A/Prof Ben Woodcroft

Modern studies of microbial ecology are often data-rich since they involve 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. The computational microbiology group led by A/Prof Ben Woodcroft aims to advance the science of microbial ecology in several ways: Community profiling: which microorganisms are present in a sample? A simple question to ask, but not easy to answer, especially when most microorganisms are not known to science. Public databases now contain ~5 Pbp (5×1015 base pairs) of high quality shotgun metagenomic data, representing >700,000 weird and wonderful communities from across the planet. Our tools – SingleM, CoverM and Lyrebird – each tackle community profiling from different angles. The Sandpiper website provides results for all these data and allows users to rapidly identify samples containing specific species of interest. Free software tools for microbial ecology: We focus on developing open-source software to be widely useful. For instance, Aviary can be used for extracting genomes from metagenomes, while Bin Chicken suggests which metagenomes to coassemble – we used it to recover the genomes of 24,000 new species (the ‘Rare Biosphere Genomes’). The group has released over 200 free software projects to date. Evolution: We apply machine learning and gene/species tree reconciliation to understand microbial evolution across deep time, including viral evolution. In a recent Science study, we showed how machine learning can be used to calibrate the bacterial tree of life. Climate change and soil microbiology: We study how microbial communities interact with — and are impacted by — climate change. Our work focuses especially on thawing permafrost in high-latitude peatlands, which store vast quantities of carbon currently locked in frozen soils but are warming at a rate faster than the rest of Earth.