Gene Presence Does Not Uniformly Predict Digoxin Metabolism by the Human Gut Bacterium Eggerthella lenta

Abstract

There are a wide variety of pharmaceutical compounds that are metabolized by bacteria within the human gut microbiome, leading to different effects. A keystone example of microbiome-derived metabolism (MDM) is the cardiac drug digoxin, which is metabolized into an inactive form by Eggerthella lenta through enzymes encoded in the cgr gene operon. A high-throughput screening method was recently developed to test for MDM-interactions in ex vivo cultures of human gut microbiome communities from healthy donors. This screen revealed that three donor’s ex vivo cultures metabolized digoxin at significant levels, yet these cultures did not initially appear to contain E. lenta. Using PCR, I confirmed that E. lenta was the causative agent of digoxin metabolism in these samples. Through this process, I also discovered that twelve additional ex vivo cultures possessed cgr2, the gene necessary for digoxin metabolism, but did not metabolize digoxin. In one of these ex vivo cultures, a previously undocumented mutation was discovered in the cgr2 gene which causes a non-functional form of the protein to be produced, preventing digoxin metabolism. This discovery of nucleotide-level variation in an MDM gene provides a novel explanation for why MDM interactions may vary between individuals that possess the same MDM+ bacteria. The lack of digoxin metabolism in the other 80% of donors possessing cgr2 remains unexplained. Experimental frameworks to interrogate the cause of variation in these donors are proposed, but require further optimization. Elucidating the factors which lead to interindividual variation in MDM will allow for personalization of medical treatments with MDM+ drugs like digoxin, improving health outcomes.