Oral and rectal microbiome composition in intracranial aneurysm patients: a 16 S rRNA amplicon sequencing study

Intracranial aneurysms can rupture and cause subarachnoid haemorrhage, yet their pathophysiology remains incompletely understood. Bacterial involvement has been proposed, although evidence remains inconsistent. We investigated the presence of bacterial genomic material in aneurysm vessel walls and characterised the oral and rectal microbiome using high-resolution 16 S rRNA amplicon sequencing with DADA2-based amplicon sequence variant (ASV) analysis and PICRUSt2-inferred functional profiling. In this cross-sectional study, 34 neurosurgical patients (16 with intracranial aneurysms, 18 neurosurgical controls) were included. No bacterial genomic material was detected in aneurysm walls or surrounding intracranial tissues. Microbiome profiling of oral ( n = 29) and rectal ( n = 27) mucosal swabs identified 9,132 ASVs across all samples. Alpha diversity (Shannon entropy, Chao1 richness, Pielou’s evenness, observed ASVs, and Faith’s phylogenetic diversity) did not differ between groups at either site. Beta diversity community composition was similar across Bray–Curtis dissimilarity and weighted and unweighted UniFrac distances (all PERMANOVA p ≥ 0.27, R²<0.05). No genus reached FDR significance after Benjamini–Hochberg correction (178 oral and 201 rectal genera tested). Machine learning classifiers showed no discriminatory ability (Random Forest and XGBoost AUC 0.53–0.60). PICRUSt2-inferred functional profiling of MetaCyc pathways, EC numbers, and KEGG Orthology gene families likewise revealed no FDR-significant differences at either site; nominally elevated pathways in intracranial aneurysm patients included galactitol degradation and NAD biosynthesis II, consistent with trends in Bifidobacterium abundance, but none survived multiple-testing correction. A preliminary OTU-based analysis suggested oral microbiome differences, but these were not reproduced with ASV-level resolution. These findings do not support a distinct mucosal microbiome or functional signature in intracranial aneurysm patients and highlight the importance of high-resolution analytical methods and adequate study power for microbiome research.