A significant portion of the bacterial domain, comprising more than 15%, is represented by a group of bacteria known as the Candidate Phyla Radiation (CPR). This group includes over 35 phyla, with more than 789 draft genomes reconstructed from microbial communities sampled from an aquifer near the Colorado River. These genomes are small, often lacking numerous biosynthetic pathways, and exhibit unique features such as self-splicing introns and proteins encoded within their rRNA genes. CPR bacteria also have unusual ribosome compositions, lacking certain ribosomal proteins and biogenesis factors typically present in bacteria. The CPR is distinguished by its shared evolutionary history and unique genetic characteristics. These bacteria often have ultra-small cells, which makes them difficult to detect in typical cultivation-independent surveys. Their 16S rRNA genes frequently contain insertions, some of which encode catalytic RNA introns or open reading frames, suggesting self-splicing. These insertions are not retained in transcribed RNAs and are likely rapidly degraded. The CPR bacteria's unusual biology is further highlighted by their metabolic limitations, including incomplete tricarboxylic acid cycles and lack of electron transport chain complexes. They are likely obligate fermenters dependent on other organisms for survival. Despite these limitations, CPR bacteria have a distinct phylogeny and are a significant portion of the bacterial domain. The study used metagenomic and metatranscriptomic sequencing to analyze CPR bacteria, revealing their unique genomic features and evolutionary relationships. The CPR is monophyletic, indicating a common ancestry. The research also identified several new phyla within the CPR, based on 16S rRNA gene sequence divergence and phylogenetic analysis. The CPR represents a significant portion of the bacterial domain, with over 250 phyla estimated to be part of this group. The study's findings highlight the importance of CPR bacteria in understanding the diversity and evolution of life on Earth. The research underscores the need for advanced methods to detect and study these previously unknown bacterial groups.A significant portion of the bacterial domain, comprising more than 15%, is represented by a group of bacteria known as the Candidate Phyla Radiation (CPR). This group includes over 35 phyla, with more than 789 draft genomes reconstructed from microbial communities sampled from an aquifer near the Colorado River. These genomes are small, often lacking numerous biosynthetic pathways, and exhibit unique features such as self-splicing introns and proteins encoded within their rRNA genes. CPR bacteria also have unusual ribosome compositions, lacking certain ribosomal proteins and biogenesis factors typically present in bacteria. The CPR is distinguished by its shared evolutionary history and unique genetic characteristics. These bacteria often have ultra-small cells, which makes them difficult to detect in typical cultivation-independent surveys. Their 16S rRNA genes frequently contain insertions, some of which encode catalytic RNA introns or open reading frames, suggesting self-splicing. These insertions are not retained in transcribed RNAs and are likely rapidly degraded. The CPR bacteria's unusual biology is further highlighted by their metabolic limitations, including incomplete tricarboxylic acid cycles and lack of electron transport chain complexes. They are likely obligate fermenters dependent on other organisms for survival. Despite these limitations, CPR bacteria have a distinct phylogeny and are a significant portion of the bacterial domain. The study used metagenomic and metatranscriptomic sequencing to analyze CPR bacteria, revealing their unique genomic features and evolutionary relationships. The CPR is monophyletic, indicating a common ancestry. The research also identified several new phyla within the CPR, based on 16S rRNA gene sequence divergence and phylogenetic analysis. The CPR represents a significant portion of the bacterial domain, with over 250 phyla estimated to be part of this group. The study's findings highlight the importance of CPR bacteria in understanding the diversity and evolution of life on Earth. The research underscores the need for advanced methods to detect and study these previously unknown bacterial groups.