“Genomes from metagenomes: new technologies and algorithms”
Thursday, February 12, 2015. 6:00pm
University of Birmingham, Inst. of Microbiology for Microbiology and Infection
URL: Nick Loman
Dr. Loman is an Independent Research Fellow in the Institute for Microbiology and Infection at the University of Birmingham. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. He has so far used high-throughput sequencing to investigate outbreaks of important bacterial pathogens. He was involved in the crowd-sourced analysis of genomics data from the Shiga-toxin producing E. coli O104:H4 outbreak in Germany. He helped to spark a flurry of crowd-sourced analysis by putting the initial genome assembly on his blog for anyone to access. A more general aim in his group is to develop bioinformatics tools to aid the interpretation of genome and metagenome-scale data in routine clinical practice.
The ability to reliably reconstruct whole genomes of bacterial strains from mixed samples would enable diagnostic microbiology and environmental applications. I will present CONCOCT, an algorithm and bioinformatics package which uses both composition and read abundance from multiple samples to help assign metagenomics contigs into genome bins. I will show how CONCOCT can used to reconstruct pathogen genomes from a large E. coli outbreak and its use when comparing microbiomes. Short read de novo assembly techniques are limited in their ability to resolve closely related strains and to deal with low coverage genomes. I will discuss how the technique of phylogenetic placement can be used to analyse mixed microbial samples with low coverage, and discuss how new technologies such as Oxford Nanopore, Moleculo and metagenomics Hi-C may continue to transform this field.
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC
- Binning metagenomic contigs by coverage and composition.
- Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing.
Mike Peabody (PhD Student, Dr. Fiona Brinkman’s Lab, SFU)
“Improving Water Quality Through Novel Genetic Tests Identified Using Metagenomics”