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<i>Boswellia serrata</i>, commonly known as frankincense, has been used for centuries as a natural anti-inflammatory and anti-microbial remedy for many illnesses. However, the effect of the bioactive ingredient of it, 3-O-acetyl-11-keto-b-boswellic acid (AKBA), on both the gut microbiome and blood metabolites, is not known. In this study, we observe the effect of this isolated active ingredient orally on both male and female mice. Gut microbiota and blood metabolites were determined at the beginning and end of a 14-day consumption period. AKBA significantly decreased gut bacterial richness in male mice, and had no effect on female mice. <i>Akkermansia muciniphila</i>, associated with weight loss and anti-inflammation, was found to be significantly increased in both male and female mice, along with an increase in <i>Bifidobacterium</i> in female mice. <i>Akkermansia muciniphila</i> and <i>Bifidobacterium</i> were plated on media containing varying levels of AKBA (0%, 0.001%, 0.01%, and 0.1%). All concentrations of AKBA completely inhibited growth of <i>Akkermansia muciniphila</i> but had no effect on <i>Bifidobacterium</i>. Several blood metabolites differed with AKBA between both males and females. These results show the potential benefits of dietary <i>Boswellia serrata</i> on the modulation of gut microbiome composition, along with differences between sexes.