Microorganisms are the most abundant and diverse forms of life on Earth. Characterizing species diversity and the composition of microbes hosted by biota is revolutionizing our understanding of the impact on the maintenance of human health, crop improvement, and species conservation. The accessibility of high-throughput sequencing has exponentially increased the number of microbial genomes. However, the commonly employed short-read strategies have extreme limitations, e.g., GC bias, difficulties in mapping repetitive elements, discriminating paralogous sequences, and phasing alleles. Long-read sequencing technologies, PacBio SMRT and Nanopore sequencing, have been seeing a dramatic increase in reading quality, throughput,cost-efficiency, and accuracy.