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Background  The gut microbiota has emerged as an important environmental factor associated with obesity, type 2 diabetes, and cardiovascular disease, through its interactions with dietary factors. Therefore, we analyzed the composition of the fecal microbiota and levels of biochemical markers related to metabolic disease according to dietary pattern in Korean adolescents.    Methods  We collected fecal samples from 112 student subjects aged 13–16 years with sufficient information available regarding clinical biomarkers and diet, and performed 16S rRNA targeted gene sequencing.    Results  Regarding bacterial composition according to taxonomic rank, we found that traditional dietary patterns enriched in plant-based and fermented foods were associated with higher proportions of  Bacteroides  ( Bacteroidaceae ) and  Bifidobacterium  ( Bifidobacteriaceae - Actinobacteria ) and a lower proportion of  Prevotella  ( Prevotellaceae ) relative to modified Western dietary patterns (a greater proportion of animal-based foods). Specifically, the proportion of  Bacteroides  ( Bacteroidaceae ) was associated with intake of plant-based nutrients such as fiber; however, that of  Prevotella  ( Prevotellaceae ) was negatively associated with these factors. Additionally, we observed that the increase of  prevotella  ( Prevotellaceae ) and decrease of  Bacteroides  ( Bacteroidaceae ) and  Ruminococcaceae  had a higher risk of obesity. We also found that the traditional dietary pattern was negatively associated with general and central adiposity and levels of clinical biomarkers, including AST, ALT, total cholesterol, triglyceride, hs-CRP, insulin, and HOMA-IR, whereas the positive associations were found for a modified Western dietary pattern.    Conclusions  These findings suggest that the gut microbiota composition differs markedly according to dietary intake and suggest a role for diet in promoting a gut microbiome associated with the pathogenesis of metabolic disease.    Electronic supplementary material  The online version of this article (doi:10.1186/s40795-016-0125-z) contains supplementary material, which is available to authorized users.

Association of dietary patterns with the fecal microbiota in Korean adolescents