Abstract
The diversity of the human gut microbiota is integral to gastrointestinal health and is largely influenced by diet. Probiotics are living bacteria that can provide health benefits when consumed. Fermentation of food encourages the growth of microbes with potential probiotic properties. Previous research studied the relationship between the human gut microbiome and consumption of different diets–specifically fresh versus fermented vegetables–with a focus on taxonomic composition rather than functional profiles. The analysis also focused on non-sex-specific microbiome responses and had poor characterization of the durability and long-term effects of microbial changes from fermented vegetables on the gut. We compared the consumption of fermented vegetables to fresh vegetables to see if they enhance gut microbiota composition and function to promote long-term gut health in women over time. We employed beta diversity analysis with linear mixed-effects of alpha and beta diversity modeling, differential abundance analysis, and functional analysis to investigate the longitudinal outcomes and functional metabolic pathways of fresh versus fermented vegetable consumption on the gut microbiomes of individuals with and without constipation. Our findings show that although cross-sectional analyses revealed no significant difference in gut microbiome beta diversity between the two diets, both diets induced immediate and sustained longitudinal shifts in microbial composition. Longitudinal analysis of alpha diversity revealed consumption of fermented vegetables led to more sustained shifts in microbial composition compared to fresh vegetables. Differential abundance analysis supports the finding that consumption of fermented vegetables created stronger and broader changes in microbial taxa, having both predicted beneficial and non-beneficial host effects. Compared to fresh vegetable consumption, fermented vegetable consumption also enriched specific functional pathways with variable host benefits. These findings can assist the development of dietary strategies that benefit the long-term gut microbial function and health in women.