The Microbiome’s Overlooked Role in Drug Discovery and Development
Cristiano Ruch Werneck Guimarães
Katia Sivieri
Miller Freitas
Stephani Saverio
Nintx – Next Innovative Therapeutics

he human microbiome is a complex ecosystem that can mediate the interaction of the human host with their environment, playing a central role in several cardiometabolic, immunological, and neurological processes. While the importance of the gut microbiota has been acknowledged for many years, the relevance of investigating the complex interactions between the gut microbiome and drugs in preclinical and clinical settings has been generally ignored by researchers and regulatory bodies.

The Human Microbiome

The microbiome comprises the genomes of all symbiotic and pathogenic microbes living on the inside and outside of vertebrate bodies. It refers to both the microorganisms and their genes, whereas the term microbiota only refers to the microorganisms themselves. The Human Microbiome Project initiated by the National Institutes of Health (NIH) in 2007 has identified microbiota at various environmentally exposed sites of the human body such as the mouth, gut, skin, respiratory system, and urogenital tract. The microbiota therein contains diverse groups of bacteria, archaea, viruses, and fungi. Ninety-five percent of microbes reside in the gut, and they collectively encode 150-fold more genes than the human genome. Among them, bacteria are the most studied. As most gut bacteria are oxygen-intolerant bacteria or bacteria that can survive in both oxygen-rich and oxygen-poor environments (i.e., obligate or facultative anaerobes), they live in a part of your large intestine called the cecum, with a concentration of 1011 cells/ml versus 108 cells/ml in the small intestine.

Humans have coevolved with these symbiotic microbes and maintain an overall mutualistic relationship. Diverse gut microbial communities harvest energy from foods and produce micronutrients, receiving food and a suitable environment for growth in return. In this way, they can outcompete the pathogenic microbes. The shift in this interspecies balance favoring pathogenic microbiota, i.e., changing from a state of eubiosis (balance) to dysbiosis (imbalance), is connected to many pathologies. Numerous discoveries link the composition and function of the human gut microbiome to several diseases, demonstrating not only the association but also the causality of the gut microbiome in relation to gastrointestinal diseases, including inflammatory bowel disease and colorectal cancer, and diseases of other systems and organs, such as obesity, type 2 diabetes (T2D), autoimmune conditions, various cancers, and neurodegenerative and psychiatric disorders. Several R&D companies are now looking into how to develop therapies that modulate the human gut microbiome in order to address unmet medical needs.

The colonization of the intestine begins at birth and then continues with the onset of feeding, breast milk or formula. The presence of oligosaccharides in human milk (HMO) promotes distinct shifts in microbiota composition and metabolism affecting the overall gut development. Following breastfeeding, the introduction of solid foods initiates a rapid increase in the structural and functional diversity of the infant microbiota, creating a mature, adultlike state. This mature microbiome is dominated by species capable of degrading glycans, mucin, and complex carbohydrates, as well as producing short-chain fatty acids. Continuing maturation, the microbiota changes significantly with exposure to various environmental factors. As a person grows older, the microbiome tends to be stable because of reduced frequency of activities and motility, lower exposure to new environmental conditions, etc. Much like genetic individuality, everyone has a unique microbiota, even though approximately one-third of the species are common across most humans.

The Overlooked Interactions Between the Gut Microbiome and Drugs

Many factors influence the individual’s gut microbiota including age, hygiene, diet, lifestyle, geographical location, host genotype, environmental factors, diseases, and physiological and psychological changes. As most drugs are delivered orally, and more than 70% exhibit low solubility, low permeability, or both, it should be expected that they reach the microbes in the small intestine and, most importantly, in the large intestine, being another factor to impact the gut microbiome composition and function. On the other hand, gut microbes collectively encode a rich repository of enzymes with the potential to metabolize drugs and influence their bioavailability, efficacy, and toxicity. This complex bidirectional interaction between both antibiotic and nonantibiotic drugs and the gut microbiome, largely ignored, has been named pharmacomicrobiomics.

A correlation between the use of antibiotics in early life and excessive weight gain in later childhood has been demonstrated in worldwide cohort studies. One possibility for this association is the lasting impact that antibiotics may have on the gut microbiota. Excessive use of antibiotics in adulthood was found to result in irreversible changes in the gut microbiota, contributing to the loss of microbial diversity and shifting the microbiota from a state of eubiosis to dysbiosis. One very important recent finding is that many commonly used nonantibiotic drugs change microbiome composition and function, such as anticholinergics, steroid inhalers, nonsteroidal anti-inflammatory drugs (NSAIDs), proton pump inhibitors (PPIs), lipid-lowering statins, laxatives, opioids, metformin, beta-blockers, angiotensin-converting enzyme (ACE) inhibitors, selective serotonin reuptake inhibitors (SSRI), etc. Suggested mechanisms for drug impact on the gut microbiome, most of them negative, have been proposed, such as (i) translocation of the microbiome from other body sites to the gut, as described for PPIs, (ii) antimicrobial activities of nonantibiotic drugs, and (iii) bioaccumulation of drugs in gut bacteria, altering their metabolism as the drugs bind to several metabolic enzymes and change the secreted metabolites.

The other direction in pharmacomicrobiomics is related to the ability of the gut microbiota to act as an organ with metabolic potential that rivals that of the liver. The microbial enzymatic repertoire in the human gut is incredibly diverse and powerful. While there are similarities with the host in terms of enzymatic reactions carried out, the gut microbial metabolism of drugs is in many ways opposite to the host biotransformation. Host enzymes mainly perform oxidation and conjugation of molecules, while microbial enzymes mostly carry out reduction and hydrolysis. A major effect of hydrolytic enzymes, widely distributed across a range of species, is the hydrolysis of conjugated metabolites of drugs and natural products present in food and health products excreted via the biliary system as glucuronides/glucosides. The liberation of the aglycones (i.e., glucosides/glucuronides whose glycosyl/glucuronyl group is replaced by a hydrogen atom) by microbial enzymes enables their absorption or resorption by the host and may increase exposure to the drug itself or bioactive/toxic metabolites.

It is clear then that the human gut microbiome should greatly contribute to interindividual variations, not only because microbial enzymes differ from one species to another in sequence, activity, and abundance, but also due to the diversity of microbial types between individuals (again, only one-third of the species are common across most humans). This is possibly one of the missing links that would explain the complexity of interindividual variability in drug bioavailability, efficacy, and toxicity that cannot be rationalized in terms of host genetic, epigenetic, and regulatory variations.

The Microbiome’s Contribution in Drug Discovery and Development

The drug discovery and development field established over the years an arsenal of in vitro and in vivo models in order to project the pharmacodynamics (PD), pharmacokinetics (PK), and toxicity of drug candidates in humans and reduce attrition in clinical development. While the importance of the gut microbiota has been acknowledged for many years, it was nevertheless generally ignored by those working in the field. When transitioning from in vitro assays to animal models to patients, the range of effects that the human gut microbiota might have on drugs, and vice versa, has the potential to produce unexpected, and potentially undesirable, outcomes on PK, PD, and toxicity in response to the administration of drugs to patients.

Rarely are those effects investigated, simulated, modeled, projected, or monitored in drug research and development. Unfortunately, little action has been taken by regulatory bodies in terms of awareness of the importance of investigating the complex interactions between the gut microbiome and drugs in preclinical and clinical settings. The potential for these microorganisms to affect drugs and at the same time be affected by them with unpredictable consequences with respect to normal body homeostasis, especially in the long run, clearly warrants attention from the drug discovery and development community.

References available upon request.

Look for our follow-up article about new microbiome initiatives and activities in drug development in your next Global Forum.