
Overview
Background
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.
Availability
- Professor Phil Hugenholtz is:
- Available for supervision
Fields of research
Qualifications
- Bachelor (Honours) of Science (Advanced), The University of Queensland
- Doctor of Philosophy, The University of Queensland
Research interests
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Metagenomics
culture-independent sequence-based characterisation of microbial communities
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Microbial diversity and evolution
with a focus on a systematic genome-based prokaryotic taxonomy
Research impacts
Phil has been at the forefront of major advances in molecular microbial ecology over the last 30 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, he 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 (57 Science & Nature series papers ) and he has established a premier research facility at The University of Queensland, the Australian Centre for Ecogenomics (ACE), dedicated to this mission.
Works
Search Professor Phil Hugenholtz’s works on UQ eSpace
2002
Journal Article
In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth
Thomsen, TR, Kjellerup, BV, Nielsen, JL, Hugenholtz, P and Nielsen, PH (2002). In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environmental Microbiology, 4 (7), 383-391. doi: 10.1046/j.1462-2920.2002.00316.x
2002
Journal Article
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes
McDevitt, Christopher A., Hugenholtz, Philip, Hanson, Graeme R. and McEwan, Alastair G. (2002). Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Molecular Microbiology, 44 (6), 1575-1587. doi: 10.1046/j.1365-2958.2002.02978.x
2002
Journal Article
Exploring prokaryotic diversity in the genomic era
Hugenholtz, P (2002). Exploring prokaryotic diversity in the genomic era. Genome Biology, 3 (2) 0003, REVIEWS0003. doi: 10.1186/gb-2002-3-2-reviews0003
2002
Journal Article
The development and use of real-time PCR for the quantification of nitrifiers in activated sludge
Hall, S. J., Hugenholtz, P., Siyambalapitiya, N., Keller, J. and Blackall, L. L. (2002). The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Science And Technology, 46 (1-2), 267-272. doi: 10.2166/wst.2002.0488
2002
Book Chapter
Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH)
Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). Gene Probes - Principles and Protocols. (pp. 1-17) edited by Aquino de Muro. M and Rapley. R. London: Humana Press.
2002
Journal Article
The DMSO reductase family of microbial molybdenum enzymes; Molecular properties and role in the dissimilatory reduction of toxic elements
McEwan, A. G., Ridge, J. P., McDevitt, C. A. and Hugenholtz, P. (2002). The DMSO reductase family of microbial molybdenum enzymes; Molecular properties and role in the dissimilatory reduction of toxic elements. Geomicrobiology Journal, 19 (1), 3-21. doi: 10.1080/014904502317246138
2002
Journal Article
Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization
Hugenholtz, P., Tyson, G. W. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods in molecular biology (Clifton, N.J.), 179, 29-42.
2001
Journal Article
Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes
Klein, M., Friedrich, M., Roger, A. J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L. L., Stahl, D. A. and Wagner, M. (2001). Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Journal of Bacteriology, 183 (20), 6028-6035. doi: 10.1128/JB.183.20.6028-6035.2001
2001
Journal Article
A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data
Dalevi, D, Hugenholtz, P and Blackall, LL (2001). A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. International Journal of Systematic And Evolutionary Microbiology, 51 (2), 385-391. doi: 10.1099/00207713-51-2-385
2001
Journal Article
Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives
Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M. and Blackall, Linda L. (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Applied And Environmental Microbiology, 67 (1), 411-419. doi: 10.1128/AEM.67.1.411-419.2001
2000
Journal Article
Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed Probes for their detection and quantitation
Crocetti, GR, Hugenholtz, P, Bond, PL, Schuler, A, Keller, J, Jenkins, D and Blackall, LL (2000). Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed Probes for their detection and quantitation. Applied and Environmental Microbiology, 66 (3), 1175-1182. doi: 10.1128/AEM.66.3.1175-1182.2000
2000
Conference Publication
Diverted Cultivation of Phylogenetically Novell Bacteria
Hugenholtz, Phil (2000). Diverted Cultivation of Phylogenetically Novell Bacteria. ICCC9 9th International Congress for Culture Collections, Brisbane, Australia, 23-28 July, 2000. Australia: UQ Press/World Federation for Culture Studies.
2000
Journal Article
Microorganisms should be high on DNA preservation list
Fuerst, J. A. and Hugenholtz, P. (2000). Microorganisms should be high on DNA preservation list. Science, 290 (5496), 1503-1503. doi: 10.1126/science.290.5496.1503b
2000
Conference Publication
Real-Time PCR: Can it accurately assess specific members in a mixed microbial community
Blackall, L. L., Hall, S. J., Hugenholtz, P., Keller, J. and Siyambalapitiya, N. (2000). Real-Time PCR: Can it accurately assess specific members in a mixed microbial community. 4th Annual Australian Environmental Engineering Research Event, Victor Harbor, South Australia, Australia, 21-24 November, 2000. Australia: EERE Organising Committee.
1999
Journal Article
Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker
Sandler, S. J., Hugenholtz, P., Schleper, C., DeLong, E. F., Pace, N. R. and Clark, A. J. (1999). Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker. Journal of Bacteriology, 181 (3), 907-915.
1999
Conference Publication
The determination of the bacteria involved in biological phosphorus removal from wastewater
Blackall, L. L., Bond, P. L., Crocetti, G., Hugenholtz, P., Jenkins, D., Keller, J. and Schuler, A. (1999). The determination of the bacteria involved in biological phosphorus removal from wastewater. IXth International Congress of Bacteriology and Applied Microbiology, Sydney, August 2-6, 1999.
1999
Conference Publication
The microbiology of biological nutrient removal - latest discoveries and developments
Blackall, L. L., Bond, P. L., Burrell, P. C., Crocetti, G. and Hugenholtz, P. (1999). The microbiology of biological nutrient removal - latest discoveries and developments. IBC Conference on Advanced Wastewater and Sludge Treatment, Sydney, Australia, 27-28 Jan 1999. not available: not available.
1998
Journal Article
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998)
Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998). Journal of Bacteriology, 180 (24), 6793-6793. doi: 10.1128/jb.180.24.6793-6793.1998
1998
Journal Article
Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation
Dojka, M. A., Hugenholtz, P., Haack, S. K. and Pace, N. R. (1998). Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Applied and Environmental Microbiology, 64 (10), 3869-3877.
1998
Journal Article
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180 (18), 4765-4774.
Funding
Current funding
Past funding
Supervision
Availability
- Professor Phil Hugenholtz is:
- Available for supervision
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Available projects
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Dual-function ribonucleases: unexpected agents of antibiotic resistance
Bacterial pathogens use a group of enzymes called metallo-β-lactamases (or MBLs) that enable them to be multi-drug resistant. Our project aims to determine how MBLs have evolved from harmless and widespread ribonucleases, both deep in the past and potentially very recently in response to modern use of antibiotics. These insights will provide valuable functional and structural information that will enable the development of urgently needed strategies to combat β-lactam antibiotic resistance.
Supervision history
Current supervision
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Doctor Philosophy
Changing the prokaryotic classification status quo with a global genome-based taxonomy
Principal Advisor
Other advisors: Professor Mikael Boden
-
Doctor Philosophy
Use of structural phylogeny and reconciliation in molecular phylogenetics
Principal Advisor
Other advisors: Professor David Ascher, Dr Kate Bowerman
-
Doctor Philosophy
Exploration of the Genome Taxonomy Database at the Species and Subspecies Level
Principal Advisor
-
Doctor Philosophy
Diversity, ecology and biotechnological potential of chain elongating microorganisms from natural and engineered ecosystems
Principal Advisor
Other advisors: Dr Paul Evans, Dr Kate Bowerman
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Doctor Philosophy
Changing the prokaryotic classification status quo with a global genome-based taxonomy
Principal Advisor
Other advisors: Professor Mikael Boden
-
Doctor Philosophy
Characterization of Uncultured Basal Clades of Planctomycetota
Principal Advisor
Other advisors: Dr Kate Bowerman
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Doctor Philosophy
Extant and Evolutionary Analysis of Uncultured Bacterial Lineages Phylogenetically Affiliated with the Orders Rickettsiales and Mycoplasmatales
Principal Advisor
Other advisors: Dr Kate Bowerman
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Doctor Philosophy
Dual-function ribonucleases: unexpected agents of antibiotic resistance
Associate Advisor
Other advisors: Professor Mikael Boden
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Doctor Philosophy
Protein structure guided precision medicine
Associate Advisor
Other advisors: Dr Stephanie Portelli, Professor David Ascher
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Doctor Philosophy
Understanding the metabolic capabilities and evolutionary relatiosnhips of novel microorganisms from hot springs
Associate Advisor
Other advisors: Associate Professor Cheong Xin Chan, Dr Paul Evans
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Doctor Philosophy
The Role of Bacterially Induced Inflammation in Squamous Cell Carcinoma Development
Associate Advisor
Other advisors: Professor Mark Morrison, Dr Debottam Sinha, Dr Janin Chandra, Professor Ian Frazer
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Doctor Philosophy
Functionalisation of Metalloproteins and Applications in Biotechnology
Associate Advisor
Other advisors: Professor Gary Schenk
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Doctor Philosophy
Evolution of an efficient antibiotic resistance mechanism from a common enzymatic fold.
Associate Advisor
Other advisors: Professor Gary Schenk
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Doctor Philosophy
Building a better understanding of acetogen's metabolism
Associate Advisor
Other advisors: Dr Kate Bowerman, Dr Paul Evans
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Doctor Philosophy
Identification and characterisation of virally-encoded, antibiotic-degrading metalloenzymes
Associate Advisor
Other advisors: Professor Gary Schenk
Completed supervision
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2024
Doctor Philosophy
Extant and Evolutionary Analysis of Uncultured Bacterial Lineages Phylogenetically Affiliated with the Orders Rickettsiales and Mycoplasmatales
Principal Advisor
Other advisors: Dr Kate Bowerman
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2021
Doctor Philosophy
A phylogenomic investigation of the largely uncharacterised Firmicutes classes, Dehalobacteriia and TC1
Principal Advisor
Other advisors: Professor Ulrike Kappler
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2021
Doctor Philosophy
Classification and functional characterisation of the murine gut bacterial family Muribaculaceae
Principal Advisor
Other advisors: Dr Antiopi Varelias
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2020
Doctor Philosophy
Exploring a Genome-Based Taxonomy for Tailed Double-Stranded DNA Viruses
Principal Advisor
-
2016
Doctor Philosophy
Molecular Investigation of Australian Termites and their Gut Symbionts
Principal Advisor
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2015
Doctor Philosophy
Investigation of root and associated soil microbiomes of sugarcane and other plants
Principal Advisor
Other advisors: Professor Susanne Schmidt
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2024
Doctor Philosophy
The Role of Bacterially Induced Inflammation in Squamous Cell Carcinoma Development
Associate Advisor
Other advisors: Professor Mark Morrison, Dr Debottam Sinha, Dr Janin Chandra, Professor Ian Frazer
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2024
Doctor Philosophy
The ecology and evolution of non-photosynthetic Cyanobacteria
Associate Advisor
Other advisors: Dr Paul Evans
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2023
Doctor Philosophy
Culture-independent exploration of microbial dark matter with a focus on Asgardarchaeota
Associate Advisor
Other advisors: Dr Paul Evans
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2017
Doctor Philosophy
Microbial Community Structure and Functionality in Ruminants Fed the Probiotic Bacillus amyloliquefaciens H57
Associate Advisor
Other advisors: Dr Peter Dart
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2017
Doctor Philosophy
Functional and comparative studies of members of the genus Methanosphaera, and their adaptations to the gut environment
Associate Advisor
Other advisors: Professor Mark Morrison
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2017
Doctor Philosophy
Viral/bacterial respiratory tract co-infections in children
Associate Advisor
Other advisors: Professor Keith Chappell
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2016
Doctor Philosophy
Moving targets: Microevolution of pathogenic species within the laboratory and the human host
Associate Advisor
Other advisors: Professor James Fraser
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2015
Doctor Philosophy
Molecular characterisation of microbial communities involved in coal bed methane production
Associate Advisor
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2015
Doctor Philosophy
Molecular characterisation of microbial communities involved in nitrate-driven anaerobic oxidation of methane
Associate Advisor
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2014
Doctor Philosophy
Microbial Ecology of Fermentative Microbes in Anaerobic Granules
Associate Advisor
Other advisors: Professor Damien Batstone, Associate Professor Paul Jensen
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2013
Master Philosophy
The characterisation of the microbiome of the demosponge Amphimedon queenslandica reveals host immune responses to changes in the symbiotic bacterial community
Associate Advisor
Other advisors: Professor Bernard Degnan, Professor Sandie Degnan
Media
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