We may not think about it often, but our gut is home to a complex ecosystem of microorganisms that play a critical role in how we function. The system is delicate—one small change can cause a major shift in the microbiome, resulting in serious consequences. When a person takes an antibiotic, it can wipe out multiple bacterial species and throw this delicate balance off-kilter. Clostridioides difficile is a common pathogen that colonizes a disrupted gut microbiota. Fecal microbiota transplantation (FMT), in which stool from a healthy donor is transplanted into the colon of a recipient, is a successful treatment for recurrent C. difficile infection (rCDI). In a recently published study, investigators from Brigham and Women's Hospital explore how the dynamics of bacterial species may influence the success of FMT in treating rCDI. In Nature Communications, the team presents an algorithm to design personalized probiotic cocktails for patients with unhealthy gut microbiomes due to rCDI.