Associate Professor
Ben Woodcroft

Biography

As the informatics group leader at the Centre for Microbiome Research, Ben has the happy knack of enjoying most things but gravitates towards the development and application of bioinformatic techniques to study the microbial communities that drive the health of our planet. He currently holds an ARC Future fellowship and has published >200 free software projects.

The study of microbial ecology is almost always data-heavy since it involves the study of microbes in the context of their microbial community. Bioinformatics provides the statistical analysis, data science-based approaches and scalable computational toolsets necessary to study the structure and function of microbiomes from a wide range of environments. The group aims to advance the science of microbial bioinformatics by developing novel and widely applicable techniques, and implementing them with tools named after Australian birds.

Main research areas:

1) The global microbiome and big data

2) Climate change, permafrost thaw and the positive feedback of soil microorganisms

3) Tools for genome-centric metagenomics

4) Phylogenetic method development to find structure/symbiosis in microbial communities

Biography:

Starting from a computational background at the University of Queensland, Ben’s broad 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 for his PhD, under the guidance of A/Prof. Stuart Ralph and Prof. Terry Speed, concentrating on the development of bioinformatic tools to understand the malaria parasite’s complex cell biology.

During his post-doctoral studies with Prof. Gene Tyson at the Australian Centre for Ecogenomics, UQ, and continuing until the present time as microbial informatics team leader within the Centre for Microbiome Research at QUT, he has studied the microbial world using informatic techniques. Direct sequencing of DNA and RNA derived from natural microbial systems has great scientific and applied potential, and the wealth of sequencing data bring many bioinformatic opportunities and challenges, including the recovery and annotation of genomes with strain-level specificity, exploring large public datasets and linking microbial communities with their function.

A primary study site he has been involved with is Stordalen Mire, in northern Sweden, a permafrost thaw gradient home to complex microbial ecosystems. This system serves as a model for understanding how climate change is affecting microbial communities in thawing permafrost, which are in turn generating the potent greenhouse gas methane, exacerbating global warming. Primary contributions at this site involved the recovery of >1000 high quality genomes from the site, discovery of novel methanogenic lineages and linking specific community members to the isotopic composition of released methane, with implications for global climate modeling.