Dynamical and highly personalized responses in the microbial composition and short-chain fatty acids of the human gut microbiome to inulin intervention

Inulin is widely used as a prebiotic to modulate the composition and short-chain fatty acids (SCFAs) metabolism of the human gut microbiota. While studies have revealed that the response of gut microbiota to inulin intervention can be personalized, characterization of the individualized dynamics following inulin intervention remains incomplete and requires further investigation, aimed at enhancing personalized nutritional interventions. In this study, we tracked the compositional and SCFAs metabolic shifts in the gut microbiome for 10 days of inulin intervention in a cohort of 20 healthy volunteers. We found that inulin exerts profound and personalized effects on the dynamics of the human gut microbiota compositions, while exhibiting a relatively moderate influence on the stool SCFA profiles. In addition, we observed inter-individual differences in the response patterns to inulin during temporal microbial shifts. Furthermore, we observed that alterations in stool SCFA profiles did not consistently align with changes in the gut microbiota compositional profiles, and notably, the baseline microbiota profile did not exhibit a correlation with the inulin-induced microbiota response. Specifically, inulin selectively enriched particular species, including Bifidobacterium adolescentis, Bifidobacterium longum, Anaerostipes hadrus, and Bacteroides xylanisolvens. Moreover, we evaluated whether in vitro culture of human stool-derived microbial communities can be used to predict the personalized responses to inulin. We found that the compositional changes in vitro (i.e. inulin stimulates the growth for certain species) were comparable with in vivo observations, while personalized responses in SCFAs were not consistent between in vitro and in vivo. Our study highlights significant individual differences in response to inulin, thereby advocating for further research based on larger cohort studies in human populations rather than relying on in vitro culturing to assess and predict inulin's prebiotic benefits.

菊糖（Inulin）作为一种益生元被广泛应用，用于调控人体肠道菌群的组成与短链脂肪酸（short-chain fatty acids, SCFAs）代谢。尽管已有研究表明肠道菌群对菊糖干预的响应存在个体化差异，但目前对于菊糖干预后菌群的个体化动态变化特征仍未完全阐明，有待进一步研究以优化个性化营养干预策略。本研究针对由20名健康志愿者组成的队列开展了为期10天的菊糖干预试验，追踪了肠道微生物组组成与SCFAs代谢的动态变化。研究结果显示，菊糖对人体肠道菌群组成的动态变化具有显著且个体化的调控作用，但对粪便SCFAs谱的影响相对温和。此外，本研究观察到在菌群随时间变化的过程中，个体对菊糖干预的响应模式存在显著差异。进一步分析发现，粪便SCFAs谱的变化与肠道菌群组成的变化并不完全一致；值得注意的是，受试者的基础菌群特征与菊糖诱导的菌群响应之间并无相关性。具体而言，菊糖可选择性富集特定菌种，包括青春双歧杆菌（Bifidobacterium adolescentis）、长双歧杆菌（Bifidobacterium longum）、哈氏厌氧杆状菌（Anaerostipes hadrus）和解木聚糖拟杆菌（Bacteroides xylanisolvens）。此外，本研究还评估了基于人体粪便来源菌群的体外培养体系是否可用于预测个体对菊糖的响应情况。研究发现，体外体系中的菌群组成变化（即菊糖可促进特定菌种的增殖）与体内观测结果较为一致，但粪便SCFAs的个体化响应在体外与体内实验中并不一致。本研究凸显了个体对菊糖干预响应的显著差异，因此呼吁未来开展基于更大规模人体队列的研究，而非仅依靠体外培养体系来评估和预测菊糖的益生元功效。