Despite the therapeutic efficacy of immune checkpoint inhibitors against some tumours, immune-related side effects remain a large concern. Dubin et al. show in a prospective study of patients with melanoma that new-onset colitis associated with the cytotoxic T lymphocyte-associated antigen 4 (CTLA4) inhibitor ipilimumab correlates with the pre-treatment faecal microbiota. An increase in bacteria from the Bacteroidetes phylum and in microbial pathways of polyamine transport and B vitamin synthesis correlated with increased colitis resistance.