IS-Seq reads of Bacteroides strains

Insertion sequence (IS) elements are mobile genetic elements present in nearly all bacterial genomes. IS elements contribute to bacterial genome plasticity that supports bacterial adaptation. Despite their importance to bacterial evolution, we know very little about the function of IS elements within polymicrobial communities such as the human microbiota. To address this knowledge gap, we developed a novel database of IS element sequences coupled to a computational pipeline that can identify diverse IS element insertions in complex microbial populations using DNA sequencing short-reads and used this tool to understand how IS elements function in the human intestinal microbiota. We discovered that multiple classes of IS elements insert into the genomes of diverse intestinal bacteria regardless of human host lifestyle. These insertions targeted bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using ISOSDB412 (IS4351) expansion in the model intestinal bacteria Bacteroides thetaiotaomicron and Bacteroides fragilis, we show that IS element activity leads to predictable insertions in similar accessory genes indicating preferred “hot spots” of IS element insertion within the microbiota. We show that IS element insertions are stably maintained for years in the absence of strong selective pressure and they can be transferred between humans. Additionally, new IS insertions consistently arise within the microbiota of healthy individuals supporting promiscuous active transposition as a mechanism to diversify bacterial genomes. Extreme environmental perturbations such as antibiotic treatment and diet intervention force IS insertions to fall out of the microbiota and many of these IS elements fail to rebound following homeostasis. Together our work shows that IS elements are major drivers of bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.