Background: Mucosal barrier injury (MBI) is a recognized risk factor for blood stream infection (BSI) in people undergoing chemotherapy, permitting expansion and translocation of enteric pathobionts; a phenomenon now clinically referred to as MBI-associated laboratory-confirmed BSI. Although recognized to originate from endogenous gastrointestinal sources, MBI-associated BSI continue to be treated with antibiotics; a counterintuitive approach that may increase infection risk by depletion of the host microbiome. While this point has been argued in numerous clinical studies and opinion pieces, there are few data describing mechanistic strategies to decrease MBI-associated BSI, reflecting a lack of translationally robust preclinical models. Here, we report on a new translational model of MBI caused by the chemotherapeutic drug, melphalan. We aimed to identify candidate pathways to strengthen the mucosal barrier and prevent infection, prompting new antibiotic stewardship initiatives. Results: Melphalan caused dose-dependent, systemic toxicity characterized by severe neutropenia, self-limiting intestinal injury, inflammation and biphasic fever, all of which were clinically and molecularly consistent with the dynamics of melphalan conditioning. The fecal microbiome following melphalan was depleted in richness and commensal taxa, impairing colonization resistance and the microbial metabolome and prompting expansion of enteric pathogens. Breakdown of the intestinal barrier was initiated by melphalan and exacerbated by mucotoxic bile acids.Conclusions: MBI-associated BSI is simply a form of collateral damage resulting from breakdown of the gastrointestinal microenvironment and self-perpetuating injury. Efforts to intervene early in these sequelae are therefore of great clinical significance to restrict antibiotic use and mitigate their detrimental consequences on treatment outcomes and antibiotic resistance. Our data support interventions targeting the host microbiome and metabolome due to its ubiquitous control of inflammation, mucosal injury, bile acid transformation; all of which contribute to infection risk in cancer.