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

Abstract

The class Clostridia in the phylum Firmicutes (formerly low-G+C Gram-positive bacteria) includes diverse bacteria of medical, environmental and biotechnological importance. The Selenomonas-Megasphaera-Sporomusa branch, which unifies members of the Firmicutes with Gram-negative-type cell envelopes, was recently moved from Clostridia to a separate class Negativicutes. However, draft genome sequences of the spore-forming members of the Negativicutes 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 Selenomonas-Megasphaera-Sporomusa group back within the Clostridia. They also support placement of Clostridium difficile and its close relatives within the family Peptostreptococcaceae; we suggest resolving the long-standing naming conundrum by renaming it Peptoclostridium difficile. These data also indicate the existence of a group of cellulolytic clostridia that belong to the family Ruminococcaceae. As a tentative solution to resolve the current taxonomical problems, we propose assigning 78 validly described Clostridium species that clearly fall outside the family Clostridiaceae to six new genera: Peptoclostridium, Lachnoclostridium, Ruminiclostridium, Erysipelatoclostridium, Gottschalkia and Tyzzerella. 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 Gram-staining pattern.

Figure 1

A ribosomal proteins-based phylogenetic tree of the Firmicutes that shows the positions of (A) Gram-negative members of the Firmicutes and (B) mis-assigned Clostridium spp. The maximum-likelihood tree was built from a concatenated alignment of 50 ribosomal proteins from 70 organisms with a total of 6,164 unambiguously aligned positions, essentially as described in Yutin et al. (2012). The tree was rooted using two members of the Fusobacteria, Fusobacterium nucleatum and Leptotrichia buccalis, as an outgroup. The numbers on the branches show TreeFinder confidence values. Those branches shared with the RpoB tree are indicated with thick lines, bootstrap values of those branches that are shared with the GyrB tree are shown in bold. The Roman numerals on the right correspond to the clusters of Collins et al. (1994). Grey triangles indicate clusters that are shown in more details on the other panel (see Supplementary Materials for details, original trees, and Table S9 for the full list of organisms).