Welcome and introduction: James Brayer, Oxford Nanopore Technologies
Ami Bhatt, Stanford University: Structural variation analysis enabled by generating complete genomes from microbiomes
Abstract: Microbes abound in our environment. They are the most successful life forms that exist on earth and this is, in part, enabled by their incredible ability to adapt their genomes in relative rapid timescales. Through the acquisition of mutations and by allowing intra- and inter-molecular gene transfer, microbes can acquire and lose critical biological functions. To date, microbiome-focused research has made great strides in measuring taxonomic composition of bacteria and archaea within complex mixtures. While powerful, these methods do not provide a window into the vast genetic variation that exists within these evolving genomes. To understand these variations and how they contribute to bacterial fitness, we must be able to directly “view” these complete genomes. Recent advances in sequencing technology, including read cloud and long read sequencing, are helping us overcome the barriers that have prevented the effective and complete recovery of genomes from metagenomes. As a result, we are now able to generate complete, closed, circular bacterial genomes directly from microbiome samples without isolating and culturing these strains. In this presentation, I will describe the methods we have used to generate complete, closed genomes for prominent human-associated gut microbes such as Prevotella copri. Both the strengths and limitations of the current approaches will be described, and I will also consider the implications of our genome findings on the role of structural variation in genome evolution.