Intestinal dysbiosis in critically ill patients: a case–control study of Enterobacteriaceae enrichment and reduced microbial diversity

Introduction Critical illness disrupts gut microbiota homeostasis, potentially exacerbating systemic inflammation and adverse outcomes. This study investigates gut dysbiosis patterns in ICU patients, with a focus on Enterobacteriaceae enrichment and microbial diversity loss, to identify biomarkers and therapeutic targets. Methods In this case–control study, 37 ICU patients (sepsis: n = 17; non-sepsis: n = 20) and 20 healthy controls were enrolled. Fecal samples underwent 16S rRNA sequencing (V3–V4 regions). Microbial diversity (Shannon/Simpson indices), <mark>beta diversity (Bray–Curtis PCoA)</mark>, and taxonomic differences (LEfSe, LDA > 2.5) were analyzed using QIIME2 and R. Results Critically ill patients showed reduced alpha diversity vs. controls (Shannon p = 0.04; Simpson p = 0.04). Enterobacteriaceae (phylum Proteobacteria ) were significantly enriched in ICU patients (LDA = 4.2, p < 0.01), while Ruminococcus dominated controls. Beta diversity differed markedly (PERMANOVA R 2 = 0.199, p = 0.001). No diversity differences were observed between sepsis/non-sepsis subgroups ( p > 0.05). Conclusion ICU patients exhibit gut dysbiosis characterized by Enterobacteriaceae expansion and diversity loss, independent of sepsis status. These findings underscore the gut microbiome’s role in critical illness and support exploring microbiota-targeted interventions (e.g., selective probiotics) to improve outcomes.