PROJECT SUMMARY Fecal microbiota transplantation (FMT) is an established treatment for patients with recurrent Clostridioides difficile infection (CDI). Although most patients with CDI can be successfully treated, the subset of acutely ill patients with severe and fulminant CDI is a much greater challenge, with high rates of colectomy and mortality. Furthermore, a variety of safety concerns remain for FMT. The risk of transmission of harmful microbes is highlighted by recent reports of transmission of multi-drug resistant organisms and enteropathogenic E. coli (EPEC). In addition, although most work has focused on bacteria, FMT also transfers non-bacterial microorganisms, and the clinical impact of these microbes may be important in fully understanding the clinical implications of FMT. Because the gut microbiota also plays a role in the pathogenesis of chronic medical conditions (e.g., diabetes, cancer, heart disease), FMT has the potential to cause chronic conditions that might take years to manifest clinically. Finally, the field is rapidly evolving with the development of commercial products formulated with live microorganisms, known as live biotherapeutic products (LBPs). Thus, critically important questions regarding the real-world safety and effectiveness of FMT and LBPs remain unanswered. The FMT National Registry is a uniquely suited resource to study these key issues. The Registry includes 32 North American sites (and 19 additional centers pending) with an established infrastructure to collect clinical data on FMT donors and recipients and a separate portal to collect information from FMT recipients. The Registry’s link to an independent biobank also provides a rich source for studying manipulation of the gut microbiota in humans. Our first specific aim is to expand knowledge on the long-term safety and effectiveness of FMT by A) continuing systematic collection of clinical metadata up to 10 years post-FMT to better define safety, including risk of developing chronic medical conditions, with incidence rates for predefined chronic conditions in Registry participants compared with a control group of patients from a national database with multiply recurrent CDI not treated with FMT; B) determining real-world estimates of effectiveness of FMT and LBPs to treat hospitalized patients with severe/fulminant CDI and identify factors associated with cure; and C) expanding the registry to include new LBPs, assessing effectiveness for CDI as compared to FMT in real-world populations and examining off-label use of LBPs for indications beyond CDI. The second specific aim is to characterize the potential value of shotgun metagenomics sequencing (SMS) and data analytics as a platform technology to identify and characterize potentially harmful microbes transmitted by FMT or LBPs by first determining the sensitivity and specificity of SMS to identify and characterize bacterial pathogens using the emerging pathogen, atypical EPEC (aEPEC) as a prototype....