<p>Carbapenem-resistant <i>Enterobacteriaceae</i> (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of <i>Bacteroidetes</i> to <i>Proteobacteria</i>. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.</p> Graphical abstract <p>Restoring gut eubiosis using microbiome therapeutic PMC101 to mitigate dysbiosis and combat CRE infections. The graphical abstract illustrates the role of microbiome therapeutic PMC101 in maintaining and restoring gut eubiosis. The diagram illustrates how the administration of antibiotics and CRE disrupts the gut microbiota, leading to dysbiosis characterized by reduced microbial diversity and increased severity of infections. PMC101 mitigates microbial disruption and promotes the restoration of eubiosis, thereby reducing the severity of infections and restoring gut health. The left-to-right flow of the illustration highlights the progression from a healthy eubiotic state to dysbiosis caused by external factors and the prophylactic intervention of PMC101 to reverse these adverse effects. Key indicators include eubiosis state on the left y-axis and infection severity on the right y-axis. The transition arrows represent the changes in microbial balance with or without the intervention of PMC101.</p>