Metagenomic and meta-transcriptomic changes in the salivary microbiome of female xerostomic patients

Xerostomia is the subjective complaint of dry mouth mainly associated with salivary flow reduction and salivary gland hypofunction. The condition significantly impacts individuals’ oral health and quality of life. Complications of xerostomia include difficulty speaking, chewing, and swallowing. Autoimmune diseases, xerogenic medications, and radiation therapy are common causes of xerostomia. Our objective was to determine oral targeted 16S metagenomic and full meta-transcriptomic taxonomic profiles associated with xerostomia caused by polypharmacy and auto-immune disease by using integrative multi-omics analysis. Female individuals ( N = 41 total) consisting of xerostomic patients (XP; n = 28), and non-xerostomic control subjects (NX; n = 13) were recruited. Salivary V1-V3 16S rRNA gene next generation sequencing (NGS) was performed. Metagenomic 16S gene sequence reads were processed with DADA2 and QIIME2 pipelines for taxonomic composition. Meta-transcriptomic RNA sequences were processed with SAMSA2 program to identify active microbial taxa. DESeq2 and DIABLO programs were used for differential analysis and multi-omics integration. Metagenomic 16S gene sequence analysis revealed a shift in beta -diversity community composition between NX and XP groups (Unweighted UniFrac and Bray-Curtis PERMANOVA 9999 permutations, p < 0.05). Prevotella veroralis , Actinomyces unclassified , Scardovia inopinata and Veillonella atypica species were enriched in XP group (p adj < 0.05). Meta-transcriptomic analyses revealed a shift in both alpha- and beta- diversity (Shannon and Simpson; Bray-Curtis PERMANOVA 9999 permutations, p adj < 0.05) and 54 significant differentiating species in XP groups (p adj < 0.05). Based on meta-transcriptome analysis alone, Rothia mucilaginosa enrichment and depletion of Haemophilus parainfluenzae and Fusobacterium nucleatum were observed in XP group. DIABLO integration revealed 30 correlated species pairs across metagenome and meta-transcriptome analysis. Xerostomic patients exhibited significant restructuring of oral microbial composition based on combined metagenomic and meta-transcriptomic analyses. Key taxa associated with xerostomia included S. inopinata , V. atypica , R. mucilaginosa , H. parainfluenzae , and F. nucleatum , reflecting a shift toward acidogenic and hypoxia-associated species consistent with lasting salivary hypofunction. These taxonomic shifts highlight the potential for microbiome-informed intervention strategies to mitigate xerostomic progression. Further research is needed to assess microbiome related pathway alterations to devise targeted treatment.