FIGURE 4.

In vitro cultures of gut microbiota strains or stool to identify microbiota‐drug interactions. (a) Anaerobic gut microbial strains are arrayed into 96‐well plates and cultured in the presence of drugs. After growth, drugs are extracted from culture supernatants and analyzed by LC–MS. Extracted ion chromatograms for drugs present in supernatants of each strain can reveal drug‐microbe interactions. (b) Stool samples from human donors are inoculated into different culture media. After growth, 16S rRNA gene profiling of cultures can be compared to the original stool donor to identify media that best recapitulate the donor community composition. After identifying optimal media, stool is cultured in the presence of drugs and drug remaining in the supernatant after growth is analyzed by LC–MS. Extracted ion chromatograms for drugs present in supernatants of different stool donors can reveal individualized drug‐microbiota interactions. LC–MS, liquid‐chromatography mass spectrometry.