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

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.  He has helped pioneer the use of culture-independent molecular methods to characterize 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

University of Colorado, Boulder

University of North Carolina

Secondary Research Areas: 
Funded Projects: 

CSIRO Flagship
Functional screens for novel cellulases A (CSIRO Energy Transformed Flagship Cluster led by ANU)

ARC Linkage Infrastructure, Equipment and Facilities
A high-throughput screening and sequencing facility for single cell genomics

ARC Discovery Projects
Toward a complete view of life on Earth via single cell genomics

ARC Linkage Projects
Evaluation of Bacillus amyloliquefaciens H57 as a probiotic in livestock using animal nutrition studies and metagenomics

Queensland Government Smart Futures Co-Investment Fund
Ecogenomics of Queensland sugarcane soils

Queensland Government Smart Futures Research Partnerships Program
Future biofuels

The Prince Charles Hospital (TPCH)
The Lung Transplant Mycobiome

Clinical and psychosocial changes over late childhood and adolescence and early life determinants of long term clinical outcomes in cystic fibrosis.



MICR3004: Microbial Genetics & Genomics

BIOC3005: Molecular Systems Biology

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       Elected Fellow of the American Academy of Microbiology




1997-         Ad hoc reviewer for the following journals; Science, Nature, Nature Reviews Microbiology, PLoS-Biology, PNAS, Journal of Bacteriology, Nucleic Acids Research, Molecular Biology and Evolution, Applied and Environmental Microbiology, International Journal of Systematic Bacteriology, Archives of Microbiology, Letters in Applied Microbiology, FEMS Microbiology Letters, Journal of Industrial Microbiology, Genome Research, Genome Biology, Journal of Infectious Diseases, Microbiology, Bioinformatics.

2003-         Taxonomy curator of the greengenes database (

2005-2009  Editorial Board of Environmental Microbiology

2006-2010  Editorial Board of FEMS Microbiology Ecology

2006-2010  Editorial Board of The ISME Journal

2009-         Editorial Board of Standards in Genomic Sciences

2010-2012  Adjunct Professor in Department of Microbial and Plant Biology, UC Berkeley

2010-         Course Faculty, MBL Microbial Diversity Course, Woods Hole

2011-         JGI Metagenome and Microbial Program Advisory Committee, Walnut Creek, California

Selected Publications: