Comparative Analysis of Gut Microbiota Patterns in Irritable Bowel Syndrome, Anxiety, and Autoimmune Disorders

Background/Objectives: The gut microbiota has been increasingly studied in the context of gastrointestinal, neuropsychiatric, and immune-mediated disorders. However, comparative data across these conditions within the same population remain limited. This observational study aimed to perform a comparative analysis of gut microbiota composition across individuals with irritable bowel syndrome (IBS), anxiety disorders (AG), and autoimmune diseases (AI) and healthy controls (HC) from a Romanian cohort, aiming to identify population-specific microbial patterns. Methods: This study included 59 Romanian adults categorized into IBS (n = 27), AG (n = 13), AI (n = 11), and HC (n = 8) groups. Gut microbiota profiles were analyzed using 16S rRNA gene sequencing (NGS), and fecal short-chain fatty acids were quantified by headspace gas chromatography-mass spectrometry. Results: At the phylum level, Actinobacteria showed significantly higher relative abundance in HC compared to both the AI (adjusted p = 0.028) and the AG (adjusted p = 0.023) groups, with the AG-HC difference confirmed by LinDA analysis (FDR-adjusted p = 0.049). At the genus level, Bifidobacterium spp. was significantly lower in the AG compared to HC (adjusted p = 0.036), while Bacteroides spp. showed higher abundance in the AG compared to AI (adjusted p = 0.013), a finding supported by Kruskal-Wallis analysis. Lactate production was significantly lower in both the AI (p = 0.014) and AG (p = 0.038) compared to HC. The Simpson index revealed significantly lower microbial evenness in the AG compared to IBS and AI (FDR-adjusted p = 0.042). Beta diversity analysis identified significant differences in community composition between groups (PERMANOVA: Pseudo-F = 2.395, R² = 0.116, p = 0.039), with the most distinct separation between AI and AG (FDR-adjusted p = 0.048). Spearman correlation analysis revealed strong positive associations between Bifidobacterium and lactate, Bacteroides and the acetate/propionate ratio, and Actinobacteria and lactate (all FDR-adjusted p < 0.001). Conclusions: The present study provides exploratory evidence of disease-associated microbial and functional patterns in a Romanian cohort, with reduced Actinobacteria in the anxiety group as the most robust observation, suggesting a potential role of the gut microbiota in gut-brain-immune interactions and contributing preliminary population-specific data from an underrepresented Eastern European population.