Primary research interest

Microbial ecology and evolution

Additional roles

About me

Beginning with the recognition that we have been ignorant of most microbial diversity due to a strong cultivation bias, I have systematically directed my research to characterise “microbial dark matter” with the ultimate goal of a holistic understanding of microbial evolution and ecology. From 2004 to 2010, I directed the Microbial Ecology and Metagenomics Programs at the DOE Joint Genome Institute (JGI) in the US. In 2010 I returned home to establish the Australian Centre for Ecogenomics. The Centre was founded around myself as Director, and Deputy Director, Professor Gene Tyson. The Centre comprises 50 researchers/core staff and state-of-the-art infrastructure for conducting ecogenomics research across a wide range of environmental, engineered and clinical ecosystems underpinned by a genome-based evolutionary framework. I was recently awarded an ARC Laureate Fellowship to obtain 100,000 genomes representing uncultured microbial dark matter which will be systematically organised into natural phylogenetic relationships.

Research focus and collaborations

  • Microbial diversity, particularly novel microbial diversity
  • Microbial ecology and evolution

International collaborators

  • Aalborg University, Denmark
  • Technical University of Denmark
  • Advanced Industrial Science & Technology (AIST), Japan
  • Department of Energy, Joint Genome Institutute
  • University of Colorado, Boulder
  • University of North Carolina
  • Massachusetts Institute of Technology
  • University of Copenhagen

Group members

Dr Christian Rinke, Research Officer

Funded projects

  • UQ Microbiome Challenge
    Metagenome-enabled human and mouse microbiomics
  • ARC 2016 Linkage Project
    Rapid functional and taxonomic skin microbe characterisation
  • ARC 2015 Australian Laureate Fellowship
    Reconstructing the universal tree and network of life
  • ARC Discovery Project
    Evolution of the marsupial gut microbiome and adaptation to plant toxins.
  • ARC Linkage Project
    Understanding the koala microbiome: unlocking the secrets of koala health and dietary specialisation, and successful husbandry and translocation.
  • NHMRC Program Grant
    Immunological therapies for cancer, chronic infection and autoimmunity.
  • UQ Collaboration and Industry Engagement Fund (CIEF)
    Novel treatments for inflammatory bowel diseases.
  • NHMRC Project Grant
    Modification of the microbiome and utilisation of microbial products as novel treatments for COPD.
  • NHMRC Project Grant
  • Determinants of progression of actinic keratoses to squamous cancer.
  • The Prince Charles Hospital (TPCH)
    Normal Pulmonary Flora - fact or fiction?
  • The Prince Charles Hospital (TPCH)
    The Lung Transplant Mycobiome
  • Gordon and Betty Moore Foundation: MMI
    Microfluidomics: Functionality at the Ocean's Microscale
  • ARC Linkage Projects
    Evaluation of Bacillus amyloliquefaciens H57 as a probiotic in livestock using animal nutrition studies and metagenomics
  • ARC Discovery Projects
    Toward a complete view of life on Earth via single cell genomics
  • Queensland Government Smart Futures Research Partnerships Program
    Development of sustainable second generation biomass crops and conversion technologies for biomaterial production.

Teaching interests

Achievements and awards 


  • 2015: Australian Academy of Health and Medical Sciences (AAHMS) Fellowship
  • 2015-20: ARC Australian Laureate Fellowship
  • 2015-19: Vice-Chancellor’s Research and Teaching Fellowship, The University of Queensland
  • 2013: A novel, thermophilic bacterium was named after me: “Thermoflexus hugenholtzii”
  • 2012: Elected Fellow of the American Academy of Microbiology
  • 2012: ARC Discovery Outstanding Researcher Award (DORA)
  • 2007: CSIRO honorary fellowship
  • 2006: International Society for Microbial Ecology (ISME) Young Investigator Award for significant contribution to microbial ecology
  • 1990-92: Australian Postgraduate Research Award
  • 1989-90: Commonwealth Government Postgraduate Research Award
  • 1989: Thomas Morrow Prize for best undergraduate essay on a topic in Scientific inquiry in Australia

Appointments, memberships and service

  • ARC Australian Laureate Fellow
  • Member of:
    • American Society for Microbiology (ASM)
    • The Australian Society for Microbiology
    • The Entomological Society of Queensland (ESQ)
    • International Society for Microbial Ecology (ISME)
    • Scientific Advisory Boards for Taxon Biosciences
    • Metagenome and Microbial Program at JGI
    • editorial boards including the Environmental Microbiology, FEMS Microbiology Ecology, ISME Journal, Microbiome, Scientific Data, Applied Scientific Reports and Life.
  • I have given more than 50 invited lectures, including Plenary & Keynotes, since 2004. My most recent Plenary invitation was the ASM 116th General Meeting held in Boston, (June 2016), and as an invited speaker at the Genomic Standards Consortium (GSC18), Crete, Greece (June 2016). In 2015 I presented as Plenary at the Transplant Society of Australia & New Zealand (TSANZ) Meeting, Canberra; Microbial Eco-genomics in Agriculture symposium, Galilee Mountains, Israel; the Division N Plenary Lecture at the American Society for Microbiology  in  Boston, USA; Keynote at the 5th International Human Microbiome Congress (IHMC) Luxembourg and Plenary  Lecture at the Queenstown Molecular Biology Meeting, New Zealand (2014). In 2013, I was a keynote speaker at the JAMS (Joint Academic Microbiology Seminars) Annual Dinner at the Australian Museum, Sydney; a keynote speaker at the 12th Symposium on Bacterial Genetics and Ecology (BAGECO 12) in Ljubljana, Slovenia and was invited to present a Phyloseminar in honour of Professor Carl Woese, a biophysicist who revolutionised the structure of the evolutionary tree of life. In 2012, I was the keynote speaker at the New Zealand Microbial Ecology Symposium in Auckland, NZ; speaker at the 28th New Phytologist Symposium, Greece; Keynote at the SEIB Colloquium, Sydney and speaker and chair at the ISME14 in Copenhagen, Denmark.
  • Current reviewer for Australian Research Council (ARC) and National Health & Medical Research Council (NHMRC)
  • Previously served on Council Review Panels such as Natural Environment Research Council-UK, National Science Foundation, Netherlands Research Council and Small Business Innovation Research
  • Frequent reviewer for many journals, including Nature, Science and Nature Biotechnology
  • Presented the Van Niel International Prize to Nikos Kyrpides (2015)

Researcher biography

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 DOE Joint Genome Institute. In late 2010 Phil returned home to establish the Australian Centre for Ecogenomics. The Centre was founded around himself as Director, and ARC QEII Fellow and Deputy Director, Dr Gene Tyson. Phil has published over one hundred papers in molecular microbial ecology including several Science & Nature papers.

Currently, Phil's research interests include the microbial ecology and evolution of host-associated ecosystems such as the termite hindgut and human microbiome, and genomic mapping of the microbial tree of life. In 2006, Phil received the Young Investigators Award from the International Society of Microbial Ecology (ISME) and was elected in 2012 as a Fellow of the American Academy of Microbiology (AAM).