Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
Keywords: biosynthetic gene clusters; microbial ecology; microbiome; microbiome sequencing; mobile genetic elements; multiple displacement amplification; primary template-directed amplification; single cell genomics; unculturable bacteria; whole genome amplification.
© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.