Phil Hugenholtz

From a PhD in 1994 at the University of Queensland, Phil Hugenholtz developed a career in microbiology and genomics in the USA and in Australia. Phil’s last position in the USA was as Staff Scientist (2004-2010) at the Department of Energy, Joint Genome Institute. In late 2010 Phil returned home to establish the Australian Centre for Ecogenomics (ACE) at the University of Queensland. He has contributed to the field of culture-independent analysis of microorganisms through the discovery and characterisation of numerous previously unrecognised major bacterial and archaeal lineages each with greater evolutionary divergence than animals and plants combined. Phil has played important roles in the development and application of metagenomics, the genome-based characterisation of microbiomes, which has revolutionised our understanding of microbial ecology and evolution. This has resulted in several discoveries in environmental and clinical microbiology sometimes overturning decades of misdirected culture-based studies. He has applied his interest in comparative genomics and metagenomics to develop a systematic genome-based taxonomy for bacteria and archaea, which is facilitating scientific communication and endeavour. Phil has published over four hundred papers on molecular microbial ecology and evolution.

As Professorial Research Fellow at UQ and Director of ACE, Phil has affiliate appointments with the Institute for Molecular Bioscience and the UQ Diamantina Institute, which supports collaborative research at ACE. Currently, Phil’s research interests include the microbial ecology and evolution of environmental and host-associated ecosystems including marsupial and insect guts, biomining, marine and genomic mapping of the microbial tree of life.

Current research includes:

- A Genome Taxonomy Database for the Kingdom Fungi

- Tracing the emergence of cellular complexity in the phylum Planctomycetota

- Dual-function ribonucleases: unexpected agents of antibiotic resistance

- Breaking critical barriers in soil formation of bauxite residues

- Changing the classification status quo with a global genome-based taxonomy

- GBR Microbial Genomic Database

In 2018, Phil co-founded a start-up company, Microba Life Sciences (microba.com), which is focused on metagenome-based diagnostics and therapeutics.

Phil received the Young Investigators Award from the International Society of Microbial Ecology (ISME) in 2016, was elected in 2012 as a Fellow of the American Academy of Microbiology (AAM), elected a Fellow of the Australian Academy of Science in 2017, is a Member of the International Scientific Advisory Board (Fachbeirat) of the Max Planck Institute for Marine Microbiology, Bremen and is the outgoing President (2024-2026) of the International Society for Microbial Ecology (ISME). Phil has been a Clarivate Highly Cited Researcher since 2014 and one of only ~300 researchers worldwide to be highly cited in two fields (Microbiology and Biology & Biochemistry) from 2019-2024.