Human-derived gut microbiota alter colonic gene expression in mice, inducing upregulation of drug transporters (including P-gp, MCT1, and OCTN2), drug-metabolizing enzymes (phase I and II), and genes regulating barrier properties, while reducing small intestinal mucosal permeability compared to germ-free mice.
Key Findings
Results
Gut microbiota induced upregulation of genes encoding P-glycoprotein (P-gp) and other drug transporters in the mouse colon.
Transcriptomic analysis of colonic tissue from colonized mice versus germ-free Swiss Webster mice revealed microbiota-induced upregulation of drug transporter genes.
Upregulated transporters included P-gp (encoded by Abcb1), MCT1 (monocarboxylate transporter 1), and OCTN2 (organic cation/carnitine transporter 2).
Immunofluorescence confirmed greater P-gp protein expression and apical localization in colonized mice compared to germ-free mice.
Colonized mice received fecal microbiota transplant from a single human donor, providing a humanized microbiota model.
Results
Microbiota colonization increased colonic gene expression of phase I and phase II drug-metabolizing enzymes.
Phase I enzymes upregulated included carboxylesterase 2 paralogs.
Phase II enzymes upregulated included UDP-glucuronosyltransferases (UGTs) and glutathione S-transferases (GSTs).
Genes responsible for synthesizing co-substrates for these enzymes were also upregulated, including those involved in UDP-glucuronic acid and glutathione synthesis.
These findings suggest microbiota influence not only the enzymes themselves but also the metabolic cofactors necessary for their activity.
Results
Small intestinal mucosal permeability was lower in colonized mice than in germ-free mice.
Permeability was assessed using small intestinal mucosal explants and 14C-labeled polyethylene glycol 4000 (PEG 4000) as a paracellular permeability marker.
Colonized mice demonstrated lower permeability to 14C-PEG 4000 compared to germ-free mice.
PEG 4000 is a large, non-absorbable probe used to assess paracellular (between-cell) transport across the intestinal barrier.
This finding indicates that human-derived microbiota contribute to tightening of the small intestinal mucosal barrier.
Results
Transcriptomic analysis identified microbiota-dependent changes in colonic genes regulating paracellular tight junctions and actomyosin contractility.
Genes involved in paracellular tight junction regulation were differentially expressed in colonized versus germ-free mice.
Genes related to actomyosin contractility, which influences tight junction dynamics and epithelial barrier integrity, were also altered.
These changes were identified through colonic tissue transcriptomic analysis.
These gene expression changes provide a mechanistic basis for microbiota-associated alterations in intestinal barrier function.
Methods
The study used a germ-free to humanized mouse model to isolate microbiota-driven effects on intestinal gene expression.
Germ-free Swiss Webster mice were compared to mice colonized with fecal microbiota from a single human donor.
This design allowed attribution of transcriptomic and protein-level differences specifically to the presence of human-derived gut microbiota.
Both colonic gene expression and small intestinal permeability were evaluated in the same model.
Use of a single donor limits generalizability but controls for inter-donor variability in microbiota composition.
What This Means
This research suggests that the community of bacteria living in the gut (the gut microbiota) plays an important role in controlling how the intestines process medications. The study compared mice raised without any gut bacteria (germ-free) to mice given gut bacteria from a human donor. By examining gene activity in the colon and protein levels, the researchers found that the presence of human-derived bacteria switched on genes responsible for transporting drugs across intestinal cells (including a major drug transporter called P-glycoprotein) and for chemically modifying drugs through metabolic enzymes. The bacteria-colonized mice also had a tighter intestinal barrier, meaning less leakage between cells, compared to germ-free mice.
These findings matter because drug transporters and metabolizing enzymes in the gut directly affect how much of an oral medication actually gets absorbed into the bloodstream and how quickly it is broken down. If gut bacteria control the activity of these proteins, then differences in a person's gut microbiota composition — due to diet, antibiotics, illness, or other factors — could help explain why the same drug dose works differently in different people. This research identifies specific genes that respond to gut bacteria and could represent targets for understanding drug variability.
This research suggests that the gut microbiome should be considered as a potential factor influencing oral drug absorption and metabolism, adding to a growing body of evidence that the bacteria in our intestines affect more than just digestion. Future studies involving multiple human donors and clinical populations would be needed to understand how broadly these findings apply to human drug therapy.
Nelson D, Veerareddy V, Tang X, Kashyap P, Kalari K, Kandimalla K. (2026). Gut Microbiota Alter Colonic Expression of Genes Encoding Drug Transporters and Drug-Metabolizing Enzymes in Mice.. International journal of molecular sciences. https://doi.org/10.3390/ijms27177583