Pilot 16s rRNA-based salivary microbiome profiling reveals candidate microbial signatures in autoimmune and immunocompromised patients: An exploratory study from Iraq

Objective: Immune system disorders may disrupt the oral microbiome, but data from Middle Eastern populations remain scarce. This pilot study aimed to characterise salivary bacterial composition in autoimmune and immunocompromised patients compared with healthy controls and to identify potential disease-associated microbial signatures using 16S rRNA metagenomic sequencing. Methods: A comparative cross-sectional pilot study was conducted in Ninewa Governorate, Iraq. Saliva samples from 15 participants (five autoimmune patients, five immunocompromised patients, and five healthy controls) underwent bacterial DNA extraction, 16S rRNA gene amplification, and metagenomic sequencing. Relative abundances were compared using Kruskal–Wallis and Mann–Whitney U tests with false discovery rate (FDR) correction. Linear discriminant analysis effect size (LEfSe) identified candidate discriminatory taxa. Results: The control group showed higher abundance of commensal taxa, particularly Unclassified streptococcus, Salivarius-vestibularis, and Odontolyticus. Autoimmune and immunocompromised groups exhibited increased levels of Nigrescens, Macacae-mucosa-sicca, Fusobacterium nucleatum, and Parainfluenzae. However, no taxon remained statistically significant after FDR correction (q > 0.05). LEfSe analysis identified Nigrescens (LDA = 5.12) and Macacae-mucosa-sicca (LDA = 4.40) as the strongest discriminatory candidates. Conclusions: This pilot study reveals preliminary compositional differences in salivary microbiomes associated with immune dysfunction. The candidate microbial signatures, particularly Nigrescens and Macacae-mucosa-sicca, warrant validation in larger, adequately powered cohorts before clinical application.