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

Director, Australian Centre for Ecogenomics

Coordinator, MICR3004 Microbial Genomics


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, Associate Professor 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.  He has helped pioneer the use of culture-independent molecular methods to characterise microbial communities including marker gene and shotgun (metagenomic) approaches.  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).

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 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: 

1989        Thomas Morrow Prize for best undergraduate essay on a topic in Scientific inquiry in Australia
1989-90   Commonwealth Government Postgraduate Research Award
1990-92   Australian Postgraduate Research Award
2006    International Society for Microbial Ecology (ISME) Young Investigator Award for significant contribution to microbial ecology
2007-       CSIRO honorary fellowship
2012        ARC Discovery Outstanding Researcher Award (DORA).
2012        Elected Fellow of the American Academy of Microbiology
2013        A novel, thermophilic bacterium named after him:  “Thermoflexus hugenholtzii”
2014      Thomson Reuters Highly Cited Researcher – The most cited documents in the field of microbiology.

Professor Hugenholtz has given over 50 invited lectures since 2004. 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. 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 2014, Professor Hugenholtz presented eight invited lectures including the Division N Plenary Lecture at the American  Society  for  Microbiology  in  Boston  (May)  and  a  Plenary  Lecture  at  the Queenstown Molecular Biology Meeting, New Zealand (August). He has accepted a further four invitations to present in 2015 including the IHMC 2015 - 5th International Human Microbiome Congress (April 1st); the Microbial Eco-genomics in Agriculture symposium, Galilee Mountains, Israel (May 17th-21st) and Opening Plenary Lecture at the TxSANZ Transplant Society Meeting, Canberra (June 21st).

Professor Hugenholtz has served on several Council Review Panels such as Natural Environment Research Council-UK, National Science Foundation, Netherlands Research Council, Small Business Innovation Research and is currently a Reviewer for the Australian Research Council (ARC) and the National Health & Medical Research Council (NHMRC).

He has reviewed for many journals including high impact journals such as Nature, Science and Nature Biotechnology. He serves, and has served, on numerous Editorial Boards including the main disciplinary journals in his research domain (Environmental Microbiology, FEMS Microbiology Ecology, ISME Journal and Microbiome) and more recently has agreed to serve on the Boards of new open-access online data-oriented journals including Scientific Data, Applied Scientific Reports and Life. Professor Hugenholtz is a member of the ISME Nomination and Elections Committee and assists on the Scientific Advisory Boards for Taxon Biosciences, a company specialising in microbial genomics and bioinformatics, and the Metagenome and Microbial Program at JGI. Lastly, Professor Hugenholtz received an invitation from “The Nobel Committee for Chemistry” to nominate candidates for the award of The Nobel Prize in Chemistry for 2015.

Selected Publications: