Transduction in the mouse gut microbiome pre- and post- perturbation

Transduction, the virus facilitated horizontal transfer of genetic material between microbes, plays important roles in generating genetic diversity, spreading virulence factors, and influencing microbiome dynamics. Despite the impact that transduction has on the ability of microbes to adapt to changing conditions, current methods to detect and study transduction in microbiomes are limited. Transductomics is a relatively new sequencing-based approach that we developed to assess the presence and characteristics of transducing events actively occurring in a microbiome. With transductomics, transduction events are identified by assessing read coverage patterns formed when reads from the purified viral-like particle (VLP) fraction of a sample are mapped to contigs generated from the same sample's whole-community (WC) metagenome. Recently, we automated the transductomics data analysis with a novel pattern-matching algorithm which has now been integrated into a freely available R package named TrIdent (jlmaier12.github.io/TrIdent/). To both test TrIdent's performance and explore the transduction occurring in the gut microbiome, we generated transductomics datasets from mouse fecal pellets collected pre- and post- gut microbiome perturbation (Cefoperazone antibiotics and Clostridium difficile infection). The transductomics datasets generated consist of short-read DNA sequences for each individual sample's WC and associated VLP-fraction. The VLP-fractions of the fecal homogenates were 0.2um filtered, DNase treated and purified using CsCl density gradient ultracentrifugation.