Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Sci Rep. 2018 Aug 23;8(1):12699. doi: 10.1038/s41598-018-30783-1.
Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host's microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient's microbiota.
饮食干预可操纵人体肠道微生物组以改善健康，越来越受到关注。然而，由于缺乏对饮食对宿主微生物组的定量影响的理解，其设计受到限制。我们在健康的人类队列中进行了一项高度受控的饮食扰动实验，在该实验中，针对标准化背景添加了个体微量营养素。我们发现，在摄入益生元添加物的参与者中，特定微生物具有强烈且可预测的反应，这表明人类肠道中存在精细的资源划分。未发现对非益生元微量营养素的可预测反应。令人惊讶的是，与复杂多变的饮食相比，我们没有观察到微生物组日常可变性的降低，反而发现了饮食引起的压力和相关生物多样性丧失的证据。我们的数据提供了对低复杂性饮食对肠道微生物组影响的深入了解，并表明有效的个性化饮食干预将依赖于对患者微生物组的功能、菌株水平的特征描述。
