• The frequency of Bacteroides depends on the acidity of the product. • Body weight gain was significantly correlated with the abundance of Streptococcus sp. • β-glucans resulted in a decrease in Lactobacillus frequency. • Oat ß-glucan contributed to a higher Clostridium sensu stricto and Blautia counts. The effect of glucans on gut microbiota functions is still unclear. Therefore, this study was undertaken to describe the influence of structurally different ß-glucans (oat ß-glucan, curdlan and scleroglucan) on the structure of the gut microbiome in rats. The structure of intestinal microbiota was evaluated by high-throughput sequencing of the16S rRNA gene. Firmicutes and Bacteroidetes were the dominant bacterial phyla in all animals. Oat ß-glucan contributed to a higher prevalence of bacterial genera Clostridium sensu stricto and Blautia , whereas curdlan increased the relative abundance of Akkermansia muciniphila. A positive correlation was noted between the relative abundance of Streptococcus bacteria and the growth rate of rats. The present study demonstrated that the consumption of non-acidified milk gels or acidified milk gels with a β-glucan dose recommended by EFSA (3.0–4.0 g per day) for 28 days did not induce significant changes in the structure of the gut microbiome in rats.