Advances in microbial genomics and metagenomics have been accelerated by the arrival of long-read sequencing technologies, which now offer greatly reduced error rates and cost compared to a decade ago. My group at Rice University (www.treangenlab.com) focuses on developing scalable and sensitive approaches for extracting biological insights from long-read sequencing datasets. In my talk, I will discuss research questions specific to microbial genomics and metagenomics through the lens of long-read sequencing. Specifically, I will highlight the benefits of long-read sequencing for detecting low-abundance pathogens and tracking structural variation within microbiomes. I will conclude with thoughts on unsolved challenges and future opportunities.