Shifts in the fecal microbial community composition are associated with dietary fiber solubility

Abstract

The impact of diet on the microbial composition in the gastrointestinal tract has been well documented. However, quantitation of the role of diet in shaping microbial composition has been difficult due to the presence of factors such as host genetics and environment. We used two genetically identical pigs housed together as a system for isolating diet‐induced changes in the microbiome. We used a withdrawal design across four 14‐d periods with two diets having different solubility of dietary fiber to study the fecal microbial community by 454‐pyrosequencing of the 16S rRNA gene. Shifts in the fecal microbial community composition were assessed with respect to dietary correlations. Similarity analysis revealed that the gut microbiomes from the two different diets clustered separately. Taxa‐based approaches detected significantly different bacteria composition in two different diets. Diversity analysis showed that bacterial diversity was associated with the level of dietary fiber solubility. To conclude, the impact of diet on gut microbiome composition was isolated from host genetics and environment. Diet‐induced changes in gut microbiome composition were observed and found to be reversible within a short time. Our results show that genetically identical pigs can be used as a model system for assessing the influence of diet and other variables on the composition of the gut microbial community.Grant Funding Source: University of Illinois Agricultural Experiment Station, USDA AG 2008–34480‐19328, USDA AG 2008–34480‐19328, USDA/ARS AG 58–5438‐7–317l, USDA/ARS AG 58–5438‐2–307