Omics-analyses of Fermented Onion pickle in Shaping Gut Microbiota and Immune Response in Women: A Community-Based Trial in Pakistan

Abstract A fermented-food intervention trial conducted in Pakistan suggested beneficial changes in the composition of the gut microbiota in healthy women. Using a subset (n=17) of the same participants, this study further investigates the impact of fermented food (onion pickle) on gene expression levels using RNA transcriptomics, with a focus on host–microbiome interactions. After consuming pickles (50g/day) for eight weeks, blood and stool samples of participants were collected at baseline and post-intervention to assess inflammatory markers, 16S rRNA gene sequencing, clinical parameters, and RNA sequencing. Among inflammatory biomarkers, lipocalin (LCN-2) levels significantly decreased (pre=86.5±80.1ng/mL, post=61.0±59.0 ng/mL, p=0.04, paired T-test). Additionally, the intervention downregulated pathways (p