QUT - Academic profiles - 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.

+61 7 34437334

b.woodcroft@qut.edu.au

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Centre for Microbiome Research

Personal details

Positions

Principal Research Fellow
Faculty of Health,
School of Biomedical Sciences

Research field

Medical microbiology, Soil sciences, Medical biochemistry and metabolomics

Field of Research code, Australian and New Zealand Standard Research Classification (ANZSRC), 2020

Qualifications

PhD (University of Melbourne)

Publications

QUT ePrints

For more publications by Ben, explore their research in QUT ePrints (our digital repository).

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2025

Borton, M. A., McGivern, B. B., Willi, K. R., Woodcroft, B. J., Mosier, A. C., Singleton, D. M., Bambakidis, T., Pelly, A., Daly, R. A., Liu, F., Freiburger, A., Edirisinghe, J. N., Faria, J. P., Danczak, R., Leleiwi, I., Goldman, A. E., Wilkins, M. J., Hall, E. K., Pennacchio, C., Roux, S., Eloe-Fadrosh, E. A., Good, S. P., Sullivan, M. B., Wood-Charlson, E. M., Miller, C. S., Ross, M. R. V., Henry, C. S., Crump, B. C., Stegen, J. C. & Wrighton, K. C. (2025). A functional microbiome catalogue crowdsourced from North American rivers. Nature, 637(8044), 103–112. https://eprints.qut.edu.au/255296

2024

Ellenbogen, J. B., Borton, M. A., McGivern, B. B., Cronin, D. R., Hoyt, D. W., Freire-Zapata, V., McCalley, C. K., Varner, R. K., Crill, P. M., Wehr, R. A., Chanton, J. P., Woodcroft, B. J., Tfaily, M. M., Tyson, G. W., Rich, V. I. & Wrighton, K. C. (2024). Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems, Article e0069823, 9(1). https://eprints.qut.edu.au/245204
McGivern, B. B., Cronin, D. R., Ellenbogen, J. B., Borton, M. A., Knutson, E. L., Freire-Zapata, V., Bouranis, J. A., Bernhardt, L., Hernandez, A. I., Flynn, R. M., Woyda, R., Cory, A. B., Wilson, R. M., Chanton, J. P., Woodcroft, B. J., Ernakovich, J. G., Tfaily, M. M., Sullivan, M. B., Tyson, G. W., Rich, V. I., Hagerman, A. E. & Wrighton, K. C. (2024). Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology, 9(6), 1454–1466. https://eprints.qut.edu.au/249024
Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. (2024). Correction to: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning (Nature Methods, (2023), 20, 8, (1203-1212), 10.1038/s41592-023-01940-w). Nature Methods, 21(4), 735.
Schoelmerich, M. C., Ly, L., West-Roberts, J., Shi, L. D., Shen, C., Malvankar, N. S., Taib, N., Gribaldo, S., Woodcroft, B. J., Schadt, C. W., Al-Shayeb, B., Dai, X., Mozsary, C., Hickey, S., He, C., Beaulaurier, J., Juul, S., Sachdeva, R. & Banfield, J. F. (2024). Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nature Communications, Article 5414, 15. https://eprints.qut.edu.au/250565
Williams, T. A., Davin, A. A., Szantho, L., Stamatakis, A., Wahl, N. A., Woodcroft, B. J., Soo, R. M., Eme, L., Sheridan, P. O., Gubry-Rangin, C., Spang, A., Hugenholtz, P. & Szollosi, G. J. (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, Article wrae129, 18(1). https://eprints.qut.edu.au/250781
Kobel, C. M., Aho, V. T. E., Øyås, O., Nørskov-Lauritsen, N., Woodcroft, B. J. & Pope, P. B. (2024). CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. bioRxiv.
Freire-Zapata, V., Holland-Moritz, H., Cronin, D. R., Aroney, S., Smith, D. A., Wilson, R. M., Ernakovich, J. G., Woodcroft, B. J., Bagby, S. C., Mondav, R., Hodgkins, S. B., Zayed, A. A. F., Varner, R. K., Saleska, S. R., Ibba, M., Ferriere, R., Fahnestock, M. F., E. Cross, J., Rich, V. I., Sullivan, M. B., Stegen, J. C., Tfaily, M. M. & other (2024). Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature Microbiology, 9(11), 2892–2908. https://eprints.qut.edu.au/253136
Cronin, D., Li, Y. F., Evans, P., Tyson, G. W., Woodcroft, B. J., Rich, V. I., Varner, R. K., Hough, M., Perry, A., Irwin-Raab, N., Jansen, J., Bennett, K. A. & other (2024). Impact of storage and extraction methods on peat soil microbiomes. PeerJ, Article e18745, 12(12). https://eprints.qut.edu.au/255295

2023

McIlroy, S. J., Leu, A. O., Zhang, X., Newell, R., Woodcroft, B. J., Yuan, Z., Hu, S. & Tyson, G. W. (2023). Anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens' has a pleomorphic life cycle. Nature Microbiology, 8(2), 321–331. https://eprints.qut.edu.au/237853
Volmer, J. G., Soo, R. M., Evans, P. N., Hoedt, E. C., Astorga Alsina, A. L., Woodcroft, B. J., Tyson, G. W., Hugenholtz, P. & Morrison, M. (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, Article 59, 21(1). https://eprints.qut.edu.au/239369
Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203–1212. https://eprints.qut.edu.au/242256
Hou, J., Wang, Y., Zhu, P., Yang, N., Liang, L., Yu, T., Niu, M., Konhauser, K., Woodcroft, B. J. & Wang, F. (2023). Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment. Science Advances, Article adf5069, 9(27). https://eprints.qut.edu.au/250564

2022

Wilson, R. M., Hough, M. A., Verbeke, B. A., Hodgkins, S. B., Tyson, G., Sullivan, M. B., Brodie, E., Riley, W. J., Woodcroft, B., McCalley, C., Dominguez, S. C., Crill, P. M., Varner, R. K., Frolking, S., Cooper, W. T., Chanton, J. P., Saleska, S. D., Rich, V. I., Tfaily, M. M. & other (2022). Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland. Science of the Total Environment, Article 152757, 820. https://eprints.qut.edu.au/228694
Hough, M., McCabe, S., Vining, S. R., Pickering Pedersen, E., Wilson, R. M., Lawrence, R., Chang, K. Y., Bohrer, G., Riley, W. J., Crill, P. M., Varner, R. K., Blazewicz, S. J., Dorrepaal, E., Tfaily, M. M., Saleska, S. R., Rich, V. I., Frolking, S., Hodgkins, S. B., McCalley, C. K., Cooper, W. T., Chanton, J. P., Sullivan, M. B., Tyson, G. W., Brodie, E. L., Woodcroft, B. J., Dominguez, S. & other (2022). Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland. Global Change Biology, 28(3), 950–968.

A complete list of publications is available at: https://www.qut.edu.au/about/our-people/academic-profiles/b.woodcroft

Associate ProfessorBen Woodcroft

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Associate Professor
Ben Woodcroft