Although diet is a substantial determinant of the human gut microbiome, the interplay between specific foods and microbial community structure remains poorly understood. Coffee is a habitually consumed beverage with established metabolic and health benefits. We previously found that coffee is, among >150 items, the food showing the highest correlation with microbiome components. Here we conducted a multi-cohort, multi-omic analysis of US and UK populations with detailed dietary information from a total of 22,867 participants, which we then integrated with public data from 211 cohorts (N = 54,198). The link between coffee consumption and microbiome was highly reproducible across different populations (area under the curve of 0.89), largely driven by the presence and abundance of the species Lawsonibacter asaccharolyticus. Using in vitro experiments, we show that coffee can stimulate growth of L. asaccharolyticus. Plasma metabolomics on 438 samples identified several metabolites enriched among coffee consumers, with quinic acid and its potential derivatives associated with coffee and L. asaccharolyticus. This study reveals a metabolic link between a specific gut microorganism and a specific food item, providing a framework for the understanding of microbial dietary responses at the biochemical level.

尽管饮食是人类肠道微生物组的重要决定因素，但对特定食物与微生物群落结构之间的相互作用仍然知之甚少。咖啡是一种习惯性饮用的饮料，具有公认的代谢和健康益处。我们之前发现，在 >150 项中，咖啡是与微生物组成分相关性最高的食物。在这里，我们对美国和英国人群进行了多队列、多组学分析，提供了来自总共 22,867 名参与者的详细饮食信息，然后将其与来自 211 个队列 （N = 54,198） 的公共数据进行了整合。咖啡消费与微生物组之间的联系在不同人群中具有高度可重复性（曲线下面积为 0.89），这主要是由溶糖劳森杆菌物种的存在和丰度驱动的。使用体外实验，我们表明咖啡可以刺激溶糖乳杆菌的生长。对 438 个样品的血浆代谢组学确定了咖啡消费者中富集的几种代谢物，其中奎宁酸及其与咖啡和溶糖乳杆菌相关的潜在衍生物。这项研究揭示了特定肠道微生物与特定食品之间的代谢联系，为在生化水平上理解微生物饮食反应提供了一个框架。