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.

Genomic and functional analysis ofRomboutsia ilealisCRIBTreveals adaptation to the small intestine

“…Here we describe a model driven genomic analysis of the small intestinal inhabitant Romboutsia ilealis CRIB T ( Gerritsen et al, 2014 ). R. ilealis CRIB T is currently still the only isolate of the recently descibed species R. ilealis , a species that belongs to the family Peptostreptococcaceae, of which many members are common intestinal microbes including the well-known species Clostridioides difficile (previously known as Clostridium difficile ) and Intestinibacter bartlettii (previously known as Clostridum bartlettii ) ( Galperin et al, 2016 ). An overview of the metabolic capabilities and nutritional potential of the type strain of R. ilealis CRIB T is provided here to identify potential mechanisms that enable this organism to survive in the competitive small intestinal environment.…”

An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017

“…In 2013, Yutin and Galperin (166) proposed creating a new genus, Peptoclostridium, to accommodate the Clostridium species reassigned to the family Peptostreptococcaceae. This proposal, which would have placed many diverse species into a single genus (including C. difficile), was rejected as being too simplistic (167). Subsequently, with the recognition that the proposed name Peptoclostridium difficile would change the monikers of C. difficile or C diff already ingrained in commercial products, packaging, computer systems, and clinical laboratories and to avoid tremendous confusion among clinicians, Lawson and colleagues (131) proposed a compromise with the new designation of Clostridioides difficile, thereby retaining the abbreviation commonly used for C. difficile.…”

Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov

“…Class Clostridia was divided into 19 clusters by Collins et al according to 16S rDNA gene sequences and/or some phenotypes; however, they did not report its biochemical properties . Indeed, several Clostridium species contained in the class Clostridia have since been transferred to other genera on the basis of findings on taxonomic analyses, such as biochemical properties and full genome analysis . Determining the properties of individual bacterial species may lead to a more detailed and clear classification of class Clostridia .…”