Gut microbiome changes in critically ill adults: a systematic review of longitudinal sequencing studies

Abstract

Objective: Critical illness profoundly alters the gut microbiome, yet its temporal evolution and clinical relevance remain unclear. This systematic review aimed to synthesize evidence from longitudinal sequencing studies describing gut microbiome changes in critically ill adults and their association with clinical outcomes. Methods: We systematically searched MEDLINE®, Scopus, and Cochrane CENTRAL from inception to May 2025 for longitudinal observational studies analyzing gastrointestinal samples by sequencing in adult critically ill patients at ≥ 2 times points. Extracted data included study and patient characteristics, as well as microbiome outcomes, including alpha and beta diversity metrics and taxonomic abundance profiles. Due to heterogeneity, we undertook a structured descriptive synthesis: alpha diversity results were grouped by trajectory and compared across intensive care unit populations; beta diversity findings were tabulated and narratively synthesized; and reported associations with mortality and multidrug-resistant organism colonization were summarized narratively. Risk of bias was assessed with RoBANS 2, and certainty of evidence with GRADE. Results: Thirty-six studies comprising 2,067 critically ill adults were included. Most used 16S rRNA sequencing targeting the V4 region. A decline in alpha diversity was reported in 18 out of 31 studies, while 8 found no change and 4 mixed patterns. Beta diversity shifts over time were reported in 11 studies. Taxonomic analyses consistently revealed the expansion of opportunistic taxa such as Enterococcus, Klebsiella, and other Enterobacteriaceae, alongside the depletion of obligate anaerobes, including Blautia, Coprococcus, and Faecalibacterium. Early low diversity and pathogen-dominated microbiomes were associated with increased mortality. Associations with multidrug-resistant organism colonization were inconsistent. Certainty of evidence (GRADE) for all outcomes was rated very low due to heterogeneity and imprecision. Conclusion: Longitudinal sequencing studies demonstrate progressive loss of microbial diversity and enrichment of pathogenic taxa during critical illness. These shifts, particularly Enterococcus and Klebsiella overgrowth, correlate with adverse outcomes and may reflect the combined effects of antibiotics, disease severity, and critical care interventions. Standardized sampling, sequencing, and reporting protocols are needed to enable meta-analytic synthesis and guide microbiome-targeted interventions in the intensive care unit.