A genomic update on clostridial phylogeny: Gram‐negative spore formers and other misplaced clostridia

Abstract

Summary: The class C lostridia in the phylum F irmicutes (formerly low‐ G + C G ram‐positive bacteria) includes diverse bacteria of medical, environmental and biotechnological importance. The S elenomonas ‐ M egasphaera ‐ S poromusa branch, which unifies members of the F irmicutes with G ram‐negative‐type cell envelopes, was recently moved from C lostridia to a separate class N egativicutes . However, draft genome sequences of the spore‐forming members of the N egativicutes revealed typically clostridial sets of sporulation genes. To address this and other questions in clostridial phylogeny, we have compared a phylogenetic tree for a concatenated set of 50 widespread ribosomal proteins with the trees for beta subunits of the RNA polymerase ( RpoB ) and DNA gyrase ( GyrB ) and with the 16S rRNA ‐based phylogeny. The results obtained by these methods showed remarkable consistency, suggesting that they reflect the true evolutionary history of these bacteria. These data put the S elenomonas ‐ M egasphaera ‐ S poromusa group back within the C lostridia . They also support placement of C lostridium difficile and its close relatives within the family P eptostreptococcaceae ; we suggest resolving the long‐standing naming conundrum by renaming it P eptoclostridium difficile . These data also indicate the existence of a group of cellulolytic clostridia that belong to the family R uminococcaceae . As a tentative solution to resolve the current taxonomical problems, we propose assigning 78 validly described C lostridium species that clearly fall outside the family C lostridiaceae to six new genera: P eptoclostridium , L achnoclostridium , R uminiclostridium , E rysipelatoclostridium , G ottschalkia and T yzzerella . This work reaffirms that 16S rRNA and ribosomal protein sequences are better indicators of evolutionary proximity than phenotypic traits, even such key ones as the structure of the cell envelope and G ram‐staining pattern.