Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov

Abstract

In 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18 species to Clostridium cluster XI, separating them from Clostridium sensu stricto (Clostridium cluster I). Subsequently, most cluster XI species have been assigned to the family Peptostreptococcaceae with some species being reassigned to new genera. However, several misclassified Clostridium species remained, creating a taxonomic conundrum and confusion regarding their status. Here, we have re-examined the phylogeny of cluster XI species by comparing the 16S rRNA gene-based trees with protein- and genome-based trees, where available. The resulting phylogeny of the Peptostreptococcaceae was consistent with the recent proposals on creating seven new genera within this family. This analysis also revealed a tight clustering of Clostridium litorale and Eubacterium acidaminophilum. Based on these data, we propose reassigning these two organisms to the new genus Peptoclostridium as Peptoclostridium litorale gen. nov. comb. nov. (the type species of the genus) and Peptoclostridium acidaminophilum comb. nov., respectively. As correctly noted in the original publications, the genera Acetoanaerobium and Proteocatella also fall within cluster XI, and can be assigned to the Peptostreptococcaceae. Clostridium sticklandii, which falls within radiation of genus Acetoanaerobium, is proposed to be reclassified as Acetoanaerobium sticklandii comb. nov. The remaining misnamed members of the Peptostreptococcaceae, [Clostridium] hiranonis, [Clostridium] paradoxum and [Clostridium] thermoalcaliphilum, still remain to be properly classified.

Fig. 1.

16S rRNA gene-based phylogenetic tree of the family Peptostreptococcaceae. The sequences from type strains (indicated with superscript T) were used and listed under their DSM accession numbers, where available. GenBank accession numbers are listed in parentheses. For Clostridioides difficile 630, Clostridioides mangenotii TR, Paraclostridium benzoelyticum JC272^T, and ‘Terrisporobacter othiniensis’, 16S rRNA gene sequences were taken from the respective genomic entries. Quotation marks indicate the organisms whose names have not yet been validly published. The organisms that this work proposes to be renamed are indicated in boldtype. The sequences were aligned using muscle (Edgar, 2004) and the tree was inferred using the maximum-likelihood method based on the Tamura–Nei model (Tamura & Nei, 1993) as implemented in mega6 (Tamura et al., 2013); for the initial neighbour-joining tree, see Fig. S1. The tree was rooted using sequences from C. butyricum and C. botulinum, members of Clostridium sensu stricto.

Fig. 2.

Ribosomal protein-based tree of the members of Peptostreptococcaceae. A maximum-likelihood tree was built using the PhyML program (Guindon et al., 2010) from a concatenated alignment of 50 ribosomal proteins (L1–L7, L9–L11, L13–L24, L27–L29, L31–L36 and S2–S20), with a total of 6269 aligned positions, as described previously (Yutin et al., 2012; Yutin & Galperin, 2013). The organisms proposed for renaming are indicated in boldtype. The names of the organisms that have not been validly published are in quotation marks. The tree was rooted using sequences from C. butyricum and C. botulinum.