Long-read nanopore metagenomics for reconstruction of bacterial genomes

Samuel Nicholls

Samuel Nicholls, University of Birmingham - University of Queensland - INIA


Effective analysis of bacterial communities requires a coordinated attack on two problems: DNA extraction and genome assembly. We demonstrate the effectiveness of the “three peaks” extraction method developed by Josh Quick, which combines chemical, enzymatic and physical lysis to achieve long-reads without loss of representation. We also introduce Reticulatus: a Snakemake-based assembly and polishing pipeline that attempts to codify current best practice for long-read metagenomics. We have applied our novel DNA extraction method to the previously characterised Zymo Mock Community Standard; a more realistic Gut Microbiome Mock and on a real faecal microbiota transplant. We use Reticulatus to assemble, polish and validate our long-read metagenomic assemblies and demonstrate the current state-of-the-art for long-read nanopore metagenomics.


Sam is a computer scientist specialising in novel data structures and algorithms for the analysis of microbial communities. He is a post-doctoral fellow in Nick Loman’s lab at the University of Birmingham which explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. Sam’s PhD thesis and recent work focused on the recovery of gene-haplotypes from microbial communities. He is currently working on accelerating metagenomic analysis pipelines with GPU and applying his haplotyping work to identify the transmission of strains between donors and patients in faecal microbiota transplants, and to investigate the lung microbiome of cystic fibrosis patients infected with Pseudomonas aeruginosa.