Variations of phylogenetic niches mediate response patterns of gut bacteria to dietary herbal supplements

Botanical dietary supplements (herbs) are widely used in alternative therapy, but their therapeutic mechanisms are still not fully revealed. A growing number of studies suggest that gut microbiota play a crucial role in therapy with herbal medicines through complicated interplay with the components of these natural products. However, the gut bacterial response and coexistence patterns under treatment with herbal medicines remain unexplored, especially the underlying ecological mechanisms. This has limited the clinical application of herbal medicines. Here, five herbal medicines with different properties were selected to investigate their effects upon the gut bacterial community and identify the drivers which shape gut bacterial diversity and mediate species coexistence patterns in mice. Clarifying the response patterns of gut bacteria to herbal medicines and their drivers will improve our understanding of the interaction mechanisms between them. Our results demonstrate that gut bacterial responses and coexistence patterns were significantly phylogenetically conserved. Variations of phylogenetic niches, affected by community assembly mechanisms, mediated the bacterial response patterns and influenced the robustness of bacterial co-occurrence network. Furthermore, community assembly processes and species pool co-shape the b-diversity patterns of gut microbiota. In conclusion, our study clearly illustrates the variations of gut bacterial response and coexistence patterns under treatments with herbal medicines and the ecological mechanisms behind them. These findings improve our ability to predict how gut bacteria respond to dietary herbal supplements and help to account for the potential therapy mechanism of herbs.