Compositional and functional aberrance of the gut microbiota in treatment-naïve patients with primary Sjögren's syndrome

•Lactobacillus salivarius is the most discriminating enriched species in pSS and is even higher in pSS with ILD.•pSS-related gut microbiota carries more virulence genes, most of which are involved in bacterial colonization and invasion.•pSS shares numerous changes of species, pathways and virulence genes in gut microbiata with SLE.•Ruminococcus torques is depleted in pSS but enriched in SLE compared to healthy controls.