The distinction of CPR bacteria from other bacteria based on protein family content

Jillian F. Banfield,Raphaël Méheust,Cindy J. Castelle,David Burstein

doi:10.1038/s41467-019-12171-z

Abstract

Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.

Highlights

Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear
The CPR was placed as the basal group in the bacterial domain in a concatenated ribosomal protein tree, but the deep branch positions were not sufficiently well supported to enable a conclusion regarding the point of divergence of CPR from other bacteria
By focusing only on protein families that are common in CPR bacteria and/or non-CPR bacteria, we demonstrate a major subdivision within the bacterial domain without reliance on gene or protein sequence phylogenies

Summary

Introduction

Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. 800 genomes from a remarkable variety of lineages that were placed together phylogenetically This monophyletic group was described as the candidate phyla radiation (CPR)[5]. CPR bacterial genomes have since been recovered from the human microbiome[6], drinking water[7], marine sediment[8], deep subsurface sediments[9], soil[10], the dolphin mouth[11] and other environments[12] It appears that CPR bacteria are both hugely diverse and widespread across earth’s environments. Cultivation from human oral samples highlighted the attachment of a CPR member of the lineage Saccharibacteria (TM7) to the surface of an Actinomyces odontolyticus bacteria[6] Another episymbiotic association has been described between a CPR organism from the Parcubacteria superphylum and an eukaryotic host[13]. Parks et al.[15] suggested that the group comprises no more than 26.3% of bacterial phylum-level lineages

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Results

Conclusion