The intestinal microbiota consists of complex populations of microbes that contribute to nutrient absorption, vitamin production, immune development and resistance to infection. Antibiotics, while highly effective at treating and preventing infections, can have adverse effects on the intestinal microbiota. We have found that antibiotic-administration can dramatically reduce the density and diversity of bacteria in the intestines of mice (Ubeda et al. Journal of Clinical Investigation, 2010; Buffie et al. Infection and Immunity, 2012).
We have found that patients undergoing allogeneic hematopoietic stem cell transplantation undergo dramatic changes in microbiota composition, some of which correlate with the subsequent development of bloodstream infection (Taur et al. Clinical Infectious Diseases, 2012), and our studies have also demonstrated that loss of microbiota diversity following transplantation is correlated with higher mortality rate (Taur et al. Blood, 2014).