Dr Ben Woodcroft
Australian Centre for Ecogenomics
The University of Queensland
However, unlike traditional methods which group sequences into operational taxonomic units (OTUs), bioinformatic synthesis of metagenome data do not resolve sequence types and simply instead estimate abundances of taxonomic groups. This presentation will focus on the applications of SingleM, a tool for finding OTUs from metagenomes and determining microbial community structure.
Resolving community profiles into sequence-based rather than taxonomy-based groupings enables community profiles to be resolved more finely. Ecological alpha and beta diversity metrics can be calculated even for complex communities containing novel lineages, and community profiles derived from metagenome sequences can be directly linked to recovered population genomes. Comparison made between unrelated metagenomic studies can also empower genome recovery efforts. An associated NeCTAR-hosted website allows searching of >4 million distinct sequence types from thousands of public metagenomes.
Starting from a computational background at the University of Queensland, Ben’s interest in biological systems was sparked by an undergraduate project in protein structure with Dr Nicholas Hamilton, then an honours project in Prof. Bernie Degnan’s marine biology laboratory studying the genome structure of the most basal animals, sponges. Then he moved south to the University of Melbourne, in doing so moving further away evolutionarily from animals, studying malaria parasites. Specifically, under the guidance of Dr Stuart Ralph (University of Melbourne) and Prof. Terry Speed (Walter & Eliza Hall Institute of Medical Research) his PhD concentrated on the development and application bioinformatic tools to understand the parasite’s complex cell biology. He recently continued his evolutionary trajectory by taking up this position at Australian Centre for Ecogenomics with Prof. Gene Tyson, using metagenomic approaches to try to understand the carbon cycle in thawing permafrost, concentrating particularly on the role of methanogens in climate change. He is now pursuing scalable hypothetical gene annotation approaches through coupling of genome-centric metagenomics with ultra-high resolution mass-spectrometry based large molecule metabolomics.