From root to tips: sporulation evolution and specialization inBacillus subtilisand the intestinal pathogenClostridioides difficile

Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the modelBacillus subtilis, an aerobic species, and in the intestinal pathogenClostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation. Using the genes involved in the process inB. subtilisandC. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macro-evolutionary framework we show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of theB. subtilisgroup and within the Peptostreptococcaceae family, which includesC. difficile. We also show that early and late sporulation regulons have been co-evolving and that sporulation genes entail greater innovation inB. subtiliswith many Bacilli-lineage restricted genes. In contrast,C. difficilemore often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota and an adjustment of sporulation to this particular ecosystem.