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.

饮食可以调节肠道微生物群，进而影响免疫系统。在这里，我们确定了两种针对微生物群的饮食干预措施，即植物性纤维和发酵食品，如何影响健康成年人的人体微生物群和免疫系统。使用为期 17 周的随机前瞻性研究（n = 18/组）结合微生物组和宿主的组学测量，包括广泛的免疫分析，我们发现了饮食特异性效应。尽管微生物群落多样性稳定，但高纤维饮食增加了微生物组编码的聚糖降解碳水化合物活性酶 (CAZymes)。尽管细胞因子反应评分（主要结果）没有变化，但高纤维消费者的三个不同的免疫轨迹与基线微生物群多样性相对应。或者，高发酵食品饮食稳步增加了微生物群的多样性并减少了炎症标志物。这些数据强调了将饮食干预与深度和纵向免疫和微生物组分析相结合如何提供个性化和全人群的洞察力。发酵食品可能有助于对抗工业化社会中普遍存在的微生物组多样性减少和炎症增加。