Saccharibacteria are ultrasmall epiparasitic bacteria within the Candidate Phylum Radiation (CPR), and are found across diverse environments including soil, wastewater, and the human oral, vaginal, and gut microbiomes. These obligate parasites are of particular interest due to their ability to lyse their hosts, and recent evidence demonstrated that host attachment requires an intact mycolic acid cell wall. This structure occurs in Actinobacteria genera, including Mycobacterium, Gordonia and Rhodococcus. Despite their ubiquity, Saccharibacteria remain recalcitrant to laboratory cultivation, limiting in vitro investigation of their biology and host interactions.
This study aimed to isolate, culture, and characterise Saccharibacteria from Australian wastewater treatment plants (WWTPs) and freshwater systems that are lytic to their Actinobacterial hosts. Candidatus Mycosynbacter amalyticus JR1 was the first Saccharibacteria isolate recovered from WWTP and demonstrated obligate epibiotic parasitism, including lysis of its host Gordonia amarae. Given the antiviral capabilities of G. amarae, this host presents a promising platform for isolating lytic Saccharibacteria. Using this host, we isolated 30 Saccharibacteria strains from WWTPs and one freshwater creek, representing 14 distinct species spanning two genera. Genomic analysis revealed a conserved core genome, including genes associated with type IV secretion systems, filament formation, and arabinogalactan degradation. Evidence of bacteriophage infection, defence responses and genomic islands were detected. Representative strains were subjected to imaging to examine their physical characteristics, and screened against a panel of potential Actinobacterial hosts, demonstrating broad, but consistent infection capabilities. Our findings show that Saccharibacteria can be studied using methods beyond metagenomic, with WWTP and waterways as a reservoir for diverse epibiotic bacteria. The isolates, which lyse mycolic acid producing hosts, provide new avenues to study mycolic acid attachment, broaden our understanding of bacterial host–parasite interactions, and may inform future biocontrol strategies against these pathogens.