Longitudinal gut microbiome dynamics in neurosurgical ICU patients: Enterococcus expansion as a feature of microbial restructuring

Background Gut microbiota alterations are commonly observed in critical illness, but their temporal dynamics in neurosurgical ICU patients remain insufficiently characterized. This study aimed to describe postoperative microbial trajectories and their clinical context during ICU stay. Methods We conducted a longitudinal study of 39 postoperative neurosurgical ICU patients, with 101 rectal swab samples collected on ICU Days 1, 7, and 14. Microbiota profiles were generated using 16S rRNA sequencing. Temporal shifts and configurations were analyzed using diversity analyses, PERMANOVA, and OTU-level clustering. Clinical features associated with Enterococcus (OTU502) abundance were examined using regression models, and microbiota–clinical relationships were further explored using redundancy and variance partitioning analyses. Results Patients were stratified into short-stay (< 14 days) and long-stay (≥ 14 days) groups. Alpha diversity showed a mild, non-significant decline by Day 7 with a slight increase at Day 14 in long-stay patients, while beta diversity demonstrated significant temporal restructuring. Genus-level analyses revealed stay-dependent changes: short-stay patients showed early loss of anaerobic genera and enrichment of Enterococcus by Day 7, whereas long-stay patients exhibited persistent anaerobe depletion and later emergence of Enterococcus . OTU clustering identified two profiles dominated by Enterococcus (OTU502) or Escherichia–Shigella (OTU967). Higher OTU502 abundance at Day 7 was more frequently observed in patients with greater illness severity and lower GCS scores. Prolonged probiotic use showed a non-significant trend toward a lower likelihood of high OTU502 abundance. Measured clinical variables accounted for a limited proportion of observed microbial variance (3–7%). Conclusions Neurosurgical ICU patients displayed time-stratified microbial trajectories. Enterococcus (OTU502) enrichment represents a consistent feature of microbiota restructuring during ICU stay. These findings provide a descriptive framework for understanding microbiome dynamics in neurosurgical ICU patients. Trial registration Chinese Clinical Trial Registry (ChiCTR2000031760). Registered on 9 April 2020.