Currently, lung infections caused by multidrug-resistant organisms (MDROs) represent a significant global health burden. In the intensive care unit (ICU), the administration of antibiotics, opioids, proton pump inhibitors (PPIs), vasoconstrictors, and parenteral nutrition-combined with the underlying severity of critical illness-leads to profound disruption of the gut microbiota, which may concurrently impair pulmonary microecology and negatively influence long-term patient outcomes. Although pulmonary microecology has garnered increasing scientific attention, the potential causal link between gut dysbiosis and the development of pulmonary microbial imbalance remains poorly elucidated. As such, it is currently unclear whether gut dysbiosis in patients with MDRO-related pulmonary infection contributes to or exacerbates pulmonary microecological disturbances. This study aims to characterize differences in gut microbiota composition and pulmonary microecology between ICU patients with and without MDRO-associated pulmonary infection, and to investigate the association between alterations in gut microbiota and changes in the pulmonary microbial environment. Fecal microbiota transplantation (FMT) is a therapeutic intervention involving the transfer of functionally intact microbial communities from healthy donors to recipients, with the objective of restoring a disrupted gut microbiota and treating both gastrointestinal and systemic conditions. Evidence suggests that FMT effectively reduces intestinal colonization by MDROs and prevents secondary infections in non-ICU populations. Over the past decade, FMT has demonstrated transformative potential in managing refractory intestinal and extra-intestinal diseases, offering a novel, mechanism-driven strategy for modulating host microbial ecosystems. These findings indicate that FMT not only facilitates the restoration of a balanced gut microbiota but may also reduce recurrent infections by suppressing the proliferation of drug-resistant bacterial strains. Given that gut-resident microorganisms serve as a major reservoir for enterogenic infections, hospital-acquired bacteremia, and ventilator-associated pneumonia, this project will conduct a prospective, randomized controlled trial (RCT) in critically ill patients admitted to the ICU with pulmonary infection-specifically targeting those eligible for antibiotic de-escalation and exhibiting clinical features of food intolerance syndrome. FMT will be administered via a nasojejunal tube to correct gut dysbiosis induced by broad-spectrum antimicrobials and other iatrogenic factors. The primary objectives are to evaluate the efficacy and safety of FMT in promoting the restoration of pulmonary microbial homeostasis and to assess its impact on clinically relevant outcomes, including length of stay in the ICU, ICU mortality, in-hospital mortality, and 28-day all-cause mortality.