1887

Abstract

The species of comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of that form a distinct cluster in the 16S rRNA tree (cluster I) should be regarded as the true representatives of the genus (i.e. ). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other species that are not part of this cluster grouped reliably with other species of clostridia in a number of well-resolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of cluster I and are not found in any other bacteria. searches on various proteins in the genomes of and SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus in more definitive terms. We have also identified a 7–9 aa conserved insert in the enzyme phosphoglycerate dehydrogenase that is uniquely found in the , , and homologues, and is absent from all other bacteria. These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster.

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2009-02-01
2019-12-11
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Neighbour-joining distance tree for the set II protein sequences for the clostridia. [PDF](468 KB)

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