Abstract: Autoimmune hepatitis (AIH) is a chronic inflammatory disorder with complex
immunopathogenesis. Dysbiosis has been linked to many autoimmune diseases, but its detailed role
in autoimmune hepatitis (AIH) still needs rigorous evaluation, especially in Egypt. We aimed to
identify the shift in the gut microbiota profile and resultant metabolic pathways in AIH Egyptian
patients compared to healthy individuals. Stool samples were collected from 15 AIH-naive patients
and from 10 healthy individuals. The V3-V4 hyper-variable regions in16S rRNA gene was amplified
and sequenced using Illumina MiSeq platform. Significantly lower bacterial diversity in AIH patients
was found compared to the controls. A phylum-level analysis showed the overrepresentation of
Firmicutes, Bacteroides, and Proteobacteria. At the genus level, AIH-associated enrichment of
Faecalibacterium, Blautia, Streptococcus, Haemophilus, Bacteroides, Veillonella, Eubacterium, Lachnospiraceae
and Butyricicoccus was reported in contrast to Prevotella, Parabacteroides and Dilaster, which were
significantly retracted in such patients. Overall, the predicted metabolic pathways associated with
dysbiosis in AIH patients could orchestrate the potential pathogenic roles of gut microbiota in
autoimmune disease, though not in a disease-specific manner, calling for future large-scale studies.
Keywords: bioinformatics; microbiome; autoimmune hepatitis