Researchers unveiled long‑read sequencing pipelines that resolve donor microbial strains after fecal microbiota transplant (FMT) with high precision. Mount Sinai’s LongTrack workflow and companion long‑read metagenomics studies used Oxford Nanopore and PacBio platforms to assemble donor‑resolved genomes, identify nearly 650 engrafted strains, and follow their adaptations for up to five years. The methods promise more accurate tracking of engraftment, persistence, and strain‑level evolution in microbiome therapeutics and safety monitoring.