This article explores the persistent dysbiosis of the gut mycobiome (fungal microbiome) in patients who have experienced sepsis or trauma, particularly those with chronic critical illness (CCI). The study reveals that the fungal community in CCI patients shifts toward a pathobiome state, which is more susceptible to infection. The fungal community in these patients is dominated by *Candida* spp., while commensal fungal species are depleted. These changes correlate with alterations in the micro-ecological niche involving specific gut bacteria and gut-blood metabolites. The findings indicate that mycobiome dysbiosis persists in both sepsis and trauma settings, even up to two weeks post-injury, highlighting the need to address the increased risk of fungal infections in CCI patients. The study used a prospective observational cohort design, collecting stool and blood samples from healthy controls, sepsis patients, and trauma patients. The mycobiome was analyzed using high-throughput sequencing, and the results showed significant differences in fungal community composition between the groups. The study also found that *Candida* was the most prevalent and significant genus in sepsis and trauma patients, with a strong correlation to pathobiome and metabolomic changes. The findings suggest that targeting mycobiome dysbiosis could be a viable approach to reduce the risk of subsequent fungal infections in critically ill patients. The study has limitations, including the single timepoint sample collection and potential confounding factors. However, it provides important insights into the role of the gut mycobiome in sepsis and trauma and highlights the need for further research into fungal infections in critically ill patients.This article explores the persistent dysbiosis of the gut mycobiome (fungal microbiome) in patients who have experienced sepsis or trauma, particularly those with chronic critical illness (CCI). The study reveals that the fungal community in CCI patients shifts toward a pathobiome state, which is more susceptible to infection. The fungal community in these patients is dominated by *Candida* spp., while commensal fungal species are depleted. These changes correlate with alterations in the micro-ecological niche involving specific gut bacteria and gut-blood metabolites. The findings indicate that mycobiome dysbiosis persists in both sepsis and trauma settings, even up to two weeks post-injury, highlighting the need to address the increased risk of fungal infections in CCI patients. The study used a prospective observational cohort design, collecting stool and blood samples from healthy controls, sepsis patients, and trauma patients. The mycobiome was analyzed using high-throughput sequencing, and the results showed significant differences in fungal community composition between the groups. The study also found that *Candida* was the most prevalent and significant genus in sepsis and trauma patients, with a strong correlation to pathobiome and metabolomic changes. The findings suggest that targeting mycobiome dysbiosis could be a viable approach to reduce the risk of subsequent fungal infections in critically ill patients. The study has limitations, including the single timepoint sample collection and potential confounding factors. However, it provides important insights into the role of the gut mycobiome in sepsis and trauma and highlights the need for further research into fungal infections in critically ill patients.