Unlocking high-resolution, strain-resolved microbiome analyses with modern nanopore sequencing

Abstract: Microbiome sequencing is dominated by two paradigms: shotgun metagenomics and metabarcoding (e.g., 16S rRNA sequencing). Both aim to recover biological units—genomes or exact sequence variants—but short-read technologies have limitations: assemblies are fragmented and collapse co-existing strains, and amplicons capture only a small portion of the 16S rRNA gene. Nanopore sequencing is a promising solution, but existing algorithms don't leverage the high accuracy of modern simplex reads; new computational methods are needed. First, I will present myloasm, a new long-read metagenome assembler. Myloasm recovers 3-fold more circular genomes than previous nanopore assemblers and unveils hidden strain diversity. Strikingly, on a gut metagenome jointly sequenced with nanopore simplex and PacBio HiFi, myloasm assembled more circular genomes with nanopore than any previous method with HiFi. Lastly, I will present savont, an algorithm for recovering exact full-length 16S rRNA amplicon sequence variants (ASVs). Savont can routinely recover 16S sequences that differ by even a single nucleotide while requiring 10x less sequencing depth than existing methods. Savont makes full-length, high-resolution 16S profiling possible from shallow nanopore amplicon sequencing. Jim Shaw is a postdoctoral researcher at Harvard Medical School and Dana-Farber Cancer Institute, advised by Professor Heng Li. #NanoporeSequencing#MicrobiomeAnalysis#Bioinformatics#Genomics#ComputationalBiology