EpicPCR-Directed Cultivation of a Candidatus Saccharibacteria Symbiont Reveals a Type IV Pili-dependent Epibiotic Lifestyle

Abstract

Candidate phyla radiations (CPR), accounting for a major microbial supergroup with remarkably small genomes and reduced sizes, are widely distributed yet mostly uncultured. Limited culture and its obligate reliance upon other bacteria hindered investigation of their lifestyles. In this work we isolated a CPR bacterium, TM7i, with its host Leucobacter aridocollis J1, by combination of Emulsion, Paired Isolation and Concatenation PCR (epicPCR) detection and filtrate co-culture. Genomic profiling of TM7 genomes and microscopic investigation of TM7i-J1 symbiosis suggest the conservation of type IV pili and a pili-dependent lifestyle of TM7. Further, we observed twitching motility of TM7i mediated by pili and its role played in the interaction with its host. Our results shed a light on the lifestyle about this enigmatic bacterial radiation, which may also be adopted by other CPR organisms. The epicPCR-directed isolation method underlines high efficiency of CPR bacteria isolation and thus may be used in other symbiotic or epibiotic microorganisms.

Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria

“…Among these, Saccharibacteria (formerly known as TM7) contain the first cultured representative, “ Candidatus Nanosynbacter lyticus” TM7x, from the human oral cavity and is associated with the human microbiome ( 9 ). In recent years, cultivation of additional TM7 strains from human and environmental sources has been achieved ( 3 – 5 , 10 , 11 ). All known TM7 strains are obligate episymbionts that grow on the surface of host bacteria ( 12 , 13 ).…”

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

“…They adhere to lifestyles dependent upon other cells, either by episymbiotic attachment -whereby CPR bacteria attach to, and obtain nutrients from, a larger host bacterium -or by deriving essential compounds such as lipids 3 from the surrounding microbial community. In most cases, the hosts of CPR bacteria are unknown, but in the case of certain oral and environmental Saccharibacteria, the hosts have been experimentally established to be species of Actinobacteria [4][5][6][7][8] . The attachment by Saccharibacteria can have a profound impact on the Actinobacteria host, leading to cycles of rapid host evolution and drastic changes in host physiology 4,6,9 .…”