Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains

<i>Clostridium scindens</i> is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, <i>C. scindens</i> ATCC 35704 and <i>C. scindens</i> VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of <i>Clostridioides difficile</i> infection. We determined the presence and absence of bile acid inducible (<i>bai</i>) and steroid-17,20-desmolase (<i>des</i>) genes among <i>C. scindens</i> strains and the features of the pangenome of 34 cultured strains of <i>C. scindens</i> and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the <i>C. scindens</i> cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that <i>C. scindens</i> strains are distributed into two clades, indicating the possible onset of <i>C. scindens</i> separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the <i>C. scindens</i> pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.