Abstract

Interactions between the microbiome and medical therapies are distinct and bidirectional. The existing term “pharmacomicrobiomics” describes the effects of the microbiome on drug distribution, metabolism, efficacy, and toxicity. We propose that the term “pharmacoecology” be used to describe the effects that drugs and other medical interventions such as probiotics have on microbiome composition and function. We suggest that the terms are complementary but distinct and that both are potentially important when assessing drug safety and efficacy as well as drug–microbiome interactions. As a proof of principle, we describe the ways in which these concepts apply to antimicrobial and non-antimicrobial medications.

“Pharmacokinetics” (PK) refers to drug absorption, distribution, and metabolism. “Pharmacodynamics” (PD) refers to the biochemical, physiological, and therapeutic effects of drugs on target tissue/organ(s). The impact of host genetics on drug metabolism, safety, and efficacy is referred to as “pharmacogenomics” (PG) (Figure 1). These terms and concepts are well established in drug development, clinical research, and practice. However, the bidirectional interactions between drugs and the microbiome are not as thoroughly described, nor are they routinely incorporated into research and clinical care. We define the microbiome here as microbes and their genomic content in the human host [1]. The host genome is relatively stable; however, the microbiome is susceptible to change and may be influenced by diet, drug co-administration, environmental exposures, age, and sex (Figure 1). Indeed, numerous studies have demonstrated that drugs, including both antimicrobials and non-antimicrobials (such as antidiabetics, proton pump inhibitors, antipsychotics, and nonsteroidal anti-inflammatory drugs), can affect microbiome composition and function, both as a therapeutic target and as an off-target effect [2–4]. Likewise the microbiome may affect responses to, and toxicities of, some drugs by metabolizing drugs and their byproducts or through synergism or antagonism [5, 6]. While interactions between the microbiome and therapeutics are bidirectional—that is, drugs may induce changes to the microbiome and the microbiome may also alter drug PK/PD—these represent two directionally distinguishable concepts that can be defined independently (Supplementary Figure 1). We propose employing the existing term “pharmacomicrobiomics” to describe exclusively the effects of the microbiome on PK and PD and using “pharmacoecology” to describe the effects of therapeutic interventions on microbiome composition and function (e.g., microbial metabolic enzymes) (Figure 1).

Schematic representation of directionality of terminology used to understand pharmacology and how these features collectively impact clinical response. For simplicity, gut microbiota is represented in the schematic. Figure created in Biorender. Abbreviations: PD, pharmacodynamics; PK, pharmacokinetics.
Figure 1.

Schematic representation of directionality of terminology used to understand pharmacology and how these features collectively impact clinical response. For simplicity, gut microbiota is represented in the schematic. Figure created in Biorender. Abbreviations: PD, pharmacodynamics; PK, pharmacokinetics.

Pharmacomicrobiomics: The Effects of Microbiomes on Drug Pharmacokinetics, Pharmacodynamics, Efficacy, and Toxicity

Although Rizkallah et al. coined the term pharmacomicrobiomics in 2010 [7], examples of microbial metabolism of therapeutic drugs antedate that term by several decades [8, 9]. With the emergence of the Human Microbiome Project [10] and high-throughput sequencing technologies, we now have a better understanding of the role of the microbiome in health, disease, and drug metabolism. Rizkallah et al. described pharmacomicrobiomics as “the study of how intra- and inter-individual microbiome variations affect drug action, disposition, efficacy and toxicity, with an emphasis on the effect of microbiome variations on pharmacokinetics and pharmacodynamics of drug therapy, rather than interactions between drugs and individual microbes” [7, 11–13]. Thus, pharmacomicrobiomics represent the unidirectional effects of microbiomes on drugs, which can either be direct through biotransformation and bioaccumulation or indirect through effects on host gene expression and the immune system.

Microbes can decrease effective drug concentration by biotransformation and bioaccumulation. Biotransformation of drugs by microbes that may alter bioavailability and/or bioactivity [14–16] is a prototypic pharmacomicrobiomic effect. Likely the best known example of microbial production of drug-degrading enzymes is antimicrobial resistance by enzymes such as beta-lactamases [17]. Notably, this form of biotransformation can be from either the target organism of antimicrobial therapy or by nontarget resident microbial species [18–21]. Microbes also transform non-antimicrobial drugs, including degradation of levodopa (an agent used to treat Parkinson's disease) by specific strains of Enterococcus faecalis and E. lenta [14] and digoxin (an anti-arrhythmic cardiac glycoside), whose degradation by E. lenta strains was described almost four decades ago [15, 22]. Bioaccumulation refers to the intracellular accumulation of unmodified drugs by microbes with minimal impact on bacterial growth, which may also alter drug disposition [23]. Klunemann et al. screened 15 non-antibacterial drugs against 25 gut microbes and found 29 novel bacterial–drug interactions, 17 of which were defined as bioaccumulation events [23]. In vivo experiments using Caenorhabditis elegans showed that bioaccumulation of duloxetine (an antidepressant) by Escherichia coli attenuated response to the drug [23].

Bacteria also indirectly alter drug response through their effects on host gene expression and immune response. Germ-free mice demonstrate decreased hepatic expression of cytochrome CYP450 genes compared with mice colonized by bacteria, suggesting that bacteria play an important role in shaping the expression of the metabolic genes involved in drug metabolism [24]. Microbes can influence response to drugs through immune effects, for example by stimulating T cells through antigen presentation and biomimicry or production of immune-active microbial metabolites, mechanisms that have been implicated in response to cancer immunotherapy [25–27]. Thus, there remains potential to optimize immune system tone during the treatment of infectious, inflammatory, and neoplastic diseases via manipulation of the microbiome [28].

As these concepts illustrate, microbial modification of drug concentration or activity is in many ways parallel to that of pharmacogenomics; that is, it represents a category of unidirectional influences of the microbiome on drug activity that needs to be taken into account in pharmacological research and clinical practice.

Pharmacoecology: The Effect of Interventions on Microbiome Composition and Function

Pharmacoecology was first coined by C. Flexner to define the environmental influence on drug pharmacokinetics and response [29], but the term is no longer in wide use. We propose to adapt the term pharmacoecology to refer to the ecological impact of medications on the microbiome. Many and varied interventions, such as diet, antimicrobials, and non-antimicrobials, can alter the microbiome directly through gains and losses (or increases and decreases) in taxa or their functions, or indirectly by modifying host physiological and immune responses, which in turn affect microbial community composition and function [2, 3, 30–36]. Pharmacoecological effects are the unidirectional effects of drugs on microbiome composition and function and are thus a complementary concept to the unidirectional effects constituting pharmacomicrobiomics. Below we summarize and exemplify pharmacoecological effects and their clinical implications.

We propose that pharmacoecological effects are any gains or losses in microbial taxa or microbe-specific function due to the direct or indirect microbicidal or promicrobial activity of a drug, regardless of whether its indicated use is microbiome-targeting. Antimicrobials including antibacterials, antifungals, antivirals, and antiparasitic agents kill or suppress pathogenic organisms and may have effects on both their target (usually a disease-causing pathogen) and off-target effects on other microbiome members [37]. However, microbicidal drug effects are not restricted to drugs whose therapeutic indication is treatment of infection. In an extensive screening of 1197 compounds against 40 representative gut bacteria, 203/835 (24%) of the non-antibiotic compounds demonstrated in vitro antimicrobial activity [3]. These effects have been described in clinical studies of antidiabetic medications [38] and proton pump inhibitors [30, 31]. Conversely, promicrobials including prebiotics, probiotics, defined microbial consortia, and fecal microbiome transplantation (FMT) are intended to promote the health benefits commensals provide [39]. As such, uncovering the ecological shifts in the microbiome following treatment will allow researchers and clinicians to better understand the impact of interventions on the microbiome and potential associations with and mechanisms of clinical benefit. Pharmacoecologic assessment aims to answer the following question: How does the intervention impact microbial community composition/function?

Pharmacoecologic assessment of the microbiome is intended to complement PK/PD during investigations of new interventions. The utility of this assessment is most intuitive when investigating interventions in which a pathologically perturbed microbiome is the therapeutic target, such as treatment of recurrent Clostridioides difficile infection (rCDI) with FMT [40–42] or microbial consortia [43–45]; novel microbiome-targeting therapies can also be used for other indications in which the microbiome has been mechanistically implicated in disease or treatment response [45]. However, this assessment is also valuable when the intervention does not target the microbiome and effects on the microbiome are unintentional.

Implications: Pharmacoecology and Disease Risk, Drug Metabolism, and Clinical Outcomes

Drug-induced changes in the microbiome can increase risk of both infectious and noninfectious diseases. For example, the use of antibiotics or proton pump inhibitors (PPIs) alters risk of infection and colonization with antimicrobial-resistant organisms including C. difficile or vancomycin-resistant Enterococcus [46]. Antimicrobial exposure early in life has been associated with increased risks of allergic and respiratory diseases, likely through the impact of antimicrobials on the microbiome [47–49]. Unlike the human genome, the microbiome is not fixed, and therefore pharmacoecological changes induced by one therapy may affect the pharmacomicrobiomics of subsequent (or coincident) therapies. Understanding the pharmacoecology of treatments and how they may shape response to other therapeutics will be critical to personalization of medicine in the future. Such effects have already been observed in cancer immunotherapy and vaccine studies, in which prior antimicrobial exposure is associated with decreased responsiveness to subsequent therapy [26, 33]. Drug-induced changes in the microbiome can increase risk or harms, but also decrease risk or confer health benefits. However, data from clinical trials assessing the effects of promicrobials such as probiotics, FMTs, and microbial consortia have been demonstrated to exert taxonomic and functional changes in the microbiome with varied clinical benefit for both infectious and noninfectious diseases [41, 43, 44, 50, 51]. It is crucial to understand the long-term, on- and off-target effects of therapies on the microbiome, and assessment of these effects may help elucidate the underlying reasons for variability in therapeutic efficacy.

How to Assess Pharmacomicrobiomics and Pharmacoecology

Measures of pharmacomicrobiomics and pharmacoecology can be achieved using several methods including culturomics, targeted amplicon sequencing of the 16S (bacteria) or 18S (fungi) rRNA genes, 16S/18S quantitative polymerase chain reaction, microbial-derived targeted metabolomics, or more comprehensively using shotgun metagenomics (SGM). However, as the microbiome field is continuously evolving and there is a lack of standardized technical, analytical, and computational techniques, it is challenging to establish standardized criteria (similar to those established for PK/PD) to assess pharmacoecology. Nonetheless, pharmacoecology can be measured by assessing changes in (1) the abundance of target and nontarget taxa; (2) summary taxonomic composition metrics including alpha- and beta-diversity; (3) metagenomic compositional metrics including microbial gene/pathway abundances; (4) direct measurement of microbial metabolites; and/or (5) measures of host–microbiome interactions (such as antimicrobe immune responses). Examples of current methods available to better understand pharmacoecology along with their strengths and limitations are listed in Table 1. For pharmacomicrobiomics, we refer readers to a review written by J. Bisanz et al., which provides a guide on how to assess the effects of microbes on the absorption, distribution, metabolism, and excretion of drugs [59].

Table 1.

Technical Approaches Used to Measure Pharmacoecology, Strengths Limitation, and Examples From the Literature

Technical ApproachesPE MeasureStrengthsLimitationsPE Examples
CulturomicsCompositionIdentify effect of drug on individual bacterial isolates.
Can identify isolates at the species and strain levels [52].
Need to culture and purify individual isolates. In vitro effect may be different than in vivo impact of drugs on microbial composition.Decrease in Pseudomonas aeruginosa density post–inhaled aztreonam compared with placebo [53].
16S/18S amplicon sequencingCompositionHigh-throughput sequencing for low cost [54].
16S rRNA gene sequencing for bacteria.
18S internal transcribed spacer region for fungi.
Inter-study differences in variable region sequencing, primer use, extraction methods, etc., limit ability to perform meta-analyses [55].
Limited taxonomic resolution [54].
Increase in alpha diversity post–Microbial Ecosystems Therapeutic 2 initiation in individuals with recurrent Clostridioides difficile infection [43].
16S/18S qPCRComposition/functionAllows you to identify microbial load in sample [55].
Can identify whether certain genes are present [55].
Amplification bias [55].
Does not allow identification of unknown species/genes [55].
Preterm neonates randomized to receive probiotics had significantly higher load of bacteria found in probiotic compared with untreated controls [56].
MetagenomicsComposition/functionHigh resolution [52, 54, 55].
Allows you to identify uncultured taxa [52, 54, 55].
Enables characterization of functional content [52, 54, 55].
Allows you to capture bacterial, fungal, DNA viruses, and other microbes [52, 54, 55].
Expensive [52, 54, 55].
Data analysis computationally demanding [52, 54, 55].
Differentially abundant microbial pathways in adolescents with obesity treated with FMT compared with placebo [50].
MetatranscriptomicsComposition/functionCaptures microbial transcribed RNA [54, 55].
May identify differential gene expression profiles [54, 55].
May be difficult to assess microbial transcripts if sample is contaminated with host nucleic acids [54, 55].
Lack of standardized protocols may result in bias [54, 55].
Study assessing impact of nonantibiotic drugs on a synthetic community of 32 human gut–derived bacteria demonstrates that antipsychotic drug chlorpromazine induces stress responses related to protein quality control [57].
MetaproteomicsComposition/functionHigh-resolution microbial protein/peptide identification [55].
Allows you to identify novel proteins/peptides and assess for differential abundance between samples [55].
Lack of standardized protocols, databases, and analytical methods makes it challenging to do meta-analyses [55].Study assessing the impact of different drugs on gut microbiome in vitro demonstrated that antibiotics, fructooligosaccharide, berberine, and diclofenac all changed the function and composition of the microbiome [58].
MetabolomicsFunctionCan be targeted panels or nontargeted discovery based [55].Can be difficult to differentiate host- vs microbiome-derived metabolites [55].
Difficult to establish standards for nontargeted approach [55].
In a randomized controlled trial, males treated with metformin had significant increases in stool butyrate and propionate [38].
Technical ApproachesPE MeasureStrengthsLimitationsPE Examples
CulturomicsCompositionIdentify effect of drug on individual bacterial isolates.
Can identify isolates at the species and strain levels [52].
Need to culture and purify individual isolates. In vitro effect may be different than in vivo impact of drugs on microbial composition.Decrease in Pseudomonas aeruginosa density post–inhaled aztreonam compared with placebo [53].
16S/18S amplicon sequencingCompositionHigh-throughput sequencing for low cost [54].
16S rRNA gene sequencing for bacteria.
18S internal transcribed spacer region for fungi.
Inter-study differences in variable region sequencing, primer use, extraction methods, etc., limit ability to perform meta-analyses [55].
Limited taxonomic resolution [54].
Increase in alpha diversity post–Microbial Ecosystems Therapeutic 2 initiation in individuals with recurrent Clostridioides difficile infection [43].
16S/18S qPCRComposition/functionAllows you to identify microbial load in sample [55].
Can identify whether certain genes are present [55].
Amplification bias [55].
Does not allow identification of unknown species/genes [55].
Preterm neonates randomized to receive probiotics had significantly higher load of bacteria found in probiotic compared with untreated controls [56].
MetagenomicsComposition/functionHigh resolution [52, 54, 55].
Allows you to identify uncultured taxa [52, 54, 55].
Enables characterization of functional content [52, 54, 55].
Allows you to capture bacterial, fungal, DNA viruses, and other microbes [52, 54, 55].
Expensive [52, 54, 55].
Data analysis computationally demanding [52, 54, 55].
Differentially abundant microbial pathways in adolescents with obesity treated with FMT compared with placebo [50].
MetatranscriptomicsComposition/functionCaptures microbial transcribed RNA [54, 55].
May identify differential gene expression profiles [54, 55].
May be difficult to assess microbial transcripts if sample is contaminated with host nucleic acids [54, 55].
Lack of standardized protocols may result in bias [54, 55].
Study assessing impact of nonantibiotic drugs on a synthetic community of 32 human gut–derived bacteria demonstrates that antipsychotic drug chlorpromazine induces stress responses related to protein quality control [57].
MetaproteomicsComposition/functionHigh-resolution microbial protein/peptide identification [55].
Allows you to identify novel proteins/peptides and assess for differential abundance between samples [55].
Lack of standardized protocols, databases, and analytical methods makes it challenging to do meta-analyses [55].Study assessing the impact of different drugs on gut microbiome in vitro demonstrated that antibiotics, fructooligosaccharide, berberine, and diclofenac all changed the function and composition of the microbiome [58].
MetabolomicsFunctionCan be targeted panels or nontargeted discovery based [55].Can be difficult to differentiate host- vs microbiome-derived metabolites [55].
Difficult to establish standards for nontargeted approach [55].
In a randomized controlled trial, males treated with metformin had significant increases in stool butyrate and propionate [38].
Table 1.

Technical Approaches Used to Measure Pharmacoecology, Strengths Limitation, and Examples From the Literature

Technical ApproachesPE MeasureStrengthsLimitationsPE Examples
CulturomicsCompositionIdentify effect of drug on individual bacterial isolates.
Can identify isolates at the species and strain levels [52].
Need to culture and purify individual isolates. In vitro effect may be different than in vivo impact of drugs on microbial composition.Decrease in Pseudomonas aeruginosa density post–inhaled aztreonam compared with placebo [53].
16S/18S amplicon sequencingCompositionHigh-throughput sequencing for low cost [54].
16S rRNA gene sequencing for bacteria.
18S internal transcribed spacer region for fungi.
Inter-study differences in variable region sequencing, primer use, extraction methods, etc., limit ability to perform meta-analyses [55].
Limited taxonomic resolution [54].
Increase in alpha diversity post–Microbial Ecosystems Therapeutic 2 initiation in individuals with recurrent Clostridioides difficile infection [43].
16S/18S qPCRComposition/functionAllows you to identify microbial load in sample [55].
Can identify whether certain genes are present [55].
Amplification bias [55].
Does not allow identification of unknown species/genes [55].
Preterm neonates randomized to receive probiotics had significantly higher load of bacteria found in probiotic compared with untreated controls [56].
MetagenomicsComposition/functionHigh resolution [52, 54, 55].
Allows you to identify uncultured taxa [52, 54, 55].
Enables characterization of functional content [52, 54, 55].
Allows you to capture bacterial, fungal, DNA viruses, and other microbes [52, 54, 55].
Expensive [52, 54, 55].
Data analysis computationally demanding [52, 54, 55].
Differentially abundant microbial pathways in adolescents with obesity treated with FMT compared with placebo [50].
MetatranscriptomicsComposition/functionCaptures microbial transcribed RNA [54, 55].
May identify differential gene expression profiles [54, 55].
May be difficult to assess microbial transcripts if sample is contaminated with host nucleic acids [54, 55].
Lack of standardized protocols may result in bias [54, 55].
Study assessing impact of nonantibiotic drugs on a synthetic community of 32 human gut–derived bacteria demonstrates that antipsychotic drug chlorpromazine induces stress responses related to protein quality control [57].
MetaproteomicsComposition/functionHigh-resolution microbial protein/peptide identification [55].
Allows you to identify novel proteins/peptides and assess for differential abundance between samples [55].
Lack of standardized protocols, databases, and analytical methods makes it challenging to do meta-analyses [55].Study assessing the impact of different drugs on gut microbiome in vitro demonstrated that antibiotics, fructooligosaccharide, berberine, and diclofenac all changed the function and composition of the microbiome [58].
MetabolomicsFunctionCan be targeted panels or nontargeted discovery based [55].Can be difficult to differentiate host- vs microbiome-derived metabolites [55].
Difficult to establish standards for nontargeted approach [55].
In a randomized controlled trial, males treated with metformin had significant increases in stool butyrate and propionate [38].
Technical ApproachesPE MeasureStrengthsLimitationsPE Examples
CulturomicsCompositionIdentify effect of drug on individual bacterial isolates.
Can identify isolates at the species and strain levels [52].
Need to culture and purify individual isolates. In vitro effect may be different than in vivo impact of drugs on microbial composition.Decrease in Pseudomonas aeruginosa density post–inhaled aztreonam compared with placebo [53].
16S/18S amplicon sequencingCompositionHigh-throughput sequencing for low cost [54].
16S rRNA gene sequencing for bacteria.
18S internal transcribed spacer region for fungi.
Inter-study differences in variable region sequencing, primer use, extraction methods, etc., limit ability to perform meta-analyses [55].
Limited taxonomic resolution [54].
Increase in alpha diversity post–Microbial Ecosystems Therapeutic 2 initiation in individuals with recurrent Clostridioides difficile infection [43].
16S/18S qPCRComposition/functionAllows you to identify microbial load in sample [55].
Can identify whether certain genes are present [55].
Amplification bias [55].
Does not allow identification of unknown species/genes [55].
Preterm neonates randomized to receive probiotics had significantly higher load of bacteria found in probiotic compared with untreated controls [56].
MetagenomicsComposition/functionHigh resolution [52, 54, 55].
Allows you to identify uncultured taxa [52, 54, 55].
Enables characterization of functional content [52, 54, 55].
Allows you to capture bacterial, fungal, DNA viruses, and other microbes [52, 54, 55].
Expensive [52, 54, 55].
Data analysis computationally demanding [52, 54, 55].
Differentially abundant microbial pathways in adolescents with obesity treated with FMT compared with placebo [50].
MetatranscriptomicsComposition/functionCaptures microbial transcribed RNA [54, 55].
May identify differential gene expression profiles [54, 55].
May be difficult to assess microbial transcripts if sample is contaminated with host nucleic acids [54, 55].
Lack of standardized protocols may result in bias [54, 55].
Study assessing impact of nonantibiotic drugs on a synthetic community of 32 human gut–derived bacteria demonstrates that antipsychotic drug chlorpromazine induces stress responses related to protein quality control [57].
MetaproteomicsComposition/functionHigh-resolution microbial protein/peptide identification [55].
Allows you to identify novel proteins/peptides and assess for differential abundance between samples [55].
Lack of standardized protocols, databases, and analytical methods makes it challenging to do meta-analyses [55].Study assessing the impact of different drugs on gut microbiome in vitro demonstrated that antibiotics, fructooligosaccharide, berberine, and diclofenac all changed the function and composition of the microbiome [58].
MetabolomicsFunctionCan be targeted panels or nontargeted discovery based [55].Can be difficult to differentiate host- vs microbiome-derived metabolites [55].
Difficult to establish standards for nontargeted approach [55].
In a randomized controlled trial, males treated with metformin had significant increases in stool butyrate and propionate [38].

Additional Considerations

Several factors may alter pharmacomicrobiomics and pharmacoecology [13]. For example, age, diet, lifestyle, polypharmacy, comorbidities, and hormonal changes may result in temporal shifts in the microbiome. Similarly, spatial differences in microbial ecosystems such as differences in the physiology of the target site, pH, and oxygen gradients may further impact host–microbiome–drug interactions [13]. It is important to consider these variables when assessing pharmacomicrobiomoics and pharmacoecology. Careful study design and randomized controlled trials will help us better understand how drugs impact the microbiome and how the microbiome may impact drugs.

Our proposed use of the terms pharmacomicrobiomics and pharmacoecology attempts to clarify the terminology used to assess these distinct interactions. We suggest that the use of this framework meet the following criteria for their use:

  1. The concepts/terms apply to drug–microbiome interactions regardless of the drug target, therapeutic indication, or host.

  2. They are taxonomically generalizable—that is, they can be applied to any host-associated organisms (bacterial, fungal, viral, or protists).

  3. They distinguish between the directional effects of microbiomes on drugs and drugs on microbiomes.

  4. They are measurable with existing technologies.

As integration of drug–microbiome interactions into clinical practice progresses, we propose that the incorporation of these terms will be useful to help clarify and consolidate concepts and measures relevant to understanding the outcomes of disease treatments across a range of diseases and drug classes.

Supplementary Data

Supplementary materials are available at Open Forum Infectious Diseases online. Consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author.

Acknowledgments

We would like to thank Coburn lab members for their feedback and suggestions. We would like to thank the peer reviewers at Open Forum Infectious Diseases for taking the time to review the manuscript. We sincerely appreciate all their valuable comments and suggestions, which helped us improve the quality of the manuscript. We acknowledge and are grateful for the support of the Tomcyzk AI and Microbiome Working Group.

Financial support. A.H. was supported by the Tomcyzk AI and Microbiome Working Group and the Princess Margaret Cancer Foundation. S.M. was supported by CIHR and Killam Postdoctoral Fellowships.

Author contributions. A.H. conceived the manuscript. A.H. created the figures and table. All authors contributed to revising and editing the manuscript. M.C.A. and B.C. supervised the work.

Patient consent. This manuscript does not include factors necessitating patient consent.

References

1

Berg
G
,
Rybakova
D
,
Fischer
D
, et al.
Microbiome definition re-visited: old concepts and new challenges
.
Microbiome
2020
;
8
:
103
.

2

Vich Vila
A
,
Collij
V
,
Sanna
S
, et al.
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota
.
Nat Commun
2020
;
11
:
362
.

3

Maier
L
,
Pruteanu
M
,
Kuhn
M
, et al.
Extensive impact of non-antibiotic drugs on human gut bacteria
.
Nature
2018
;
555
:
623–8
.

4

Weersma
RK
,
Zhernakova
A
,
Fu
J
.
Interaction between drugs and the gut microbiome
.
Gut
2020
;
69
:
1510
9
.

5

Zimmermann
M
,
Zimmermann-Kogadeeva
M
,
Wegmann
R
,
Goodman
AL
.
Mapping human microbiome drug metabolism by gut bacteria and their genes
.
Nature
2019
;
570
:
462
7
.

6

Hitchings
R
,
Kelly
L
.
Predicting and understanding the human microbiome's impact on pharmacology
.
Trends Pharmacol Sci
2019
;
40
:
495
505
.

7

Rizkallah
M
,
Saad
R
,
Aziz
R
.
The Human Microbiome Project, personalized medicine and the birth of pharmacomicrobiomics
.
Curr Pharmacogenomics Person Med
2010
;
8
:
182
93
. doi:

8

Dobkin
JF
,
Saha
JR
,
Butler
VP
,
Neu
HC
,
Lindenbaum
J
.
Digoxin-inactivating bacteria: identification in human gut flora
.
Science
1983
;
220
:
325
7
.

9

Lindenbaum
J
,
Rund
DG
,
Butler
VP
,
Tse-Eng
D
,
Saha
JR
.
Inactivation of digoxin by the gut flora: reversal by antibiotic therapy
.
N Engl J Med
1981
;
305
:
789
94
.

10

Methé
BA
,
Nelson
KE
,
Pop
M
, et al.
A framework for human microbiome research
.
Nature
2012
;
486
:
215
21
.

11

Aziz
RK
,
Rizkallah
MR
,
Saad
R
,
Elrakaiby
MT
.
Translating pharmacomicrobiomics: three actionable challenges/prospects in 2020
.
Omi A J Integr Biol
2020
;
24
:
60
1
.

12

Saad
R
,
Rizkallah
MR
,
Aziz
RK
.
Gut pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes
.
Gut Pathog
2012
;
4
:
16
.

13

ElRakaiby
M
,
Dutilh
BE
,
Rizkallah
MR
,
Boleij
A
,
Cole
JN
,
Aziz
RK
.
Review articles pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics
.
OMICS
2014
;
18
:
402
14
.

14

Rekdal
VM
,
Bess
EN
,
Bisanz
JE
,
Turnbaugh
PJ
,
Balskus
EP
.
Discovery and inhibition of an interspecies gut bacterial pathway for levodopa metabolism
.
Science
2019
;
364:
eaau6323
.

15

Haiser
HJ
,
Seim
KL
,
Balskus
EP
,
Turnbaugh
PJ
.
Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics
.
Gut Microbes
2014
;
5
:
233
8
.

16

Okuda
H
,
Ogura
K
,
Kato
A
,
Takubo
H
,
Watabe
T
.
A possible mechanism of eighteen patient deaths caused by interactions of sorivudine, a new antiviral drug, with oral 5-fluorouracil prodrugs
.
J Pharmacol Exp Ther
1998
;
287
:
791
9
.

17

Tomás
M
,
Doumith
M
,
Warner
M
, et al.
Efflux pumps, OprD porin, AmpC β-lactamase, and multiresistance in Pseudomonas aeruginosa isolates from cystic fibrosis patients
.
Antimicrob Agents Chemother
2010
;
54
:
2219
24
.

18

Sherrard
LJ
,
McGrath
SJ
,
McIlreavey
L
, et al.
Production of extended-spectrum β-lactamases and the potential indirect pathogenic role of Prevotella isolates from the cystic fibrosis respiratory microbiota
.
Int J Antimicrob Agents
2015
;
47
:
140
5
.

19

Sherrard
LJ
,
Schaible
B
,
Graham
KA
, et al.
Mechanisms of reduced susceptibility and genotypic prediction of antibiotic resistance in Prevotella isolated from cystic fibrosis (CF) and non-CF patients
.
J Antimicrob Chemother
2014
;
69
:
2690
8
.

20

Gjonbalaj
M
,
Keith
JW
,
Do
MH
,
Hohl
TM
,
Pamer
EG
,
Becattini
S
.
Antibiotic degradation by commensal microbes shields pathogens
.
Infect Immun
2020
;
88
:
e00012
20
.

21

Stiefel
U
,
Tima
MA
,
Nerzic
MM
.
Metallo-β-lactamase-producing Bacteroides species can shield other members of the gut microbiota from antibiotics
.
Antimicrob Agents Chemother
2015
;
59
:
650
3
.

22

Haiser
HJ
,
Gootenberg
DB
,
Chatman
K
,
Sirasani
G
,
Balskus
EP
,
Turnbaugh
PJ
.
Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta
.
Science
2013
;
341
:
295
8
.

23

Klünemann
M
,
Andrejev
S
,
Blasche
S
, et al.
Bioaccumulation of therapeutic drugs by human gut bacteria
.
Nature
2021
;
597:
533
8
.

24

Togao
M
,
Kawakami
K
,
Otsuka
J
, et al.
Effects of gut microbiota on in vivo metabolism and tissue accumulation of cytochrome P450 3A metabolized drug: midazolam
.
Biopharm Drug Dispos
2020
;
41
:
275
82
.

25

Fluckiger
A
,
Daillère
R
,
Sassi
M
, et al.
Cross-reactivity between tumor MHC class I–restricted antigens and an enterococcal bacteriophage
.
Science
2020
;
369
:
936
42
.

26

Hagan
T
,
Cortese
M
,
Rouphael
N
, et al.
Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans
.
Cell
2019
;
178
:
1313
28.e13
.

27

Mager
LF
,
Burkhard
R
,
Pett
N
, et al.
Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy
.
Science
2020
;
369
:
1481
9
.

28

Zheng
D
,
Liwinski
T
,
Elinav
E
.
Interaction between microbiota and immunity in health and disease
.
Cell Res
2020
;
30
:
492
506
.

29

Flexner
C
.
Pharmacoecology: a new name for an old science
.
Clin Pharmacol Ther
2008
;
83
:
375
9
.

30

Imhann
F
,
Bonder
MJ
,
Vich Vila
A
, et al.
Proton pump inhibitors affect the gut microbiome
.
Gut
2016
;
65
:
740
8
.

31

Imhann
F
,
Vich Vila
A
,
Bonder
MJ
, et al.
The influence of proton pump inhibitors and other commonly used medication on the gut microbiota
.
Gut Microbes
2017
;
8
:
351
8
.

32

Jackson
MA
,
Goodrich
JK
,
Maxan
ME
, et al.
Proton pump inhibitors alter the composition of the gut microbiota
.
Gut
2016
;
65
:
749
56
.

33

Routy
B
,
Le Chatelier
E
,
Derosa
L
, et al.
Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors
.
Science
2018
;
359
:
91
7
.

34

Ahmed
J
,
Kumar
A
,
Parikh
K
, et al.
Use of broad-spectrum antibiotics impacts outcome in patients treated with immune checkpoint inhibitors
.
Oncoimmunology
2018
;
7
:
e1507670
.

35

Tsikala-Vafea
M
,
Belani
N
,
Vieira
K
,
Khan
H
,
Farmakiotis
D
.
Use of antibiotics is associated with worse clinical outcomes in patients with cancer treated with immune checkpoint inhibitors: a systematic review and meta-analysis
.
Int J Infect Dis
2021
;
106
:
142
54
.

36

Spencer
CN
,
McQuade
JL
,
Gopalakrishnan
V
, et al.
Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response
.
Science
2021
;
374
:
1632
40
.

37

Heirali
AA
,
Workentine
ML
,
Acosta
N
, et al.
The effects of inhaled aztreonam on the cystic fibrosis lung microbiome
.
Microbiome
2017
;
5
:
51
.

38

Wu
H
,
Esteve
E
,
Tremaroli
V
, et al.
Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug
.
Nat Med
2017
;
23
:
850
8
.

39

Mimee
M
,
Citorik
RJ
,
Lu
TK
.
Microbiome therapeutics—advances and challenges
.
Adv Drug Deliv Rev
2016
;
105
:
44
54
.

40

Verma
S
,
Dutta
SK
,
Firnberg
E
,
Phillips
L
,
Vinayek
R
,
Nair
PP
.
Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects
.
PLoS One
2021
;
16
:
e0251590
.

41

Baunwall
SMD
,
Lee
MM
,
Eriksen
MK
, et al.
Faecal microbiota transplantation for recurrent Clostridioides difficile infection: an updated systematic review and meta-analysis
.
EClinicalMedicine
2020
;
29–30
:
100642
.

42

Lee
CH
,
Belanger
JE
,
Kassam
Z
, et al.
The outcome and long-term follow-up of 94 patients with recurrent and refractory Clostridium difficile infection using single to multiple fecal microbiota transplantation via retention enema
.
Eur J Clin Microbiol Infect Dis
2014
;
33
:
1425
8
.

43

Kao
D
,
Wong
K
,
Franz
R
, et al.
The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial
.
Lancet Gastroenterol Hepatol
2021
;
6
:
282
91
.

44

Feuerstadt
P
,
Louie
TJ
,
Lashner
B
, et al.
SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection
.
N Engl J Med
2022
;
386
:
220
9
.

45

Spreafico
A
,
Heirali
AA
,
Araujo
DV
, et al.
First-in-class microbial ecosystem therapeutic 4 (MET4) in combination with immune checkpoint inhibitors in patients with advanced solid tumors (MET4-IO trial)
.
Ann Oncol.
2023
. doi:

46

Mullish
BH
,
Williams
HRT
.
Clostridium difficile infection and antibiotic-associated diarrhoea
.
Clin Med J R Coll Physicians London
2018
;
18
:
237
41
.

47

Patrick
DM
,
Sbihi
H
,
Dai
DLY
, et al.
Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies
.
Lancet Respir Med
2020
;
8
:
1094
105
.

48

Russell
SL
,
Gold
MJ
,
Hartmann
M
, et al.
Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma
.
EMBO Rep
2012
;
13
:
440
7
.

49

Pettersen
VK
,
Arrieta
MC
.
Host-microbiome intestinal interactions during early life: considerations for atopy and asthma development
.
Curr Opin Allergy Clin Immunol
2020
;
20
:
138
48
.

50

Wilson
BC
,
Vatanen
T
,
Jayasinghe
TN
, et al.
Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity
.
Microbiome
2021
;
9
:
107
.

51

Cohen
CR
,
Wierzbicki
MR
,
French
AL
, et al.
Randomized trial of lactin-V to prevent recurrence of bacterial vaginosis
.
N Engl J Med
2020
;
382
:
1906
15
.

52

Lagier
J.-C.
,
Dubourg
G
,
Million
M
, et al.
Culturing the human microbiota and culturomics
.
Nat Rev Microbiol
2018
;
16
:
540
50
.

53

McCoy
KS
,
Quittner
AL
,
Oermann
CM
,
Gibson
RL
,
Retsch-Bogart
GZ
,
Montgomery
AB
.
Inhaled aztreonam lysine for chronic airway Pseudomonas aeruginosa in cystic fibrosis
.
Am J Respir Crit Care Med
2008
;
178
:
921
8
.

54

Knight
R
,
Vrbanac
A
,
Taylor
BC
, et al.
Best practices for analysing microbiomes
.
Nat Rev Microbiol
2018
;
16
:
410
22
.

55

Rezasoltani
S
,
Bashirzadeh
DA
,
Mojarad
EN
,
Aghdaei
HA
,
Norouzinia
M
,
Shahrokh
S
.
Signature of gut microbiome by conventional and advanced analysis techniques: advantages and disadvantages
.
Middle East J Dig Dis
2020
;
12
:
5
11
.

56

Samara
J
,
Moossavi
S
,
Alshaikh
B
, et al.
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants
.
Cell Host Microbe
2022
;
30
:
696
711.e5
.

57

Wuyts
S
,
Alves
R
,
Zimmermann-Kogadeeva
M
, et al.
Consistency across multi-omics layers in a drug-perturbed gut microbial community
.
bioRxiv 519475 [Preprint]. January 3,
2023
. Available at:
https://doi.org/10.1101/2023.01.03.519475. Accessed March 21, 2023.

58

Li
L
,
Ning
Z
,
Zhang
X
, et al.
RapidAIM: a culture- and metaproteomics-based rapid assay of individual microbiome responses to drugs
.
Microbiome
2020
;
8
:
33
.

59

Bisanz
JE
,
Spanogiannopoulos
P
,
Pieper
LM
,
Bustion
AE
,
Turnbaugh
PJ
.
How to determine the role of the microbiome in drug disposition
.
Drug Metab Dispos
2018
;
46
:
1588
95
.

Author notes

Potential conflicts of interest. All authors have no conflicts to report.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact [email protected]

Supplementary data

Comments

0 Comments
Submit a comment
You have entered an invalid code
Thank you for submitting a comment on this article. Your comment will be reviewed and published at the journal's discretion. Please check for further notifications by email.