Fecal microbiota transplantation (FMT) has changed the standard of care for Clostridium difficile infection. However, there is limited data focusing on efficacy and safety profile of FMT in patients with C. difficile infection with underlying inflammatory bowel disease (IBD), including the risk of IBD flare. Recently, there is also emerging evidence supporting the role of FMT to treat IBD including promising randomized trials in ulcerative colitis. However, with heterogeneity across these studies, the clinical application of this emerging therapy has yet to be fully elucidated. Here, we aim to review the current landscape of this rapidly developing field, mapping the efficacy and safety of FMT (1) to treat C. difficile infection in patients with IBD, (2) to treat underlying IBD, and (3) outline ongoing clinical trials and the future of the microbiome space.

The gastrointestinal microbiome is intrinsically linked to the spread of antibiotic resistance. Antibiotic treatment puts patients at risk for colonization by opportunistic pathogens like vancomycin resistant Enterococcus and Clostridioides difficile by destroying the colonization resistance provided by the commensal microbiota. Once colonized, the host is at a much higher risk for infection by that pathogen. Furthermore, we know that microbiome community differences are associated with disease states, but we do not have a good understanding of how we can use these changes to classify different patient populations. To that end, we have performed a multicenter retrospective analysis on patients who received fecal microbiota transplants to treat recurrent Clostridioides difficile infection. We performed 16S rRNA gene sequencing on fecal samples collected as part of this study and used these data to develop a microbiome disruption index. Our microbiome disruption index is a simple index that is predictive across cohorts, indications, and batch effects. We are able to classify pre-fecal transplant vs post-fecal transplant samples in patients with recurrent C. difficile infection, and we are able to predict, using previously-published data from a cohort of patients receiving hematopoietic stem cell transplants, which patients would go on to develop bloodstream infections. Finally, we also identified patients in this cohort that were initially colonized with vancomycin resistant Enterococcus and that 92% (11/12) were decolonized after the transplant, but the microbiome disruption index was unable to predict such decolonization. We, however, were able to compare the relative abundance of different taxa between the two groups, and we found that increased abundance of Enterobacteriaceae predicts whether patients were colonized with vancomycin resistant Enterococcus. This work is an early step towards a better understanding of how microbiome predictors can be used to help improve patient care and patient outcomes.

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The opioid epidemic has claimed the lives of more than 183,000 individuals since 1999 and is now the leading cause of accidental death in the United States. Meanwhile, rates of incarceration have quadrupled in recent decades, and drug use is the leading cause of incarceration. Medication-assisted treatment or MAT (i.e. methadone, buprenorphine) is the gold standard for treatment of opioid use disorder. Incarcerated individuals with opioid use disorder treated with methadone or buprenorphine have a lower risk of overdose, lower rates of hepatitis C transmission, and lower rates of re-incarceration. Despite evidence of improved outcomes, many jails and prisons do not offer MAT to individuals with opioid use disorder. This seems partly due to a scientifically unjustified preference for an abstinence-only treatment approach. The absence of MAT in prisons and jails results in poor outcomes for individuals and poses a public health threat to communities. Furthermore, it disproportionately harms poor communities and communities of color. Health care providers in prisons and jails have an ethical obligation to offer MAT to individuals with opioid use disorder to mitigate risk of infectious diseases, opioid overdose and health disparities associated with incarceration.