as a sub-discipline intersecting microbiology, genomics, and pharmacology, pharmacomicrobiomics studies the effects that the human microbiome has on drug exposure, activity, and toxicity. However, the field is relatively new and although there have been several reports of microbial biotransformation, there have been few in-depth investigations into the specificity of bacterial strains or the chemical determinants that may predict drug transformations.

A recent study by Zimmerman, et al. provides what may be the first in-depth examination of the molecular mechanism of biotransformation of a large number of orally administered agents by the human gut microbiota.

 The study surveyed the metabolic activity of 76 human gut bacteria, representing the major phyla of the human gut microbiome, against 271 oral drugs. High-throughput genetic analysis coupled with mass spectrometric methods was used to identify the bacterial gene products responsible for drug metabolism and the specific metabolic reaction. The investigators showed that after a 12-hour incubation period, two-thirds of the analyzed drugs were metabolized to a significant extent (>20%) by at least 1 of the bacterial strains investigated. They further showed that each bacterial strain that was studied metabolized between 11 and 95 drugs. Importantly, the investigators were able to identify phylum-specific metabolic activities by clustering the drug-metabolizing activities of the bacterial isolates. They reported that drugs containing ester or amide functionalities were specifically susceptible to metabolism by the 

, while other organisms showed a preference for nitrogen-containing functional groups.

Of key importance in this study is the investigators’ identification of specific drug-metabolizing gene products in the organisms tested. They were able to characterize 30 enzymes expressed by gut bacteria that were responsible for the metabolism of 20 drugs to 59 metabolites. This work suggests the potential for predicting drug exposure, based in part, upon genetic and microbiological analysis of a patient’s gut microbial composition and even the possibility of rationally altering a patient’s gut microflora to beneficially affect microbiome-drug interactions.

Although the field of pharmacomicrobiomics is relatively new, it is clear from recent publications that this new discipline will continue to grow. Initiatives such as the Human Microbiome Project have been started to facilitate the characterization of the human microbiota and investigate how alterations in the microbiome may affect systems pharmacology and personalized medicine.

 The Zimmerman, et al. study further highlights the large role that pharmacomicrobiomics will likely have in the near future, taking a place beside pharmacogenomics, metabolomics, and therapeutic drug monitoring in the personalized medicine armamentarium.

 year professional student at University of Tennessee College of Pharmacy, enrolled in UT’s dual PharmD/PhD program. She received a Bachelor of Science degree in Chemistry from Arkansas State University.

Hevener is an assistant professor of pharmaceutical sciences at University of Tennessee College of Pharmacy. His research focuses on the characterization and validation of narrow-spectrum antibacterial drug targets.

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A recent study provides what may be the first in-depth examination of the molecular mechanism of biotransformation of a large number of orally administered agents by the human gut microbiota.

Kirk E. Hevener, PharmD, PhD

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