Gene Tyson

Professor Tyson is internationally recognised as an expert microbial ecologist and bioinformatician. Over the last decade, he has been at the forefront in the development and application of culture-independent molecular approaches that provide direct access to microbial ‘dark matter’.

Professor Tyson’s research discoveries have been recognized by the Australian Society for Microbiology, who awarded him the Frank Fenner Award in 2015, and International Symposium on Microbial Ecology (ISME), who named him Young Investigator Award in 2016. He has been recognized as a Highly Cited Researcher (top 1% of cited scientists) for the past three years. In 2020, CI Tyson was recruited to the Queensland University of Technology (QUT) to establish the Centre for Microbiome Research (CMR).

Professor Tyson has made substantial contributions over the course of his career, including seminal papers demonstrating the development and application of metagenomics (Nature, 2004), metatranscriptomics (PNAS, 2008; Nature 2009), and metaproteomics (Science, 2005) to microbial communities. These approaches bypass traditional cultivation bottlenecks, and have revolutionised how the structure and function of microbial communities is studied. This research has paved the way for numerous important discoveries in microbiology, including work by CI Tyson’s team which has led to identifying important microbial lineages that regulate the Earth’s carbon cycle (Nature, 2015; Science 2018), previously unknown bacterial and archaeal lineages (Nature Microbiology, 2016;  Nature Microbiology, 2017), and characterisation of novel microbial metabolic functions (Nature, 2013; Nature, 2018). His team has also made important contributions to the development of novel bioinformatic tools for the analysis of meta-omic data (Nature Methods, 2012; Nucleic Acids, 2013, Bioinformatics, 2014; Genome Research, 2015; Nucleic Acids, 2018). These widely used and highly cited bioinformatic tools (>5,000 citations) have undoubtedly helped the widespread adoption of meta-omics in microbiology.

Contact

+61 7 3443 7612

gene.tyson@qut.edu.au

Project themes

• Understanding the Human microbiome
• Climate change and permafrost thaw
• Adaptive evolution of anaerobic methanotrophic (ANME) archaea mediating methane oxidation in freshwater environments
• Marine microbiology
• Single-cell approaches in microbial ecology

Selected publications

Professor Tyson has authored more than 130 peer-reviewed scientific papers and five book chapters. His research has been published in top tier journals, including seven papers in Nature, five papers in Science and three papers in PNAS and leading specialty journals. To date, his papers have been cited more than 23,500 times and he has a combined h-index of 67.

• CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

  Development of a tool for estimating the completeness and contamination of microbial genomes recovered from metagenomes. Parks D, Imelfort M, Skennerton C, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research. 7:1043-1055.

• Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

  The first large-scale recovery of thousands of microbial genomes from diverse microbial lineages from metagenomes. Parks D, Rinke C, et al Tyson GW (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology. 2(11):1533-1542.

• Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

  Discovery of a new short alkane-metabolising archaeal phylum. Evans P, Parks D, et al., Golding S, Tyson GW (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science. 350(6259):434-8.

• Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

  Discovery of a new phylum of archaea capable of methylotrophic methanogenesis. Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology. 1:1-9.

• Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

  The development of a new approach for the recovery of microbial genomes from metagenomic data using differential coverage. Albertsen M, et al., Tyson GW, Nielsen PH (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology. 31:533-538.

• Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

  The discovery of a novel archaeal lineage capable of anaerobic methane oxidation coupled to nitrate reduction. Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500:567-570.

• A genomic view of the reef-building coral Porites lutea and its microbial symbionts

  Demonstrates a meta-omic system-level approach to understanding how the microbiome contributes to host health and resilience. Robbins S, Singleton C, Chan CX, Messer L, et al., Tyson GW, Bourne DB (2019). A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology. 4:2090-2. 

• First use of metatranscriptomics in the ocean’s water column revealing unique microbial small RNAs

  Revealed that a significant number of small RNAs are actively expressed in microbial assemblages in the ocean. Shi Y, Tyson GW and DeLong E (2009) First use of metatranscriptomics in the ocean’s water column revealing unique microbial small RNAs. Nature, 459:266-269.

• Microbiology: metagenomics

  A perspective on metagenomics discussing the utility, major impacts, and future directions of the field. Hugenholtz P and Tyson GW. 2008. Microbiology: metagenomics. Nature 455(7212):481-483.

• Community structure and metabolism through reconstruction of microbial genomes from the environment

  A landmark  paper  that  demonstrates  the  feasibility  of  using  metagenomics  to  reconstruct  microbial genomes directly from the environment. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, and Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978):37-43.

 

Research Impact

In addition to the knowledge impacts of CI Tyson’s academic research, significant economic impact for Australia have been achieved through commercialisation of his research. Recognising the potential of meta-omics to understand the role of the microbiome in human health and disease, CI Tyson co-founded Microba, a microbial biotechnology company that provides consumer and clinical services to characterise the human microbiome, with the ultimate goal of developing microbiome-derived diagnostics and therapeutics. Microba employs 50+ people in Australia and the United States, with operations in seven different countries. The company has secured major deals with large multinational pharmaceutical and food/supplement companies, and is currently moving into Phase 1 trials.