Data from: Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

There is growing interest in understanding how diet affects the intestinal microbiota, including its possible associations with systemic diseases such as metabolic syndrome. Here we report a comprehensive and deep microbiota analysis of fourteen obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSP), and a weight-loss diet (WL). We analyzed the composition, diversity and dynamics of the faecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR analysis. Additionally, we analyzed faecal short chain fatty acids (SCFA) as a proxy of colonic fermentation, and indices of insulin sensitivity from blood samples. The diet explained around 10% of the total variance in microbiota composition, which was substantially less than the inter-individual variance. Yet, each of the study diets induced clear and distinct changes in the microbiota. Multiple Ruminococcaceae phylotypes increased on the RS diet, whereas mostly Lachnospiraceae phylotypes increased on the NSP diet. Bifidobacteria decreased significantly on the WL diet. The RS diet decreased significantly diversity of the microbiota. The total 16S rRNA gene signal estimated by qPCR correlated positively with the three major SCFAs, while the amount of propionate specifically correlated with the Bacteroidetes. The dietary responsiveness of the individual’s microbiota varied substantially and associated inversely with its diversity, suggesting that individuals can be stratified into responders and non-responders based on the features of their intestinal microbiota.当前学界对饮食如何影响肠道菌群（包括其与代谢综合征等全身性疾病的潜在关联）的研究兴趣与日俱增。本研究针对14名肥胖男性展开全面深入的肠道菌群分析，受试者分别食用添加抗性淀粉（Resistant Starch, RS）、非淀粉多糖（Non-starch Polysaccharides, NSP）的完全可控膳食，以及减重膳食（Weight-loss Diet, WL）。研究通过系统发育微阵列与定量聚合酶链式反应（Quantitative PCR, qPCR），分析了每种膳食模式下粪便菌群的组成、多样性与动态变化；此外还通过粪便样本检测了短链脂肪酸（Short Chain Fatty Acids, SCFA，作为结肠发酵的替代指标），并通过血液样本分析了胰岛素敏感性相关指标。膳食因素仅能解释菌群组成约10%的总变异度，远低于个体间差异带来的变异水平。但本研究涉及的每种膳食均会使肠道菌群产生清晰且独特的变化：食用RS膳食的受试者体内，多种瘤胃球菌科（Ruminococcaceae）系统型丰度显著升高；食用NSP膳食的受试者则以毛螺菌科（Lachnospiraceae）系统型丰度上升为主；食用WL膳食的受试者体内双歧杆菌（Bifidobacteria）丰度显著降低。此外，RS膳食会显著降低肠道菌群的多样性。通过qPCR检测得到的总16S rRNA基因信号与三种主要短链脂肪酸呈正相关，而丙酸的含量则与拟杆菌门（Bacteroidetes）特异性相关。个体肠道菌群对膳食的响应程度存在显著差异，且与菌群多样性呈负相关，这表明可根据个体肠道菌群的特征将其划分为膳食响应者与非响应者。