Project Description

Dr Ben Woodcroft

 

Australian Centre for Ecogenomics
The University of Queensland

Community diversity in metagenomes: one, many and thousands

Ecogenomics

Friday 8 July 2016

Shotgun Illumina sequencing is an increasingly common method of studying microbial communities as it allows estimation of functional potential and recovery of population genomes. Studying communities with metagenomics is not subject to the primer biases inherent in traditional amplicon-based approaches.

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.

Ben has the happy knack of enjoying most things that are plonked in front of him, but has tended to gravitate towards development and application of bioinformatic techniques to studying biological systems in rewarding ways. Topics of interest include soil meta-omics, eukaryotic cell biology, endosymbiosis, methanogen biology and open-source software.

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.

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