BSc (Hons) (UQ) Microbiology, PhD (UQ) Microbiology
Director, Australian Centre for Ecogenomics
+61 7 336 53822

Director, Australian Centre for Ecogenomics

ARC Australian Laureate Fellow

Coordinator, MICR3004 Microbial Genomics


Professor Hugenholtz has been at the forefront of major advances in molecular microbial ecology over the last 21 years, which now form the basis of this field. Our understanding of microbiology as a whole has been profoundly changed as a result of these advances. Beginning with the recognition that we have been ignorant of most microbial diversity due to a strong cultivation bias, Hugenholtz has systematically directed his research to characterise “microbial dark matter” with the ultimate goal of a holistic understanding of microbial evolution and ecology. He has made central contributions to this grand challenge in biology as evidenced by a series of landmark papers (23 papers in Science and Nature journals).

From 2004 to 2010, he built and directed the Microbial Ecology and Metagenomics Programs at the DOE Joint Genome Institute (JGI) in the US. In 2010 Phil returned home to establish the Australian Centre for Ecogenomics.  The Centre was founded around himself as Director, and Deputy Director, Professor Gene Tyson. The Centre comprises 45 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. Hugenholtz 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.

Brief Research Description: 
Microbial ecology & evolution
Research Focus and Collaborations: 

Microbial diversity, particularly novel microbial diversity
Microbial ecology and evolution

International Collaborators:

Aalborg University, 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



Secondary Research Areas: 
Funded Projects: 

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.




MICR3004: Microbial Genetics & Genomics


Significant Professional Activities 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 named after him:  “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


Professor Hugenholtz has given over 50 invited lectures, including Plenary & Keynote, since 2004. His most recent Plenary invitation is the ASM 116th General Meeting being held in Boston, (June 17th), and as an invited speaker at the Genomic Standards Consortium (GSC18), Crete, Greece (June 12th). In 2015 he 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, he 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, he 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 & chair at the ISME14 in Copenhagen, Denmark.


Member: 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, and the 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.

Service:  Current reviewer for Australian Research Council (ARC) and National Health & Medical Research Council (NHMRC). Previously has served on Council Review Panels such as Natural Environment Research Council-UK, National Science Foundation, Netherlands Research Council and Small Business Innovation Research. Prof Hugenholtz is a frequent reviewer for many journals including Nature, Science and Nature Biotechnology. Presented the Van Niel International Prize to Nikos Kyrpides (2015).

 Group Members:

Dr Christian Rinke Research Officer

Selected Publications: