The genetic and ecological landscape of plasmids in the human gut

Abstract

AbstractPlasmids are mobile genetic elements that often carry key determinants of fitness, yet their diversity in natural systems is poorly understood. Here we trained a machine learning model on reference genomes to recognize the genetic architecture of plasmids. We applied our model to a global collection of human gut metagenomes to identify 68,350 non-redundant plasmids, which represent a 200-fold increase in the number of detectable plasmids in the human gut. This broad view of plasmid diversity revealed 1,169 ‘plasmid systems’, an evolutionary phenomenon where a backbone sequence with core plasmid functions, such as replication, is recombined with cargo functions, such as antibiotic resistance, depending on the environment. This work unearths the astonishing diversity of plasmids and provides a framework for studying their ecology and evolution.One-Sentence Summary:New computational methods enable a global search and reveal evolutionary principles of plasmids in the human gut microbiome.