Single-Cell Genomics as a Next Step for More Informative Fecal Microbiota Transplantation Research

C. difficile infection (CDI) is an infection caused by the bacterium Clostridioides difficile that can cause significant diarrhea and inflammation of the colon, particularly after gut dysbiosis caused by antibiotics. If not treated promptly, it may result in serious complications. To alleviate symptoms of CDI, a medical procedure that involves transferring stool from a healthy donor to a diseased colon, Fecal Microbiota Transplantation (FMT), is administered to patients with at least 2 episodes of CDI or refractory CDI. It is done to restore beneficial bacteria and improve the health of the patient. However, the selection of which donor, or which patient, to yield the best possible results for remission after FMT remains unknown. To gain more clarity on this selection, we want to use the cutting-edge advantage of droplet microfluidics and single-cell genomics as a high-throughput method for acquiring complete bacterial genomes in CDI patients and FMT donors. The primary objective is to reveal within-host diversity in the human gut microbiota from healthy FMT donors and patients with CDI, and to compare changes in the gut microbiota of patients with CDI before and after FMT using single-cell sequencing.