Some broad-spectrum antibiotics that disrupt the gut microbiome may raise the risk of complications from stem cell transplantation, according to a new study evaluating data from more than 850 transplant patients, as well as from mice. The findings suggest that selecting antibiotics that spare "good" bacteria may help protect against graft-versus-host disease (GVHD), which occurs when transplanted donor cells, recognizing their new home as foreign, attack the recipient's body. Transplant patients vulnerable to life-threatening bacterial infections are often treated with broad-spectrum antibiotics. To better understand the effects of antibiotic treatment on GVHD, Yusuke Shono and colleagues mined the clinical records of 857 allogeneic hematopoietic stem cell transplant patients. Treatment with some broad-spectrum antibiotics, compared to antibiotics with more limited activity, correlated with greater risk of death from GVHD. Analysis of stool samples from some of the patients revealed that broad-spectrum antibiotics perturbed the gut microbiome, killing off certain protective bugs. In mice treated with various antibiotic regimens following stem cell transplantation, those given broad-spectrum antibiotics developed more severe GVHD. The drugs seemed to spur the growth of bacteria known to degrade the protective mucus lining the colon, breaking down gut barrier function. While the findings remain to be confirmed in clinical trials, they caution against the use of broad-spectrum antibiotics in transplant patients at risk of GVHD.