New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes

Abstract

The Clostridium genus of bacteria contains the most widely studied biofuel-producing organisms such as Clostridium thermocellum and also some human pathogens, plus a few less characterized strains. Here, we present a comparative genomic analysis of 40 fully sequenced clostridial genomes, paying a particular attention to the biomass degradation ones. Our analysis indicates that some of the Clostridium botulinum strains may have been incorrectly classified in the current taxonomy and hence should be renamed according to the 16S ribosomal RNA (rRNA) phylogeny. A core-genome analysis suggests that only 169 orthologous gene groups are shared by all the strains, and the strain-specific gene pool consists of 22,668 genes, which is consistent with the fact that these bacteria live in very diverse environments and have evolved a very large number of strain-specific genes to adapt to different environments. Across the 40 genomes, 1.4–5.8 % of genes fall into the carbohydrate active enzyme (CAZyme) families, and 20 out of the 40 genomes may encode cellulosomes with each genome having 1 to 76 genes bearing the cellulosome-related modules such as dockerins and cohesins. A phylogenetic footprinting analysis identified cis-regulatory motifs that are enriched in the promoters of the CAZyme genes, giving rise to 32 statistically significant motif candidates.