Little is known about a radiation of phyla that may comprise >15% of the bacterial domain. Organisms from these phyla occur in diverse environments where they are suggested to mediate carbon and hydrogen cycles, but no members have been cultivated. Thus, this group represents a substantial gap in our understanding of bacteria. We reconstructed 8 complete and 789 draft genomes from >35 of these phyla, and show that these organisms consistently exhibit features that distinguish them from other bacteria. We infer that this group has a shared evolutionary history and refer to it as the Candidate Phyla Radiation (CPR). All genomes from the CPR are small and lack numerous biosynthetic pathways. Due to divergent 16S rRNA gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Further, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.
Each organism assembly was binned from one of 12 groundwater metagenome BioSamples: SAMN03202994, SAMN03202995, SAMN03202996, SAMN03202997, SAMN03202998, SAMN03202999, SAMN03203000, SAMN03203001, SAMN03203002, SAMN03203003, SAMN03203004, or SAMN03203005
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