Biological capacities clearly define a major subdivision in Domain Bacteria

Abstract

ResumePhylogenetic analyses separate candidate phyla radiation (CPR) bacteria from other bacteria, but the degree to which their proteomes are distinct remains unclear. Here, we leveraged a proteome database that includes sequences from thousands of uncultivated organisms to identify protein families and examine their organismal distributions. We focused on widely distributed protein families that co-occur in genomes, as they likely foundational for metabolism. Clustering of genomes using the protein family presence/absence patterns broadly recapitulates the phylogenetic structure of the tree, suggesting persistence of core sets of protein families after lineage divergence. CPR bacteria group together and away from all other bacteria and archaea, in part due to novel proteins, some of which may be involved in cell-cell interactions. The diversity of combinations of protein families in CPR may exceed that of all other bacteria. Overall, the results extend the phylogeny-based suggestion that the CPR represent a major subdivision within Bacteria.