All Publications

  • Genetic determinants of EGFR-driven lung cancer growth and therapeutic response in vivo Foggetti, G., Li, C., Cai, H., Lin, W., Ayeni, D., Hastings, K., Andrejka, L., Maghini, D., Homer, R., Petrov, D. A., Winslow, M. M., Politi, K. AMER ASSOC CANCER RESEARCH. 2020
  • Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nature biotechnology Moss, E. L., Maghini, D. G., Bhatt, A. S. 2020


    Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.

    View details for DOI 10.1038/s41587-020-0422-6

    View details for PubMedID 32042169

  • Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome. Nature protocols Maghini, D. G., Moss, E. L., Vance, S. E., Bhatt, A. S. 2020


    Short-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield draft bacterial genomes without isolation and culture. However, bacterial genomes assembled from short-read sequencing are often fragmented. Furthermore, these metagenome-assembled genomes often exclude repeated genomic elements, such as mobile genetic elements, compromising our understanding of the contribution of these elements to important bacterial phenotypes. Although long-read sequencing has been applied successfully to the assembly of contiguous bacterial isolate genomes, extraction of DNA of sufficient molecular weight, purity and quantity for metagenomic sequencing from stool samples can be challenging. Here, we present a protocol for the extraction of microgram quantities of high-molecular-weight DNA from human stool samples that are suitable for downstream long-read sequencing applications. We also present Lathe ( ), a computational workflow for long-read basecalling, assembly, consensus refinement with long reads or Illumina short reads and genome circularization. Altogether, this protocol can yield high-quality contiguous or circular bacterial genomes from a complex human gut sample in approximately 10 d, with 2 d of hands-on bench and computational effort.

    View details for DOI 10.1038/s41596-020-00424-x

    View details for PubMedID 33277629