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While some strains are used as probiotics, others have been isolated from cases of botulism and necrotizing enterocolitis (NEC) in preterm neonates. We identify a unique genomic feature of this species, namely a highly conserved extrachromosomal element of ~0.8\u2009Mb. This replicon satisfies the three principal criteria used to define a chromid, which include the possession of core genes that are encoded on the main chromosome in other species. Although <jats:italic>C. butyricum<\/jats:italic> is the type species of <jats:italic>Clostridium<\/jats:italic>, we find that the possession of a chromid is not a typical feature of members of this genus and represents a unique genomic fingerprint of the species <jats:italic>C. butyricum<\/jats:italic>. Furthermore, we show that pathogenic <jats:italic>C. butyricum<\/jats:italic> strains from the sequenced examples are not monophyletic, which suggests that virulence has evolved multiple times from related non-pathogenic ancestors. However, we were able to identify common genes which are found exclusively in these pathogenic strains. In addition to the botulinum neurotoxin genes, these include a novel set of genes involved in the biosynthesis of a capsular polysaccharide (CPS), and genes that confer the ability to utilize the mucin-derived sugar <jats:sc>l<\/jats:sc>-fucose, which may provide a competitive advantage for growth in the colon. 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