Darobactin derivatives are active in Gram-negative pneumonia and exert reduced pressure on the murine gut microbiome

Abstract Background The rise of multidrug-resistant (MDR) Gram-negative bacteria poses a global health threat. Furthermore, treatment with the remaining antibiotics of last resort often cause profound collateral damage to the host gut microbiome. This dysbiosis - characterized by the depletion of anaerobic commensals - is linked to impaired immunity and adverse clinical outcomes. We investigated the efficacy and ecological impact of optimized darobactin derivatives, a novel class of antibiotics that target the β -barrel assembly machinery (BAM)-complex, to determine if they offer a more selective alternative to broad-spectrum carbapenems. Results In murine models of pneumonia, we demonstrate that the darobactin derivatives darobactin B and B9 effectively reduce bacterial loads caused by Klebsiella pneumoniae ( K. pneumoniae ) and Pseudomonas aeruginosa ( P. aeruginosa ). Notably, darobactin B maintains potent activity against a clinical isolate of multidrug-resistant P. aeruginosa that is resistant to carbapenems and cephalosporins. To evaluate the impact on microbial homeostasis, we performed a head-to-head microbiome analysis comparing systemic administration of darobactin B with the broad-spectrum antibiotic meropenem. While meropenem treatment caused significant reductions in α -diversity and profound shifts in community composition - specifically depleting key anaerobic commensals such as the Lachnospiraceae and Muribaculaceae families - darobactin B treatment left the gut microbial community largely intact. Microbiome profiles in darobactin-treated mice remained statistically comparable to both vehicle-treated and untreated controls, preserving the abundance of critical commensal taxa. Conclusions Our findings demonstrate that darobactin derivatives are highly effective against clinically relevant Gram-negative pneumonia pathogens while exerting minimal pressure on the murine gut microbiome. By sparing the anaerobic commensal landscape, darobactin derivatives represent a promising new class of "microbiome-sparing" antibiotics. This selectivity may offer significant clinical advantages, including the prevention of antibiotic-induced dysbiosis and the maintenance of host-microbiome homeostasis during the treatment of critical infections.