The gut microbiota has been linked to various neurological disorders via the gut–brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer’s, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after 3 months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing, both taxonomic and functional profiles were established. Here we report that alpha diversity is not changed significantly during the diet, but differences in both taxonomic and functional composition are detected. Relative abundance of bifidobacteria as well as E. rectale and Dialister is significantly diminished during the intervention. An increase in relative abundance of E. coli is observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicates that bifidobacteria and Escherichia are important contributors to the observed functional shifts. As relative abundance of health-promoting, fiber-consuming bacteria becomes less abundant during KD, we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD.

肠道菌群通过肠脑轴与各种神经系统疾病有关。饮食会影响肠道菌群的组成。生酮饮食（KD）是一种高脂肪，蛋白质充足，低碳水化合物的饮食，旨在治疗儿童的抗治疗性癫痫。已经证实其在减少癫痫发作中的功效，但是其机制仍然难以捉摸。饮食还对多种其他疾病（包括老年痴呆症，抑郁症，自闭症，癌症和2型糖尿病）产生了积极影响。在开始KD之前和饮食3个月后，我们从12例具有抗治疗性癫痫病的儿童中收集了粪便样本。父母没有开始KD并担任饮食控制。应用shot弹枪宏基因组DNA测序，建立了分类学和功能谱。在这里，我们报告饮食中的α多样性没有显着变化，但是在分类学和功能组成方面都存在差异。双歧杆菌的相对丰度以及干预期间大肠埃希氏菌和迪亚尼斯特菌明显减少。在KD上观察到大肠杆菌的相对丰度增加。功能分析揭示了29个SEED子系统的变化，包括减少了涉及碳水化合物代谢的7条途径。这些转变的分解表明双歧杆菌和大肠埃希菌是观察到的功能转变的重要贡献者。随着KD期间相对丰富的促进健康，消耗纤维的细菌数量减少，我们引起人们对饮食对肠道菌群和整体健康的影响的关注。进一步的研究需要调查这些改变对于KD的治疗效果是否必要。