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

Abstract

Summary 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.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

“…2). The reference tree used by CheckM was inferred from the 155 concatenation of 43 conserved marker genes with largely congruent phylogenetic histories (Supplemental Table S5 S4) shares features in common with recently published genome trees, including the class Clostridia 160 being highly paraphyletic (Yutin and Galperin, 2013) and the class Epsilonproteobacteria residing outside the Proteobacteria phylum (Rinke et al 2013). These discrepancies between phylogeny and taxonomy will cause marker genes calculated from named lineages within the genome tree to deviate from those determine strictly from assigned taxonomy.…”

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

“…such as C. sordellii and C. bifermentans, as well as other species such as Peptostreptococcus anaerobius and Eubacterium tenue (Collins et al, 1994). After a brief incarnation as Peptoclostridium difficile (Yutin and Galperin, 2013), a name that was never -validly published‖, it has been renamed very recently as Clostridioides difficile (Lawson et al, 2016), and moved to within the Peptostreptococcaceae family (Ludwig et al, 2009). Whether the new name will be accepted by the C. difficile community around the world remains to be seen.…”

Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov.

“…Consequently, in the recent past, a number of species have been reclassified in separate genera based mainly on phylogenetic analysis of the 16S rRNA gene sequence (Liu et al, 2008;Moore & Moore, 1994). Similarly, Yutin & Galperin (2013) proposed a new genus 'Lachnoclostridium' to accommodate misassigned species of the genus Clostridium belonging to cluster XIVa (Collins et al, 1994) based on the phylogenetic reciprocal relation between the 16S rRNA gene and genes encoding the beta subunits of RNA polymerase (RpoB) and DNA gyrase (GyrB). However, the description of this genus was based only on phylogenetic analysis, and the name has not been validly published.…”