scMicrobe PTA: Near Complete Genomes From Single Bacterial Cells

Robert M. Bowers; Veronica Gonzalez-Pena; Kartika A. Wardhani; Danielle Goudeau; Matthew J. Blow; Daniel Udwary; David Klein; Albert C. Vill; Ilana Brito; Tanja Woyke; Rex R. Malmstrom; Charles Gawad

doi:10.1093/ismeco/ycae085

GenomicsISME CommunicationsJan 1, 2024

Peer-reviewed journal article

scMicrobe PTA: Near Complete Genomes From Single Bacterial Cells

Robert M. Bowers iD, Veronica Gonzalez-Pena iD, Kartika A. Wardhani iD, Danielle Goudeau iD, Matthew J. Blow iD, Daniel Udwary iD, David Klein iD, Albert C. Vill iD, Ilana Brito iD, Tanja Woyke iD, Rex R. Malmstrom iD, Charles Gawad iD

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Abstract

Microbial genomes produced by single-cell amplification are largely incomplete. Here, we show that primary template 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 amplification approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.