5-Pentadecylresorcinol (C15) is a natural alkylresorcinol that has been shown to protect against complications caused by imbalanced nutrition. Although the exact mechanisms of beneficial activity of C15 are not known, we assume that the protective effects of C15 on metabolic health are mediated by their modulatory influence on the composition of the intestinal microbiota and functional activity. Cobamides and vitamin B12 are believed to be crucial modulators of mammalian gut ecosystems. We proposed that C15 may influence the representation of enzymes and pathways for vitamin B12 synthesis in the gut microbiome, providing compositional and functional changes in the microbial community. High-throughput metagenome sequencing of the contents of the small and large intestines of C57Bl6 mice fed a regular or high-fat diet with or without C15 supplementation was performed followed by reconstruction of the metabolic activity of the microbiota to clarify the role of C15 in vitamin B12 synthesis by the gut microbiota. It has been established that C15 significantly increases the representation of the cobalamin salvage pathway and enzymes in the microbiome of the large intestine of mice fed a high-fat diet. The genera Clostridium, AF12, and [Ruminococcus] had shown the highest number of correlations with enzymes for B12 synthesis and were negatively associated with the representation of probiotic bacteria. Therefore, the beneficial effect of C15 on the gut microbiota community can be achieved by modulating B12 synthesis that, in turn, serves as one of the key regulators of gut microbiota ecology.