Gut-microbiota-targeted diets modulate human immune status

Diet modulates the gut microbiome, which in turn can impact the immune system. Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, we found diet-specific effects. The high-fiber diet increased microbiome-encoded glycan-degrading carbohydrate active enzymes (CAZymes) despite stable microbial community diversity. Although cytokine response score (primary outcome) was unchanged, three distinct immunological trajectories in high-fiber consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society. [Display omitted] •Diet intervention with systems profiling reveals links in diet-microbiome-immune axis•High-fiber diet changes microbiome function and elicits personalized immune responses•Fermented-food diet increases microbiome diversity and decreases markers of inflammation A prospective randomized multiomics study in humans investigating the longitudinal effects of a high-fiber or fermented-food diet shows their differential effects on the diversity of the microbiome, with the latter having a noticeable impact on reducing inflammatory markers and modulating immune responses.