Comparative population genomics reveal the genetic features associated with the plant host adaptation of Clostridium butyricum

Plants are increasingly considered as secondary reservoirs for enterics. However, little is known about their population dynamics and the genetic mechanisms during plant colonization. Clostridium butyricum is a gut symbiont of humans and animals and, rarely, a pathogen. Here, 55 strains of C. butyricum isolated from the roots of Paris polyphylla var. yunnanensis provided a new model for understanding plant-host adaptation of enterics. These strains, along with 67 non-endophytic C. butyricum strains (nECB), were examined for population structure, revealing that they diverged into four well-defined lineages, whereas endophytic C. butyricum strains (ECB) from different sources were scattered across two lineages. The population diversity estimate confirmed the genetic distinctiveness among four lineages and uncovered distinct evolutionary processes that might drive the divergence of ECB-related lineages. Frequent gene flow between ECB and nECB suggested that plant-host colonization does not lead to genetic isolation. Extensive recombinations within and between lineages demonstrated the major role of recombination in shaping population genetic structure and diversification in C. butyricum. Additionally, the endophytic variance analysis identified several genes associated with CRISPR, defense systems, and metabolism that contribute to endophytic colonization by C. butyricum. This study provides novel insights into the ongoing adaptation of C. butyricum to plant hosts and illuminates the genetic mechanisms underlying this host transition. By elucidating population structure, gene flow, recombination patterns, and candidate adaptive genes, our findings advance the understanding of host-associated evolution in enteric bacteria.